U.S. patent application number 11/685603 was filed with the patent office on 2007-09-20 for compositions for use in identification of bacteria.
Invention is credited to Lawrence Blyn, David J. Ecker, Thomas A. Hall, Rangarajan Sampath.
Application Number | 20070218489 11/685603 |
Document ID | / |
Family ID | 38533927 |
Filed Date | 2007-09-20 |
United States Patent
Application |
20070218489 |
Kind Code |
A1 |
Sampath; Rangarajan ; et
al. |
September 20, 2007 |
COMPOSITIONS FOR USE IN IDENTIFICATION OF BACTERIA
Abstract
The present invention provides compositions, kits and methods
for rapid identification and quantification of bacteria by
molecular mass and base composition analysis.
Inventors: |
Sampath; Rangarajan; (San
Diego, CA) ; Hall; Thomas A.; (Oceanside, CA)
; Ecker; David J.; (Encinitas, CA) ; Blyn;
Lawrence; (Mission Viejo, CA) |
Correspondence
Address: |
MEDLEN & CARROLL LLP
101 HOWARD STREET
SUITE 350
SAN FRANCISCO
CA
94105
US
|
Family ID: |
38533927 |
Appl. No.: |
11/685603 |
Filed: |
March 13, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11409535 |
Apr 21, 2006 |
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11685603 |
Mar 13, 2007 |
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11060135 |
Feb 17, 2005 |
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11409535 |
Apr 21, 2006 |
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10728486 |
Dec 5, 2003 |
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11409535 |
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60545425 |
Feb 18, 2004 |
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60559754 |
Apr 5, 2004 |
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60632862 |
Dec 3, 2004 |
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60639068 |
Dec 22, 2004 |
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60648188 |
Jan 28, 2005 |
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60501926 |
Sep 11, 2003 |
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60674118 |
Apr 21, 2005 |
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60705631 |
Aug 3, 2005 |
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60732539 |
Nov 1, 2005 |
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60773124 |
Feb 13, 2006 |
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Current U.S.
Class: |
435/6.15 ;
536/24.1 |
Current CPC
Class: |
C12Q 1/689 20130101;
C12Q 2600/156 20130101; C12Q 1/6816 20130101; C12Q 1/6858 20130101;
C12Q 1/6816 20130101; C12Q 2537/143 20130101; C12Q 1/6858 20130101;
C12Q 2565/627 20130101; C12Q 2565/627 20130101 |
Class at
Publication: |
435/006 ;
536/024.1 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; C07H 21/04 20060101 C07H021/04 |
Goverment Interests
STATEMENT OF GOVERNMENT SUPPORT
[0002] This invention was made with United States Government
support under CDC contract RO1 CI000099-01. The United States
Government has certain rights in the invention.
Claims
1. An oligonucleotide primer pair comprising a forward primer and a
reverse primer, each comprising between 13 and 35 linked
nucleotides in length, configured to generate an amplicon that is
between 45 and 200 linked nucleotides in length, said forward
primer configured to hybridize with at least 70% complementarity to
a first portion of a region of Genbank gi number: 57634611, and
said reverse primer configured to hybridize with at least 70%
complementarity to a second portion of said region of Genbank gi
number: 57634611, wherein said region of Genbank gi number:
57634611 begins with the 5' end of SEQ ID NO.: 174, and extends to
the 5' end of SEQ ID NO.: 899.
2. The oligonucleotide primer pair of claim 1, wherein said forward
primer comprises at least 70% sequence identity with SEQ ID NO:
174.
3. The oligonucleotide primer pair of claim 2, wherein said forward
primer comprises at least 80% sequence identity with SEQ ID NO:
174.
4. The oligonucleotide primer pair of claim 3, wherein said forward
primer comprises at least 90% sequence identity with SEQ ID NO:
174.
5. The oligonucleotide primer pair of claim 1, wherein said forward
primer is SEQ ID NO: 174.
6. The oligonucleotide primer pair of claim 1, wherein said reverse
primer comprises at least 70% sequence identity with SEQ ID NO:
853.
7. The oligonucleotide primer pair of claim 6, wherein said reverse
primer comprises at least 80% sequence identity with SEQ ID NO:
853.
8. The oligonucleotide primer pair of claim 7, wherein said reverse
primer comprises at least 90% sequence identity with SEQ ID NO:
853.
9. The oligonucleotide primer pair of claim 1, wherein said reverse
primer is SEQ ID NO: 853.
10. The oligonucleotide primer pair of claim 1, wherein at least
one of said forward primer and said reverse primer comprises at
least one modified nucleobase.
11. The oligonucleotide primer pair of claim 10, wherein at least
one of said at least one modified nucleobase is a mass modified
nucleobase.
12. The oligonucleotide primer pair of claim 11, wherein said mass
modified nucleobase is 5-Iodo-C.
13. The composition of claim 11, wherein said mass modified
nucleobase comprises a molecular mass modifying tag.
14. The oligonucleotide primer pair of claim 10, wherein at least
one of said at least one modified nucleobase is a universal
nucleobase.
15. The oligonucleotide primer pair of claim 14, wherein said
universal nucleobase is inosine.
16. The oligonucleotide primer pair of claim 1, wherein at least
one of said forward primer and said reverse primer comprises a
non-templated T residue at its 5' end.
17. A kit for identifying a Staphylococcus aureus bioagent
comprising: i) a first oligonucleotide primer pair comprising a
forward primer and a reverse primer, each comprising between 13 and
35 linked nucleotides in length, configured to generate an amplicon
that is between 45 and 200 linked nucleotides in length, said
forward primer configured to hybridize with at least 70%
complementarity to a first portion of a region of Genbank gi
number: 57634611, and said reverse primer configured to hybridize
with at least 70% complementarity to a second portion of said
region of Genbank gi number: 57634611, wherein said region of
Genbank gi number: 57634611 begins with the 5' end of SEQ ID NO:
174 and extends to the 5' end of SEQ ID NO: 899; and ii) at least
one additional primer pair, wherein the primers of each of said at
least one additional primer pair are configured to hybridize to
conserved sequence regions within a Staphylococcus aureus gene
selected from the group consisting of: mecA, mecRI, ermA, ermC,
pvluk, tufB and mupR.
18. The kit of claim 17, wherein each of said at least one
additional primer pair comprises SEQ ID NO: 217:SEQ ID NO: 1167,
SEQ ID NO: 399:SEQ ID NO:1041, SEQ ID NO: 456:SEQ ID NO: 1261, SEQ
ID NO: 430:SEQ ID NO: 1321, SEQ ID NO: 288:SEQ ID NO:1269, SEQ ID
NO: 698:SEQ ID NO: 1420, or SEQ ID NO: 205:SEQ ID NO: 876.
19. The kit of claim 17, wherein said first oligonucleotide primer
pair and said at least one additional primer pair consists of eight
oligonucleotide primer pairs having at least 70% sequence identity
with the primer pairs: SEQ ID NO: 217:SEQ ID NO: 1167, SEQ ID NO:
399:SEQ ID NO:1041, SEQ ID NO: 456:SEQ ID NO: 1261, SEQ ID NO:
174:SEQ ID NO: 853, SEQ ID NO: 430:SEQ ID NO: 1321, SEQ ID NO:
288:SEQ ID NO:1269, SEQ ID NO: 698:SEQ ID NO: 1420, and SEQ ID NO:
205:SEQ ID NO: 876.
20. A method for identifying a Staphylococcus aureus bioagent in a
sample comprising: a) amplifying a nucleic acid from said sample
using an oligonucleotide primer pair comprising a forward primer
and a reverse primer, each comprising between 13 and 35 linked
nucleotides in length, said forward primer configured to hybridize
with at least 70% complementarity to a first portion of a region of
Genbank gi number: 57634611, and said reverse primer configured to
hybridize with at least 70% complementarity to a second portion of
said region of Genbank gi number: 57634611, wherein said region of
Genbank gi number: 57634611 begins with the 5' end of SEQ ID NO.:
174, and extends to the 5' end of SEQ ID NO.: 899; wherein said
amplifying generates at least one amplification product that
comprises between 45 and 200 linked nucleotides; and b) determining
the molecular mass of said at least one amplification product by
mass spectrometry.
21. The method of claim 20 further comprising comparing said
determined molecular mass to a database comprising a plurality of
molecular masses of bioagent identifying amplicons, wherein a match
between said determined molecular mass and a molecular mass
comprised in said database identifies said Staphylococcus aureus
bioagent in said sample.
22. The method of claim 20 further comprising calculating a base
composition of said at least one amplification product using said
molecular mass.
23. The method of claim 22 further comprising comparing said
calculated base composition to a database comprising a plurality of
base compositions of bioagent identifying amplicons, wherein a
match between said calculated base composition and a base
composition comprised in said database identifies said
Staphylococcus aureus bioagent in said sample.
24. The method of claim 20, wherein said forward primer comprises
at least 70% sequence identity with SEQ ID NO: 174.
25. The method of claim 20, wherein said reverse primer comprises
at least 70% sequence identity with SEQ ID NO: 853.
26. The method of claim 20 further comprising repeating said
amplifying and determining steps using at least one additional
oligonucleotide primer pair wherein the primers of each of said at
least one additional primer pair are designed to hybridize to
conserved sequence regions within a Staphylococcus aureus gene
selected from the group consisting of mecA, mecRI, ermA, ermC,
pvluk, tufB, mupR, and nuc.
27. The method of claim 20, wherein said identifying comprises
detecting the presence of said Staphylococcus aureus bioagent in
said sample.
28. The method of claim 20, wherein said identifying comprises
determining either the sensitivity or the resistance of said
Staphylococcus aureus bioagent in said sample to one or more
antibiotics.
29. The method of claim 20, wherein said identifying comprises
identifying a sub-species characteristic, strain, or genotype of
said Staphylococcus aureus bioagent in said sample.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 11/409,535, filed Apr. 21, 2006, which is a
continuation-in-part of U.S. application Ser. No. 11/060,135, filed
Feb. 17, 2005 which claims the benefit of priority to U.S.
Provisional Application Ser. No. 60/545,425 filed Feb. 18, 2004;
U.S. Provisional Application Ser. No. 60/559,754, filed Apr. 5,
2004; U.S. Provisional Application Ser. No. 60/632,862, filed Dec.
3, 2004; U.S. Provisional Application Ser. No. 60/639,068, filed
Dec. 22, 2004; and U.S. Provisional Application Ser. No.
60/648,188, filed Jan. 28, 2005. U.S. application Ser. No.
11/409,535 is a also continuation-in-part of U.S. application Ser.
No. 10/728,486, filed Dec. 5, 2003 which claims the benefit of
priority to U.S. Provisional Application Ser. No. 60/501,926, filed
Sep. 11, 2003. U.S. application Ser. No. 11/409,535 also claims the
benefit of priority to: U.S. Provisional Application Ser. No.
60/674,118, filed Apr. 21, 2005; U.S. Provisional Application Ser.
No. 60/705,631, filed Aug. 3, 2005; U.S. Provisional Application
Ser. No. 60/732,539, filed Nov. 1, 2005; and U.S. Provisional
Application Ser. No. 60/773,124, filed Feb. 13, 2006. Each of the
above-referenced U.S. Applications is incorporated herein by
reference in its entirety. Methods disclosed in U.S. application
Ser. Nos. 09/891,793, 10/156,608, 10/405,756, 10/418,514,
10/660,122, 10,660,996, 10/660,997, 10/660,998, 10/728,486,
11/060,135, and 11/073,362, are commonly owned and incorporated
herein by reference in their entirety for any purpose.
SEQUENCE LISTING
[0003] The present application is being filed along with a Sequence
Listing in electronic format. The Sequence Listing is provided as a
file entitled DIBIS0083USC12SEQ.txt, created on Mar. 13, 2007 which
is 252 Kb in size. The information in the electronic format of the
sequence listing is incorporated herein by reference in its
entirety.
FIELD OF THE INVENTION
[0004] The present invention provides compositions, kits and
methods for rapid identification and quantification of bacteria by
molecular mass and base composition analysis.
BACKGROUND OF THE INVENTION
[0005] A problem in determining the cause of a natural infectious
outbreak or a bioterrorist attack is the sheer variety of organisms
that can cause human disease. There are over 1400 organisms
infectious to humans; many of these have the potential to emerge
suddenly in a natural epidemic or to be used in a malicious attack
by bioterrorists (Taylor et al. Philos. Trans. R. Soc. London B.
Biol. Sci., 2001, 356, 983-989). This number does not include
numerous strain variants, bioengineered versions, or pathogens that
infect plants or animals.
[0006] Much of the new technology being developed for detection of
biological weapons incorporates a polymerase chain reaction (PCR)
step based upon the use of highly specific primers and probes
designed to selectively detect certain pathogenic organisms.
Although this approach is appropriate for the most obvious
bioterrorist organisms, like smallpox and anthrax, experience has
shown that it is very difficult to predict which of hundreds of
possible pathogenic organisms might be employed in a terrorist
attack. Likewise, naturally emerging human disease that has caused
devastating consequence in public health has come from unexpected
families of bacteria, viruses, fungi, or protozoa. Plants and
animals also have their natural burden of infectious disease agents
and there are equally important biosafety and security concerns for
agriculture.
[0007] A major conundrum in public health protection, biodefense,
and agricultural safety and security is that these disciplines need
to be able to rapidly identify and characterize infectious agents,
while there is no existing technology with the breadth of function
to meet this need. Currently used methods for identification of
bacteria rely upon culturing the bacterium to effect isolation from
other organisms and to obtain sufficient quantities of nucleic acid
followed by sequencing of the nucleic acid, both processes which
are time and labor intensive.
[0008] Mass spectrometry provides detailed information about the
molecules being analyzed, including high mass accuracy. It is also
a process that can be easily automated. DNA chips with specific
probes can only determine the presence or absence of specifically
anticipated organisms. Because there are hundreds of thousands of
species of benign bacteria, some very similar in sequence to threat
organisms, even arrays with 10,000 probes lack the breadth needed
to identify a particular organism.
[0009] The present invention provides oligonucleotide primers and
compositions and kits containing the oligonucleotide primers, which
define bacterial bioagent identifying amplicons and, upon
amplification, produce corresponding amplification products whose
molecular masses provide the means to identify bacteria, for
example, at and below the species taxonomic level.
SUMMARY OF THE INVENTION
[0010] The present invention provides compositions, kits and
methods for rapid identification and quantification of bacteria by
molecular mass and base composition analysis.
[0011] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 456.
[0012] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1261.
[0013] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 456 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1261.
[0014] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 288.
[0015] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1269.
[0016] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 288 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1269.
[0017] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 698.
[0018] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1420.
[0019] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 698 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1420.
[0020] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 217.
[0021] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1167
[0022] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 217 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1167.
[0023] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 399.
[0024] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1041.
[0025] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 399 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1041.
[0026] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 430.
[0027] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1321.
[0028] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 430 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1321.
[0029] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 174.
[0030] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 853.
[0031] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 174 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 853.
[0032] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 172.
[0033] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1360.
[0034] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 172 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1360.
[0035] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 456 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1261.
[0036] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 456 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1261 and further comprising one or more primer pairs wherein each
member of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 288:1269, 698:1420, 217:1167, 399:1041, 430:1321,
174:853, and 172:1360.
[0037] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 681.
[0038] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1022.
[0039] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 681 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1022.
[0040] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 315.
[0041] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1379.
[0042] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 315 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1379.
[0043] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 346.
[0044] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 955.
[0045] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 346 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 955.
[0046] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 504.
[0047] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1409.
[0048] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 504 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1409.
[0049] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 323.
[0050] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1068.
[0051] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 323 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 1068.
[0052] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 479.
[0053] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 938.
[0054] Another embodiment is an oligonucleotide primer pair
including an oligonucleotide primer 14 to 35 nucleobases in length
having at least 70% sequence identity with SEQ ID NO: 479 and an
oligonucleotide primer 14 to 35 nucleobases in length having at
least 70% sequence identity with SEQ ID NO: 938.
[0055] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 681 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1022.
[0056] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 681 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1022 and further comprising one or more primer pairs wherein each
member of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 315:1379, 346:955, 504:1409, 323:1068, 479:938.
[0057] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 583.
[0058] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 923.
[0059] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 583 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
923.
[0060] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 454.
[0061] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1418.
[0062] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 454 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1418.
[0063] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 250.
[0064] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 902.
[0065] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 250 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
902.
[0066] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 384.
[0067] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 878.
[0068] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 384 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
878.
[0069] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 694.
[0070] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1215.
[0071] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 694 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1215.
[0072] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 194.
[0073] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1173.
[0074] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 194 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1173.
[0075] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 375.
[0076] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 890.
[0077] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 375 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
890.
[0078] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 656.
[0079] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1224.
[0080] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 656 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1224.
[0081] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 618.
[0082] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1157.
[0083] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 618 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1157.
[0084] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 302.
[0085] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 852.
[0086] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 302 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
852.
[0087] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 199.
[0088] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 889.
[0089] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 199 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
889.
[0090] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 596.
[0091] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1169.
[0092] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 596 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1169.
[0093] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 150.
[0094] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1242.
[0095] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 150 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1242.
[0096] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 166.
[0097] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1069.
[0098] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 166 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1069.
[0099] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 166.
[0100] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1168.
[0101] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 166 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1168.
[0102] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 583 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO: 923
and further comprising one or more primer pairs wherein each member
of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 454:1418, 250:902, 384:878, 694:1215, 194:1173,
375:890, 656:1224, 618:1157, 302:852, 199:889, 596:1169, 150:1242,
166:1069 and 166:1168.
[0103] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 437.
[0104] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1137.
[0105] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 437 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1137.
[0106] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 530.
[0107] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 891.
[0108] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 530 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
891.
[0109] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 474.
[0110] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 869.
[0111] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 474 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
869.
[0112] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 268.
[0113] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1284.
[0114] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 268 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1284.
[0115] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 418.
[0116] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1301.
[0117] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 418 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1301.
[0118] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 318.
[0119] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1300.
[0120] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 318 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1300.
[0121] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 440.
[0122] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1076.
[0123] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 440 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1076.
[0124] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 219.
[0125] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1013.
[0126] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 219 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1013.
[0127] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 437 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1137 and further comprising one or more primer pairs wherein each
member of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 530:891, 474:869, 268:1284, 418:1301, 318:1300,
440:1076 and 219:1013.
[0128] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 325.
[0129] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1163.
[0130] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 325 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1163.
[0131] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 278.
[0132] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1039.
[0133] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 278 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1039.
[0134] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 465.
[0135] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1037.
[0136] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 465 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1037.
[0137] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 148.
[0138] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1172.
[0139] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 148 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1172.
[0140] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 190.
[0141] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1254.
[0142] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 190 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1254.
[0143] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 266.
[0144] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1094.
[0145] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 266 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1094.
[0146] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 508.
[0147] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1297.
[0148] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 508 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1297.
[0149] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 259.
[0150] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1060.
[0151] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 259 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1060.
[0152] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 325 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1163 and further comprising one or more primer pairs wherein each
member of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 278:1039: 465:1037, 148:1172, 190:1254, 266:1094,
508:1297 and 259:1060.
[0153] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 376.
[0154] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1265.
[0155] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 376 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1265.
[0156] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 267.
[0157] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1341.
[0158] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 267 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1341.
[0159] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 705.
[0160] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1056.
[0161] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 705 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1056.
[0162] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 710.
[0163] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1259.
[0164] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 710 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1259.
[0165] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 374.
[0166] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1111.
[0167] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 374 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1111.
[0168] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 545.
[0169] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 978.
[0170] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 545 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
978.
[0171] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 249.
[0172] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1095.
[0173] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 249 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1095.
[0174] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 195.
[0175] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1376.
[0176] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 195 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1376.
[0177] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 311.
[0178] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1014.
[0179] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 311 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1014.
[0180] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 365.
[0181] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1052.
[0182] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 365 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1052.
[0183] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 527.
[0184] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1071.
[0185] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 527 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1071.
[0186] One embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 490.
[0187] Another embodiment is an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 1182.
[0188] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 490 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1182.
[0189] Another embodiment is a kit comprising an oligonucleotide
primer pair including an oligonucleotide primer 14 to 35
nucleobases in length having at least 70% sequence identity with
SEQ ID NO: 376 and an oligonucleotide primer 14 to 35 nucleobases
in length having at least 70% sequence identity with SEQ ID NO:
1265 and further comprising one or more primer pairs wherein each
member of said one or more primer pairs is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from the group of primer pairs represented by
SEQ ID NOs: 267:1341, 705:1056, 710:1259, 374:1111, 545:978,
249:1095, 195:1376, 311:1014, 365:1052, 527:1071 and 490:1182.
[0190] In some embodiments, either or both of the primers of a
primer pair composition contain at least one modified nucleobase
such as 5-propynyluracil or 5-propynylcytosine for example.
[0191] In some embodiments, either or both of the primers of the
primer pair comprises at least one universal nucleobase such as
inosine for example.
[0192] In some embodiments, either or both of the primers of the
primer pair comprises at least one non-templated T residue on the
5'-end.
[0193] In some embodiments, either or both of the primers of the
primer pair comprises at least one non-template tag.
[0194] In some embodiments, either or both of the primers of the
primer pair comprises at least one molecular mass modifying
tag.
[0195] In some embodiments, the present invention provides primers
and compositions comprising pairs of primers, and kits containing
the same, and methods for use in identification of bacteria. The
primers are designed to produce amplification products of DNA
encoding genes that have conserved and variable regions across
different subgroups and genotypes of bacteria.
[0196] Some embodiments are kits that contain one or more of the
primer pair compositions. In some embodiments, each member of the
one or more primer pairs of the kit is of a length of 14 to 35
nucleobases and has 70% to 100% sequence identity with the
corresponding member from any of the primer pairs listed in Table
2.
[0197] Some embodiments of the kits contain at least one
calibration polynucleotide for use in quantitiation of bacteria in
a given sample, and also for use as a positive control for
amplification.
[0198] Some embodiments of the kits contain at least one anion
exchange functional group linked to a magnetic bead.
[0199] In some embodiments, the present invention also provides
methods for identification of bacteria. Nucleic acid from the
bacterium is amplified using the primers described above to obtain
an amplification product. The molecular mass of the amplification
product is measured. Optionally, the base composition of the
amplification product is determined from the molecular mass. The
molecular mass or base composition is compared with a plurality of
molecular masses or base compositions of known analogous bacterial
identifying amplicons, wherein a match between the molecular mass
or base composition and a member of the plurality of molecular
masses or base compositions identifies the bacterium. In some
embodiments, the molecular mass is measured by mass spectrometry in
a modality such as electrospray ionization (ESI) time of flight
(TOF) mass spectrometry or ESI Fourier transform ion cyclotron
resonance (FTICR) mass spectrometry, for example. Other mass
spectrometry techniques can also be used to measure the molecular
mass of bacterial bioagent identifying amplicons.
[0200] In some embodiments, the present invention is also directed
to a method for determining the presence or absence of a bacterium
in a sample. Nucleic acid from the sample is amplified using the
composition described above to obtain an amplification product. The
molecular mass of the amplification product is determined.
Optionally, the base composition of the amplification product is
determined from the molecular mass. The molecular mass or base
composition of the amplification product is compared with the known
molecular masses or base compositions of one or more known
analogous bacterial bioagent identifying amplicons, wherein a match
between the molecular mass or base composition of the amplification
product and the molecular mass or base composition of one or more
known bacterial bioagent identifying amplicons indicates the
presence of the bacterium in the sample. In some embodiments, the
molecular mass is measured by mass spectrometry.
[0201] In some embodiments, the present invention also provides
methods for determination of the quantity of an unknown bacterium
in a sample. The sample is contacted with the composition described
above and a known quantity of a calibration polynucleotide
comprising a calibration sequence. Nucleic acid from the unknown
bacterium in the sample is concurrently amplified with the
composition described above and nucleic acid from the calibration
polynucleotide in the sample is concurrently amplified with the
composition described above to obtain a first amplification product
comprising a bacterial bioagent identifying amplicon and a second
amplification product comprising a calibration amplicon. The
molecular masses and abundances for the bacterial bioagent
identifying amplicon and the calibration amplicon are determined.
The bacterial bioagent identifying amplicon is distinguished from
the calibration amplicon based on molecular mass and comparison of
bacterial bioagent identifying amplicon abundance and calibration
amplicon abundance indicates the quantity of bacterium in the
sample. In some embodiments, the base composition of the bacterial
bioagent identifying amplicon is determined.
[0202] In some embodiments, the present invention provides methods
for detecting or quantifying bacteria by combining a nucleic acid
amplification process with a mass determination process. In some
embodiments, such methods identify or otherwise analyze the
bacterium by comparing mass information from an amplification
product with a calibration or control product. Such methods can be
carried out in a highly multiplexed and/or parallel manner allowing
for the analysis of as many as 300 samples per 24 hours on a single
mass measurement platform. The accuracy of the mass determination
methods in some embodiments of the present invention permits allows
for the ability to discriminate between different bacteria such as,
for example, various genotypes and drug resistant strains of
Staphylococcus aureus.
BRIEF DESCRIPTION OF THE DRAWINGS
[0203] The foregoing summary of the invention, as well as the
following detailed description of the invention, is better
understood when read in conjunction with the accompanying drawings
which are included by way of example and not by way of
limitation.
[0204] FIG. 1: process diagram illustrating a representative primer
pair selection process.
[0205] FIG. 2: process diagram illustrating an embodiment of the
calibration method.
[0206] FIG. 3: common pathogenic bacteria and primer pair coverage.
The primer pair number in the upper right hand corner of each
polygon indicates that the primer pair can produce a bioagent
identifying amplicon for all species within that polygon.
[0207] FIG. 4: a representative 3D diagram of base composition
(axes A, G and C) of bioagent identifying amplicons obtained with
primer pair number 14 (a precursor of primer pair number 348 which
targets 16S rRNA). The diagram indicates that the experimentally
determined base compositions of the clinical samples (labeled NHRC
samples) closely match the base compositions expected for
Streptococcus pyogenes and are distinct from the expected base
compositions of other organisms.
[0208] FIG. 5: a representative mass spectrum of amplification
products indicating the presence of bioagent identifying amplicons
of Streptococcus pyogenes, Neisseria meningitidis, and Haemophilus
influenzae obtained from amplification of nucleic acid from a
clinical sample with primer pair number 349 which targets 23S rRNA.
Experimentally determined molecular masses and base compositions
for the sense strand of each amplification product are shown.
[0209] FIG. 6: a representative mass spectrum of amplification
products representing a bioagent identifying amplicon of
Streptococcus pyogenes, and a calibration amplicon obtained from
amplification of nucleic acid from a clinical sample with primer
pair number 356 which targets rplB. The experimentally determined
molecular mass and base composition for the sense strand of the
Streptococcus pyogenes amplification product is shown.
[0210] FIG. 7: a representative mass spectrum of an amplified
nucleic acid mixture which contained the Ames strain of Bacillus
anthracis, a known quantity of combination calibration
polynucleotide (SEQ ID NO: 1464), and primer pair number 350 which
targets the capC gene on the virulence plasmid pX02 of Bacillus
anthracis. Calibration amplicons produced in the amplification
reaction are visible in the mass spectrum as indicated and
abundance data (peak height) are used to calculate the quantity of
the Ames strain of Bacillus anthracis.
DEFINITIONS
[0211] As used herein, the term "abundance" refers to an amount.
The amount may be described in terms of concentration which are
common in molecular biology such as "copy number," "pfu or
plate-forming unit" which are well known to those with ordinary
skill. Concentration may be relative to a known standard or may be
absolute.
[0212] As used herein, the term "amplifiable nucleic acid" is used
in reference to nucleic acids that may be amplified by any
amplification method. It is contemplated that "amplifiable nucleic
acid" also comprises "sample template."
[0213] As used herein the term "amplification" refers to a special
case of nucleic acid replication involving template specificity. It
is to be contrasted with non-specific template replication (i.e.,
replication that is template-dependent but not dependent on a
specific template). Template specificity is here distinguished from
fidelity of replication (i.e., synthesis of the proper
polynucleotide sequence) and nucleotide (ribo- or deoxyribo-)
specificity. Template specificity is frequently described in terms
of "target" specificity. Target sequences are "targets" in the
sense that they are sought to be sorted out from other nucleic
acid. Amplification techniques have been designed primarily for
this sorting out. Template specificity is achieved in most
amplification techniques by the choice of enzyme. Amplification
enzymes are enzymes that, under conditions they are used, will
process only specific sequences of nucleic acid in a heterogeneous
mixture of nucleic acid. For example, in the case of Q.beta.
replicase, MDV-1 RNA is the specific template for the replicase (D.
L. Kacian et al., Proc. Natl. Acad. Sci. USA 69:3038 [1972]). Other
nucleic acid will not be replicated by this amplification enzyme.
Similarly, in the case of T7 RNA polymerase, this amplification
enzyme has a stringent specificity for its own promoters
(Chamberlin et al., Nature 228:227 [1970]). In the case of T4 DNA
ligase, the enzyme will not ligate the two oligonucleotides or
polynucleotides, where there is a mismatch between the
oligonucleotide or polynucleotide substrate and the template at the
ligation junction (D. Y. Wu and R. B. Wallace, Genomics 4:560
[1989]). Finally, Taq and Pfu polymerases, by virtue of their
ability to function at high temperature, are found to display high
specificity for the sequences bounded and thus defined by the
primers; the high temperature results in thermodynamic conditions
that favor primer hybridization with the target sequences and not
hybridization with non-target sequences (H. A. Erlich (ed.), PCR
Technology, Stockton Press [1989]).
[0214] As used herein, the term "amplification reagents" refers to
those reagents (deoxyribonucleotide triphosphates, buffer, etc.),
needed for amplification, excluding primers, nucleic acid template,
and the amplification enzyme. Typically, amplification reagents
along with other reaction components are placed and contained in a
reaction vessel (test tube, microwell, etc.).
[0215] As used herein, the term "analogous" when used in context of
comparison of bioagent identifying amplicons indicates that the
bioagent identifying amplicons being compared are produced with the
same pair of primers. For example, bioagent identifying amplicon
"A" and bioagent identifying amplicon "B", produced with the same
pair of primers are analogous with respect to each other. Bioagent
identifying amplicon "C", produced with a different pair of primers
is not analogous to either bioagent identifying amplicon "A" or
bioagent identifying amplicon "B".
[0216] As used herein, the term "anion exchange functional group"
refers to a positively charged functional group capable of binding
an anion through an electrostatic interaction. The most well known
anion exchange functional groups are the amines, including primary,
secondary, tertiary and quaternary amines.
[0217] The term "bacteria" or "bacterium" refers to any member of
the groups of eubacteria and archaebacteria.
[0218] As used herein, a "base composition" is the exact number of
each nucleobase (for example, A, T, C and G) in a segment of
nucleic acid. For example, amplification of nucleic acid of
Staphylococcus aureus strain carrying the lukS-PV gene with primer
pair number 2095 (SEQ ID NOs: 456:1261) produces an amplification
product 117 nucleobases in length from nucleic acid of the lukS-PV
gene that has a base composition of A35 G17 C19 T46 (by
convention--with reference to the sense strand of the amplification
product). Because the molecular masses of each of the four natural
nucleotides and chemical modifications thereof are known (if
applicable), a measured molecular mass can be deconvoluted to a
list of possible base compositions. Identification of a base
composition of a sense strand which is complementary to the
corresponding antisense strand in terms of base composition
provides a confirmation of the true base composition of an unknown
amplification product. For example, the base composition of the
antisense strand of the 139 nucleobase amplification product
described above is A46 G19 C17 T35.
[0219] As used herein, a "base composition probability cloud" is a
representation of the diversity in base composition resulting from
a variation in sequence that occurs among different isolates of a
given species. The "base composition probability cloud" represents
the base composition constraints for each species and is typically
visualized using a pseudo four-dimensional plot.
[0220] In the context of this invention, a "bioagent" is any
organism, cell, or virus, living or dead, or a nucleic acid derived
from such an organism, cell or virus. Examples of bioagents
include, but are not limited, to cells, (including but not limited
to human clinical samples, bacterial cells and other pathogens),
viruses, fungi, protists, parasites, and pathogenicity markers
(including but not limited to: pathogenicity islands, antibiotic
resistance genes, virulence factors, toxin genes and other
bioregulating compounds). Samples may be alive or dead or in a
vegetative state (for example, vegetative bacteria or spores) and
may be encapsulated or bioengineered. In the context of this
invention, a "pathogen" is a bioagent which causes a disease or
disorder.
[0221] As used herein, a "bioagent division" is defined as group of
bioagents above the species level and includes but is not limited
to, orders, families, classes, clades, genera or other such
groupings of bioagents above the species level.
[0222] As used herein, the term "bioagent identifying amplicon"
refers to a polynucleotide that is amplified from a bioagent in an
amplification reaction and which 1) provides sufficient variability
to distinguish among bioagents from whose nucleic acid the bioagent
identifying amplicon is produced and 2) whose molecular mass is
amenable to a rapid and convenient molecular mass determination
modality such as mass spectrometry, for example.
[0223] As used herein, the term "biological product" refers to any
product originating from an organism. Biological products are often
products of processes of biotechnology. Examples of biological
products include, but are not limited to: cultured cell lines,
cellular components, antibodies, proteins and other cell-derived
biomolecules, growth media, growth harvest fluids, natural products
and bio-pharmaceutical products.
[0224] The terms "biowarfare agent" and "bioweapon" are synonymous
and refer to a bacterium, virus, fungus or protozoan that could be
deployed as a weapon to cause bodily harm to individuals. Military
or terrorist groups may be implicated in deployment of biowarfare
agents.
[0225] In context of this invention, the term "broad range survey
primer pair" refers to a primer pair designed to produce bioagent
identifying amplicons across different broad groupings of
bioagents. For example, the ribosomal RNA-targeted primer pairs are
broad range survey primer pairs which have the capability of
producing bacterial bioagent identifying amplicons for essentially
all known bacteria. With respect to broad range primer pairs
employed for identification of bacteria, a broad range survey
primer pair for bacteria such as 16S rRNA primer pair number 346
(SEQ ID NOs: 202:1110) for example, will produce an bacterial
bioagent identifying amplicon for essentially all known
bacteria.
[0226] The term "calibration amplicon" refers to a nucleic acid
segment representing an amplification product obtained by
amplification of a calibration sequence with a pair of primers
designed to produce a bioagent identifying amplicon.
[0227] The term "calibration sequence" refers to a polynucleotide
sequence to which a given pair of primers hybridizes for the
purpose of producing an internal (i.e: included in the reaction)
calibration standard amplification product for use in determining
the quantity of a bioagent in a sample. The calibration sequence
may be expressly added to an amplification reaction, or may already
be present in the sample prior to analysis.
[0228] The term "clade primer pair" refers to a primer pair
designed to produce bioagent identifying amplicons for species
belonging to a clade group. A clade primer pair may also be
considered as a "speciating" primer pair which is useful for
distinguishing among closely related species.
[0229] The term "codon" refers to a set of three adjoined
nucleotides (triplet) that codes for an amino acid or a termination
signal.
[0230] In context of this invention, the term "codon base
composition analysis," refers to determination of the base
composition of an individual codon by obtaining a bioagent
identifying amplicon that includes the codon. The bioagent
identifying amplicon will at least include regions of the target
nucleic acid sequence to which the primers hybridize for generation
of the bioagent identifying amplicon as well as the codon being
analyzed, located between the two primer hybridization regions.
[0231] As used herein, the terms "complementary" or
"complementarity" are used in reference to polynucleotides (i.e., a
sequence of nucleotides such as an oligonucleotide or a target
nucleic acid) related by the base-pairing rules. For example, for
the sequence "5'-A-G-T-3'," is complementary to the sequence
"3'-T-C-A-5'." Complementarity may be "partial," in which only some
of the nucleic acids' bases are matched according to the base
pairing rules. Or, there may be "complete" or "total"
complementarity between the nucleic acids. The degree of
complementarity between nucleic acid strands has significant
effects on the efficiency and strength of hybridization between
nucleic acid strands. This is of particular importance in
amplification reactions, as well as detection methods that depend
upon binding between nucleic acids. Either term may also be used in
reference to individual nucleotides, especially within the context
of polynucleotides. For example, a particular nucleotide within an
oligonucleotide may be noted for its complementarity, or lack
thereof, to a nucleotide within another nucleic acid strand, in
contrast or comparison to the complementarity between the rest of
the oligonucleotide and the nucleic acid strand.
[0232] The term "complement of a nucleic acid sequence" as used
herein refers to an oligonucleotide which, when aligned with the
nucleic acid sequence such that the 5' end of one sequence is
paired with the 3' end of the other, is in "antiparallel
association." Certain bases not commonly found in natural nucleic
acids may be included in the nucleic acids of the present invention
and include, for example, inosine and 7-deazaguanine.
Complementarity need not be perfect; stable duplexes may contain
mismatched base pairs or unmatched bases. Those skilled in the art
of nucleic acid technology can determine duplex stability
empirically considering a number of variables including, for
example, the length of the oligonucleotide, base composition and
sequence of the oligonucleotide, ionic strength and incidence of
mismatched base pairs. Where a first oligonucleotide is
complementary to a region of a target nucleic acid and a second
oligonucleotide has complementary to the same region (or a portion
of this region) a "region of overlap" exists along the target
nucleic acid. The degree of overlap will vary depending upon the
extent of the complementarity.
[0233] In context of this invention, the term "division-wide primer
pair" refers to a primer pair designed to produce bioagent
identifying amplicons within sections of a broader spectrum of
bioagents For example, primer pair number 352 (SEQ ID NOs:
687:1411), a division-wide primer pair, is designed to produce
bacterial bioagent identifying amplicons for members of the
Bacillus group of bacteria which comprises, for example, members of
the genera Streptococci, Enterococci, and Staphylococci. Other
division-wide primer pairs may be used to produce bacterial
bioagent identifying amplicons for other groups of bacterial
bioagents.
[0234] As used herein, the term "concurrently amplifying" used with
respect to more than one amplification reaction refers to the act
of simultaneously amplifying more than one nucleic acid in a single
reaction mixture.
[0235] As used herein, the term "drill-down primer pair" refers to
a primer pair designed to produce bioagent identifying amplicons
for identification of sub-species characteristics or confirmation
of a species assignment. For example, primer pair number 2146 (SEQ
ID NOs: 437:1137), a drill-down Staphylococcus aureus genotyping
primer pair, is designed to produce Staphylococcus aureus
genotyping amplicons. Other drill-down primer pairs may be used to
produce bioagent identifying amplicons for Staphylococcus aureus
and other bacterial species.
[0236] The term "duplex" refers to the state of nucleic acids in
which the base portions of the nucleotides on one strand are bound
through hydrogen bonding the their complementary bases arrayed on a
second strand. The condition of being in a duplex form reflects on
the state of the bases of a nucleic acid. By virtue of base
pairing, the strands of nucleic acid also generally assume the
tertiary structure of a double helix, having a major and a minor
groove. The assumption of the helical form is implicit in the act
of becoming duplexed.
[0237] As used herein, the term "etiology" refers to the causes or
origins, of diseases or abnormal physiological conditions.
[0238] The term "gene" refers to a DNA sequence that comprises
control and coding sequences necessary for the production of an RNA
having a non-coding function (e.g., a ribosomal or transfer RNA), a
polypeptide or a precursor. The RNA or polypeptide can be encoded
by a full length coding sequence or by any portion of the coding
sequence so long as the desired activity or function is
retained.
[0239] The terms "homology," "homologous" and "sequence identity"
refer to a degree of identity. There may be partial homology or
complete homology. A partially homologous sequence is one that is
less than 100% identical to another sequence. Determination of
sequence identity is described in the following example: a primer
20 nucleobases in length which is otherwise identical to another 20
nucleobase primer but having two non-identical residues has 18 of
20 identical residues (18/20=0.9 or 90% sequence identity). In
another example, a primer 15 nucleobases in length having all
residues identical to a 15 nucleobase segment of a primer 20
nucleobases in length would have 15/20=0.75 or 75% sequence
identity with the 20 nucleobase primer. In context of the present
invention, sequence identity is meant to be properly determined
when the query sequence and the subject sequence are both described
and aligned in the 5' to 3' direction. Sequence alignment
algorithms such as BLAST, will return results in two different
alignment orientations. In the Plus/Plus orientation, both the
query sequence and the subject sequence are aligned in the 5' to 3'
direction. On the other hand, in the Plus/Minus orientation, the
query sequence is in the 5' to 3' direction while the subject
sequence is in the 3' to 5' direction. It should be understood that
with respect to the primers of the present invention, sequence
identity is properly determined when the alignment is designated as
Plus/Plus. Sequence identity may also encompass alternate or
modified nucleobases that perform in a functionally similar manner
to the regular nucleobases adenine, thymine, guanine and cytosine
with respect to hybridization and primer extension in amplification
reactions. In a non-limiting example, if the 5-propynyl pyrimidines
propyne C and/or propyne T replace one or more C or T residues in
one primer which is otherwise identical to another primer in
sequence and length, the two primers will have 100% sequence
identity with each other. In another non-limiting example, Inosine
(I) may be used as a replacement for G or T and effectively
hybridize to C, A or U (uracil). Thus, if inosine replaces one or
more C, A or U residues in one primer which is otherwise identical
to another primer in sequence and length, the two primers will have
100% sequence identity with each other. Other such modified or
universal bases may exist which would perform in a functionally
similar manner for hybridization and amplification reactions and
will be understood to fall within this definition of sequence
identity.
[0240] As used herein, "housekeeping gene" refers to a gene
encoding a protein or RNA involved in basic functions required for
survival and reproduction of a bioagent. Housekeeping genes
include, but are not limited to genes encoding RNA or proteins
involved in translation, replication, recombination and repair,
transcription, nucleotide metabolism, amino acid metabolism, lipid
metabolism, energy generation, uptake, secretion and the like.
[0241] As used herein, the term "hybridization" is used in
reference to the pairing of complementary nucleic acids.
Hybridization and the strength of hybridization (i.e., the strength
of the association between the nucleic acids) is influenced by such
factors as the degree of complementary between the nucleic acids,
stringency of the conditions involved, and the T.sub.m of the
formed hybrid. "Hybridization" methods involve the annealing of one
nucleic acid to another, complementary nucleic acid, i.e., a
nucleic acid having a complementary nucleotide sequence. The
ability of two polymers of nucleic acid containing complementary
sequences to find each other and anneal through base pairing
interaction is a well-recognized phenomenon. The initial
observations of the "hybridization" process by Marmur and Lane,
Proc. Natl. Acad. Sci. USA 46:453 (1960) and Doty et al., Proc.
Natl. Acad. Sci. USA 46:461 (1960) have been followed by the
refinement of this process into an essential tool of modern
biology.
[0242] The term "in silico" refers to processes taking place via
computer calculations. For example, electronic PCR (ePCR) is a
process analogous to ordinary PCR except that it is carried out
using nucleic acid sequences and primer pair sequences stored on a
computer formatted medium.
[0243] As used herein, "intelligent primers" are primers that are
designed to bind to highly conserved sequence regions of a bioagent
identifying amplicon that flank an intervening variable region and,
upon amplification, yield amplification products which ideally
provide enough variability to distinguish individual bioagents, and
which are amenable to molecular mass analysis. By the term "highly
conserved," it is meant that the sequence regions exhibit between
about 80-100%, or between about 90-100%, or between about 95-100%
identity among all, or at least 70%, at least 80%, at least 90%, at
least 95%, or at least 99% of species or strains.
[0244] The "ligase chain reaction" (LCR; sometimes referred to as
"Ligase Amplification Reaction" (LAR) described by Barany, Proc.
Natl. Acad. Sci., 88:189 (1991); Barany, PCR Methods and Applic.,
1:5 (1991); and Wu and Wallace, Genomics 4:560 (1989) has developed
into a well-recognized alternative method for amplifying nucleic
acids. In LCR, four oligonucleotides, two adjacent oligonucleotides
which uniquely hybridize to one strand of target DNA, and a
complementary set of adjacent oligonucleotides, that hybridize to
the opposite strand are mixed and DNA ligase is added to the
mixture. Provided that there is complete complementarity at the
junction, ligase will covalently link each set of hybridized
molecules. Importantly, in LCR, two probes are ligated together
only when they base-pair with sequences in the target sample,
without gaps or mismatches. Repeated cycles of denaturation,
hybridization and ligation amplify a short segment of DNA. LCR has
also been used in combination with PCR to achieve enhanced
detection of single-base changes. However, because the four
oligonucleotides used in this assay can pair to form two short
ligatable fragments, there is the potential for the generation of
target-independent background signal. The use of LCR for mutant
screening is limited to the examination of specific nucleic acid
positions.
[0245] The term "locked nucleic acid" or "LNA" refers to a nucleic
acid analogue containing one or more 2'-O,
4'-C-methylene-o-D-ribofuranosyl nucleotide monomers in an RNA
mimicking sugar conformation. LNA oligonucleotides display
unprecedented hybridization affinity toward complementary
single-stranded RNA and complementary single- or double-stranded
DNA. LNA oligonucleotides induce A-type (RNA-like) duplex
conformations. The primers of the present invention may contain LNA
modifications.
[0246] As used herein, the term "mass-modifying tag" refers to any
modification to a given nucleotide which results in an increase in
mass relative to the analogous non-mass modified nucleotide.
Mass-modifying tags can include heavy isotopes of one or more
elements included in the nucleotide such as carbon-13 for example.
Other possible modifications include addition of substituents such
as iodine or bromine at the 5 position of the nucleobase for
example.
[0247] The term "mass spectrometry" refers to measurement of the
mass of atoms or molecules. The molecules are first converted to
ions, which are separated using electric or magnetic fields
according to the ratio of their mass to electric charge. The
measured masses are used to identity the molecules.
[0248] The term "microorganism" as used herein means an organism
too small to be observed with the unaided eye and includes, but is
not limited to bacteria, virus, protozoans, fungi; and
ciliates.
[0249] The term "multi-drug resistant" or multiple-drug resistant"
refers to a microorganism which is resistant to more than one of
the antibiotics or antimicrobial agents used in the treatment of
said microorganism.
[0250] The term "multiplex PCR" refers to a PCR reaction where more
than one primer set is included in the reaction pool allowing 2 or
more different DNA targets to be amplified by PCR in a single
reaction tube.
[0251] The term "non-template tag" refers to a stretch of at least
three guanine or cytosine nucleobases of a primer used to produce a
bioagent identifying amplicon which are not complementary to the
template. A non-template tag is incorporated into a primer for the
purpose of increasing the primer-duplex stability of later cycles
of amplification by incorporation of extra G-C pairs which each
have one additional hydrogen bond relative to an A-T pair.
[0252] The term "nucleic acid sequence" as used herein refers to
the linear composition of the nucleic acid residues A, T, C or G or
any modifications thereof, within an oligonucleotide, nucleotide or
polynucleotide, and fragments or portions thereof, and to DNA or
RNA of genomic or synthetic origin which may be single or double
stranded, and represent the sense or antisense strand
[0253] As used herein, the term "nucleobase" is synonymous with
other terms in use in the art including "nucleotide,"
"deoxynucleotide," "nucleotide residue," "deoxynucleotide residue,"
"nucleotide triphosphate (NTP)," or deoxynucleotide triphosphate
(dNTP).
[0254] The term "nucleotide analog" as used herein refers to
modified or non-naturally occurring nucleotides such as 5-propynyl
pyrimidines (i.e., 5-propynyl-dTTP and 5-propynyl-dTCP), 7-deaza
purines (i.e., 7-deaza-dATP and 7-deaza-dGTP). Nucleotide analogs
include base analogs and comprise modified forms of
deoxyribonucleotides as well as ribonucleotides.
[0255] The term "oligonucleotide" as used herein is defined as a
molecule comprising two or more deoxyribonucleotides or
ribonucleotides, preferably at least 5 nucleotides, more preferably
at least about 13 to 35 nucleotides. The exact size will depend on
many factors, which in turn depend on the ultimate function or use
of the oligonucleotide. The oligonucleotide may be generated in any
manner, including chemical synthesis, DNA replication, reverse
transcription, PCR, or a combination thereof. Because
mononucleotides are reacted to make oligonucleotides in a manner
such that the 5' phosphate of one mononucleotide pentose ring is
attached to the 3' oxygen of its neighbor in one direction via a
phosphodiester linkage, an end of an oligonucleotide is referred to
as the "5'-end" if its 5' phosphate is not linked to the 3' oxygen
of a mononucleotide pentose ring and as the "3'-end" if its 3'
oxygen is not linked to a 5' phosphate of a subsequent
mononucleotide pentose ring. As used herein, a nucleic acid
sequence, even if internal to a larger oligonucleotide, also may be
said to have 5' and 3' ends. A first region along a nucleic acid
strand is said to be upstream of another region if the 3' end of
the first region is before the 5' end of the second region when
moving along a strand of nucleic acid in a 5' to 3' direction. All
oligonucleotide primers disclosed herein are understood to be
presented in the 5' to 3' direction when reading left to right.
When two different, non-overlapping oligonucleotides anneal to
different regions of the same linear complementary nucleic acid
sequence, and the 3' end of one oligonucleotide points towards the
5' end of the other, the former may be called the "upstream"
oligonucleotide and the latter the "downstream" oligonucleotide.
Similarly, when two overlapping oligonucleotides are hybridized to
the same linear complementary nucleic acid sequence, with the first
oligonucleotide positioned such that its 5' end is upstream of the
5' end of the second oligonucleotide, and the 3' end of the first
oligonucleotide is upstream of the 3' end of the second
oligonucleotide, the first oligonucleotide may be called the
"upstream" oligonucleotide and the second oligonucleotide may be
called the "downstream" oligonucleotide.
[0256] In the context of this invention, a "pathogen" is a bioagent
which causes a disease or disorder.
[0257] As used herein, the terms "PCR product," "PCR fragment," and
"amplification product" refer to the resultant mixture of compounds
after two or more cycles of the PCR steps of denaturation,
annealing and extension are complete. These terms encompass the
case where there has been amplification of one or more segments of
one or more target sequences.
[0258] The term "peptide nucleic acid" ("PNA") as used herein
refers to a molecule comprising bases or base analogs such as would
be found in natural nucleic acid, but attached to a peptide
backbone rather than the sugar-phosphate backbone typical of
nucleic acids. The attachment of the bases to the peptide is such
as to allow the bases to base pair with complementary bases of
nucleic acid in a manner similar to that of an oligonucleotide.
These small molecules, also designated anti gene agents, stop
transcript elongation by binding to their complementary strand of
nucleic acid (Nielsen, et al. Anticancer Drug Des. 8:53 63). The
primers of the present invention may comprise PNAs.
[0259] The term "polymerase" refers to an enzyme having the ability
to synthesize a complementary strand of nucleic acid from a
starting template nucleic acid strand and free dNTPs.
[0260] As used herein, the term "polymerase chain reaction" ("PCR")
refers to the method of K. B. Mullis U.S. Pat. Nos. 4,683,195,
4,683,202, and 4,965,188, hereby incorporated by reference, that
describe a method for increasing the concentration of a segment of
a target sequence in a mixture of genomic DNA without cloning or
purification. This process for amplifying the target sequence
consists of introducing a large excess of two oligonucleotide
primers to the DNA mixture containing the desired target sequence,
followed by a precise sequence of thermal cycling in the presence
of a DNA polymerase. The two primers are complementary to their
respective strands of the double stranded target sequence. To
effect amplification, the mixture is denatured and the primers then
annealed to their complementary sequences within the target
molecule. Following annealing, the primers are extended with a
polymerase so as to form a new pair of complementary strands. The
steps of denaturation, primer annealing, and polymerase extension
can be repeated many times (i.e., denaturation, annealing and
extension constitute one "cycle"; there can be numerous "cycles")
to obtain a high concentration of an amplified segment of the
desired target sequence. The length of the amplified segment of the
desired target sequence is determined by the relative positions of
the primers with respect to each other, and therefore, this length
is a controllable parameter. By virtue of the repeating aspect of
the process, the method is referred to as the "polymerase chain
reaction" (hereinafter "PCR"). Because the desired amplified
segments of the target sequence become the predominant sequences
(in terms of concentration) in the mixture, they are said to be
"PCR amplified." With PCR, it is possible to amplify a single copy
of a specific target sequence in genomic DNA to a level detectable
by several different methodologies (e.g., hybridization with a
labeled probe; incorporation of biotinylated primers followed by
avidin-enzyme conjugate detection; incorporation of 32P-labeled
deoxynucleotide triphosphates, such as dCTP or dATP, into the
amplified segment). In addition to genomic DNA, any oligonucleotide
or polynucleotide sequence can be amplified with the appropriate
set of primer molecules. In particular, the amplified segments
created by the PCR process itself are, themselves, efficient
templates for subsequent PCR amplifications.
[0261] The term "polymerization means" or "polymerization agent"
refers to any agent capable of facilitating the addition of
nucleoside triphosphates to an oligonucleotide. Preferred
polymerization means comprise DNA and RNA polymerases.
[0262] As used herein, the terms "pair of primers," or "primer
pair" are synonymous. A primer pair is used for amplification of a
nucleic acid sequence. A pair of primers comprises a forward primer
and a reverse primer. The forward primer hybridizes to a sense
strand of a target gene sequence to be amplified and primes
synthesis of an antisense strand (complementary to the sense
strand) using the target sequence as a template. A reverse primer
hybridizes to the antisense strand of a target gene sequence to be
amplified and primes synthesis of a sense strand (complementary to
the antisense strand) using the target sequence as a template.
[0263] The primers are designed to bind to highly conserved
sequence regions of a bioagent identifying amplicon that flank an
intervening variable region and yield amplification products which
ideally provide enough variability to distinguish each individual
bioagent, and which are amenable to molecular mass analysis. In
some embodiments, the highly conserved sequence regions exhibit
between about 80-100%, or between about 90-100%, or between about
95-100% identity, or between about 99-100% identity. The molecular
mass of a given amplification product provides a means of
identifying the bioagent from which it was obtained, due to the
variability of the variable region. Thus design of the primers
requires selection of a variable region with appropriate
variability to resolve the identity of a given bioagent. Bioagent
identifying amplicons are ideally specific to the identity of the
bioagent.
[0264] Properties of the primers may include any number of
properties related to structure including, but not limited to:
nucleobase length which may be contiguous (linked together) or
non-contiguous (for example, two or more contiguous segments which
are joined by a linker or loop moiety), modified or universal
nucleobases (used for specific purposes such as for example,
increasing hybridization affinity, preventing non-templated
adenylation and modifying molecular mass) percent complementarity
to a given target sequences.
[0265] Properties of the primers also include functional features
including, but not limited to, orientation of hybridization
(forward or reverse) relative to a nucleic acid template. The
coding or sense strand is the strand to which the forward priming
primer hybridizes (forward priming orientation) while the reverse
priming primer hybridizes to the non-coding or antisense strand
(reverse priming orientation). The functional properties of a given
primer pair also include the generic template nucleic acid to which
the primer pair hybridizes. For example, identification of
bioagents can be accomplished at different levels using primers
suited to resolution of each individual level of identification.
Broad range survey primers are designed with the objective of
identifying a bioagent as a member of a particular division (e.g.,
an order, family, genus or other such grouping of bioagents above
the species level of bioagents). In some embodiments, broad range
survey intelligent primers are capable of identification of
bioagents at the species or sub-species level. Other primers may
have the functionality of producing bioagent identifying amplicons
for members of a given taxonomic genus, clade, species, sub-species
or genotype (including genetic variants which may include presence
of virulence genes or antibiotic resistance genes or mutations).
Additional functional properties of primer pairs include the
functionality of performing amplification either singly (single
primer pair per amplification reaction vessel) or in a multiplex
fashion (multiple primer pairs and multiple amplification reactions
within a single reaction vessel).
[0266] As used herein, the terms "purified" or "substantially
purified" refer to molecules, either nucleic or amino acid
sequences, that are removed from their natural environment,
isolated or separated, and are at least 60% free, preferably 75%
free, and most preferably 90% free from other components with which
they are naturally associated. An "isolated polynucleotide" or
"isolated oligonucleotide" is therefore a substantially purified
polynucleotide.
[0267] The term "reverse transcriptase" refers to an enzyme having
the ability to transcribe DNA from an RNA template. This enzymatic
activity is known as reverse transcriptase activity. Reverse
transcriptase activity is desirable in order to obtain DNA from RNA
viruses which can then be amplified and analyzed by the methods of
the present invention.
[0268] The term "ribosomal RNA" or "rRNA" refers to the primary
ribonucleic acid constituent of ribosomes. Ribosomes are the
protein-manufacturing organelles of cells and exist in the
cytoplasm. Ribosomal RNAs are transcribed from the DNA genes
encoding them.
[0269] The term "sample" in the present specification and claims is
used in its broadest sense. On the one hand it is meant to include
a specimen or culture (e.g., microbiological cultures). On the
other hand, it is meant to include both biological and
environmental samples. A sample may include a specimen of synthetic
origin. Biological samples may be animal, including human, fluid,
solid (e.g., stool) or tissue, as well as liquid and solid food and
feed products and ingredients such as dairy items, vegetables, meat
and meat by-products, and waste. Biological samples may be obtained
from all of the various families of domestic animals, as well as
feral or wild animals, including, but not limited to, such animals
as ungulates, bear, fish, lagamorphs, rodents, etc. Environmental
samples include environmental material such as surface matter,
soil, water, air and industrial samples, as well as samples
obtained from food and dairy processing instruments, apparatus,
equipment, utensils, disposable and non-disposable items. These
examples are not to be construed as limiting the sample types
applicable to the present invention. The term "source of target
nucleic acid" refers to any sample that contains nucleic acids (RNA
or DNA). Particularly preferred sources of target nucleic acids are
biological samples including, but not limited to blood, saliva,
cerebral spinal fluid, pleural fluid, milk, lymph, sputum and
semen.
[0270] As used herein, the term "sample template" refers to nucleic
acid originating from a sample that is analyzed for the presence of
"target" (defined below). In contrast, "background template" is
used in reference to nucleic acid other than sample template that
may or may not be present in a sample. Background template is often
a contaminant. It may be the result of carryover, or it may be due
to the presence of nucleic acid contaminants sought to be purified
away from the sample. For example, nucleic acids from organisms
other than those to be detected may be present as background in a
test sample.
[0271] A "segment" is defined herein as a region of nucleic acid
within a target sequence.
[0272] The "self-sustained sequence replication reaction" (3SR)
(Guatelli et al., Proc. Natl. Acad. Sci., 87:1874-1878 [1990], with
an erratum at Proc. Natl. Acad. Sci., 87:7797 [1990]) is a
transcription-based in vitro amplification system (Kwok et al.,
Proc. Natl. Acad. Sci., 86:1173-1177 [1989]) that can exponentially
amplify RNA sequences at a uniform temperature. The amplified RNA
can then be utilized for mutation detection (Fahy et al., PCR Meth.
Appl., 1:25-33 [1991]). In this method, an oligonucleotide primer
is used to add a phage RNA polymerase promoter to the 5' end of the
sequence of interest. In a cocktail of enzymes and substrates that
includes a second primer, reverse transcriptase, RNase H, RNA
polymerase and ribo- and deoxyribonucleoside triphosphates, the
target sequence undergoes repeated rounds of transcription, cDNA
synthesis and second-strand synthesis to amplify the area of
interest. The use of 3SR to detect mutations is kinetically limited
to screening small segments of DNA (e.g., 200-300 base pairs).
[0273] As used herein, the term ""sequence alignment"" refers to a
listing of multiple DNA or amino acid sequences and aligns them to
highlight their similarities. The listings can be made using
bioinformatics computer programs.
[0274] In context of this invention, the term "speciating primer
pair" refers to a primer pair designed to produce a bioagent
identifying amplicon with the diagnostic capability of identifying
species members of a group of genera or a particular genus of
bioagents. Primer pair number 2249 (SEQ ID NOs: 430:1321), for
example, is a speciating primer pair used to distinguish
Staphylococcus aureus from other species of the genus
Staphylococcus.
[0275] As used herein, a "sub-species characteristic" is a genetic
characteristic that provides the means to distinguish two members
of the same bioagent species. For example, one viral strain could
be distinguished from another viral strain of the same species by
possessing a genetic change (e.g., for example, a nucleotide
deletion, addition or substitution) in one of the viral genes, such
as the RNA-dependent RNA polymerase. Sub-species characteristics
such as virulence genes and drug--are responsible for the
phenotypic differences among the different strains of bacteria.
[0276] As used herein, the term "target" is used in a broad sense
to indicate the gene or genomic region being amplified by the
primers. Because the present invention provides a plurality of
amplification products from any given primer pair (depending on the
bioagent being analyzed), multiple amplification products from
different specific nucleic acid sequences may be obtained. Thus,
the term "target" is not used to refer to a single specific nucleic
acid sequence. The "target" is sought to be sorted out from other
nucleic acid sequences and contains a sequence that has at least
partial complementarity with an oligonucleotide primer. The target
nucleic acid may comprise single- or double-stranded DNA or RNA. A
"segment" is defined as a region of nucleic acid within the target
sequence.
[0277] The term "template" refers to a strand of nucleic acid on
which a complementary copy is built from nucleoside triphosphates
through the activity of a template-dependent nucleic acid
polymerase. Within a duplex the template strand is, by convention,
depicted and described as the "bottom" strand. Similarly, the
non-template strand is often depicted and described as the "top"
strand.
[0278] As used herein, the term "T.sub.m" is used in reference to
the "melting temperature." The melting temperature is the
temperature at which a population of double-stranded nucleic acid
molecules becomes half dissociated into single strands. Several
equations for calculating the T.sub.m of nucleic acids are well
known in the art. As indicated by standard references, a simple
estimate of the T.sub.m value may be calculated by the equation:
T.sub.m=81.5+0.41(% G+C), when a nucleic acid is in aqueous
solution at 1 M NaCl (see e.g., Anderson and Young, Quantitative
Filter Hybridization, in Nucleic Acid Hybridization (1985). Other
references (e.g., Allawi, H. T. & SantaLucia, J., Jr.
Thermodynamics and NMR of internal G.T mismatches in DNA.
Biochemistry 36, 10581-94 (1997) include more sophisticated
computations which take structural and environmental, as well as
sequence characteristics into account for the calculation of
T.sub.m.
[0279] The term "triangulation genotyping analysis" refers to a
method of genotyping a bioagent by measurement of molecular masses
or base compositions of amplification products, corresponding to
bioagent identifying amplicons, obtained by amplification of
regions of more than one gene. In this sense, the term
"triangulation" refers to a method of establishing the accuracy of
information by comparing three or more types of independent points
of view bearing on the same findings. Triangulation genotyping
analysis carried out with a plurality of triangulation genotyping
analysis primers yields a plurality of base compositions that then
provide a pattern or "barcode" from which a species type can be
assigned. The species type may represent a previously known
sub-species or strain, or may be a previously unknown strain having
a specific and previously unobserved base composition barcode
indicating the existence of a previously unknown genotype.
[0280] As used herein, the term "triangulation genotyping analysis
primer pair" is a primer pair designed to produce bioagent
identifying amplicons for determining species types in a
triangulation genotyping analysis.
[0281] The employment of more than one bioagent identifying
amplicon for identification of a bioagent is herein referred to as
"triangulation identification." Triangulation identification is
pursued by analyzing a plurality of bioagent identifying amplicons
produced with different primer pairs. This process is used to
reduce false negative and false positive signals, and enable
reconstruction of the origin of hybrid or otherwise engineered
bioagents. For example, identification of the three part toxin
genes typical of B. anthracis (Bowen et al., J. Appl. Microbiol.,
1999, 87, 270-278) in the absence of the expected signatures from
the B. anthracis genome would suggest a genetic engineering
event.
[0282] In the context of this invention, the term "unknown
bioagent" may mean either: (i) a bioagent whose existence is known
(such as the well known bacterial species Staphylococcus aureus for
example) but which is not known to be in a sample to be analyzed,
or (ii) a bioagent whose existence is not known (for example, the
SARS coronavirus was unknown prior to April 2003). For example, if
the method for identification of coronaviruses disclosed in
commonly owned U.S. patent Ser. No. 10/829,826 (incorporated herein
by reference in its entirety) was to be employed prior to April
2003 to identify the SARS coronavirus in a clinical sample, both
meanings of "unknown" bioagent are applicable since the SARS
coronavirus was unknown to science prior to April, 2003 and since
it was not known what bioagent (in this case a coronavirus) was
present in the sample. On the other hand, if the method of U.S.
patent Ser. No. 10/829,826 was to be employed subsequent to April
2003 to identify the SARS coronavirus in a clinical sample, only
the first meaning (i) of "unknown" bioagent would apply since the
SARS coronavirus became known to science subsequent to April 2003
and since it was not known what bioagent was present in the
sample.
[0283] The term "variable sequence" as used herein refers to
differences in nucleic acid sequence between two nucleic acids. For
example, the genes of two different bacterial species may vary in
sequence by the presence of single base substitutions and/or
deletions or insertions of one or more nucleotides. These two forms
of the structural gene are said to vary in sequence from one
another. In the context of the present invention, "viral nucleic
acid" includes, but is not limited to, DNA, RNA, or DNA that has
been obtained from viral RNA, such as, for example, by performing a
reverse transcription reaction. Viral RNA can either be
single-stranded (of positive or negative polarity) or
double-stranded.
[0284] The term "virus" refers to obligate, ultramicroscopic,
parasites that are incapable of autonomous replication (i.e.,
replication requires the use of the host cell's machinery). Viruses
can survive outside of a host cell but cannot replicate.
[0285] The term "wild-type" refers to a gene or a gene product that
has the characteristics of that gene or gene product when isolated
from a naturally occurring source. A wild-type gene is that which
is most frequently observed in a population and is thus arbitrarily
designated the "normal" or "wild-type" form of the gene. In
contrast, the term "modified", "mutant" or "polymorphic" refers to
a gene or gene product that displays modifications in sequence and
or functional properties (i.e., altered characteristics) when
compared to the wild-type gene or gene product. It is noted that
naturally-occurring mutants can be isolated; these are identified
by the fact that they have altered characteristics when compared to
the wild-type gene or gene product.
[0286] As used herein, a "wobble base" is a variation in a codon
found at the third nucleotide position of a DNA triplet. Variations
in conserved regions of sequence are often found at the third
nucleotide position due to redundancy in the amino acid code.
DETAILED DESCRIPTION OF EMBODIMENTS
A. Bioagent Identifying Amplicons
[0287] The present invention provides methods for detection and
identification of unknown bioagents using bioagent identifying
amplicons. Primers are selected to hybridize to conserved sequence
regions of nucleic acids derived from a bioagent, and which bracket
variable sequence regions to yield a bioagent identifying amplicon,
which can be amplified and which is amenable to molecular mass
determination. The molecular mass then provides a means to uniquely
identify the bioagent without a requirement for prior knowledge of
the possible identity of the bioagent. The molecular mass or
corresponding base composition signature of the amplification
product is then matched against a database of molecular masses or
base composition signatures. A match is obtained when an
experimentally-determined molecular mass or base composition of an
analyzed amplification product is compared with known molecular
masses or base compositions of known bioagent identifying amplicons
and the experimentally determined molecular mass or base
composition is the same as the molecular mass or base composition
of one of the known bioagent identifying amplicons. Alternatively,
the experimentally-determined molecular mass or base composition
may be within experimental error of the molecular mass or base
composition of a known bioagent identifying amplicon and still be
classified as a match. In some cases, the match may also be
classified using a probability of match model such as the models
described in U.S. Ser. No. 11/073,362, which is commonly owned and
incorporated herein by reference in entirety. Furthermore, the
method can be applied to rapid parallel multiplex analyses, the
results of which can be employed in a triangulation identification
strategy. The present method provides rapid throughput and does not
require nucleic acid sequencing of the amplified target sequence
for bioagent detection and identification.
[0288] Despite enormous biological diversity, all forms of life on
earth share sets of essential, common features in their genomes.
Since genetic data provide the underlying basis for identification
of bioagents by the methods of the present invention, it is
necessary to select segments of nucleic acids which ideally provide
enough variability to distinguish each individual bioagent and
whose molecular mass is amenable to molecular mass
determination.
[0289] Unlike bacterial genomes, which exhibit conservation of
numerous genes (i.e. housekeeping genes) across all organisms,
viruses do not share a gene that is essential and conserved among
all virus families. Therefore, viral identification is achieved
within smaller groups of related viruses, such as members of a
particular virus family or genus. For example, RNA-dependent RNA
polymerase is present in all single-stranded RNA viruses and can be
used for broad priming as well as resolution within the virus
family.
[0290] In some embodiments of the present invention, at least one
bacterial nucleic acid segment is amplified in the process of
identifying the bacterial bioagent. Thus, the nucleic acid segments
that can be amplified by the primers disclosed herein and that
provide enough variability to distinguish each individual bioagent
and whose molecular masses are amenable to molecular mass
determination are herein described as bioagent identifying
amplicons.
[0291] In some embodiments of the present invention, bioagent
identifying amplicons comprise from about 45 to about 150
nucleobases (i.e. from about 45 to about 200 linked nucleosides),
although both longer and short regions may be used. One of ordinary
skill in the art will appreciate that the invention embodies
compounds of 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,
92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,
107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145,
146, 147, 148, 149, and 150 nucleobases in length, or any range
therewithin.
[0292] It is the combination of the portions of the bioagent
nucleic acid segment to which the primers hybridize (hybridization
sites) and the variable region between the primer hybridization
sites that comprises the bioagent identifying amplicon. Thus, it
can be said that a given bioagent identifying amplicon is "defined
by" a given pair of primers.
[0293] In some embodiments, bioagent identifying amplicons amenable
to molecular mass determination which are produced by the primers
described herein are either of a length, size or mass compatible
with the particular mode of molecular mass determination or
compatible with a means of providing a predictable fragmentation
pattern in order to obtain predictable fragments of a length
compatible with the particular mode of molecular mass
determination. Such means of providing a predictable fragmentation
pattern of an amplification product include, but are not limited
to, cleavage with chemical reagents, restriction enzymes or
cleavage primers, for example. Thus, in some embodiments, bioagent
identifying amplicons are larger than 150 nucleobases and are
amenable to molecular mass determination following restriction
digestion. Methods of using restriction enzymes and cleavage
primers are well known to those with ordinary skill in the art.
[0294] In some embodiments, amplification products corresponding to
bioagent identifying amplicons are obtained using the polymerase
chain reaction (PCR) that is a routine method to those with
ordinary skill in the molecular biology arts. Other amplification
methods may be used such as ligase chain reaction (LCR),
low-stringency single primer PCR, and multiple strand displacement
amplification (MDA). These methods are also known to those with
ordinary skill.
B. Primers and Primer Pairs
[0295] In some embodiments, the primers are designed to bind to
conserved sequence regions of a bioagent identifying amplicon that
flank an intervening variable region and yield amplification
products which provide variability sufficient to distinguish each
individual bioagent, and which are amenable to molecular mass
analysis. In some embodiments, the highly conserved sequence
regions exhibit between about 80-100%, or between about 90-100%, or
between about 95-100% identity, or between about 99-100% identity.
The molecular mass of a given amplification product provides a
means of identifying the bioagent from which it was obtained, due
to the variability of the variable region. Thus, design of the
primers involves selection of a variable region with sufficient
variability to resolve the identity of a given bioagent. In some
embodiments, bioagent identifying amplicons are specific to the
identity of the bioagent.
[0296] In some embodiments, identification of bioagents is
accomplished at different levels using primers suited to resolution
of each individual level of identification. Broad range survey
primers are designed with the objective of identifying a bioagent
as a member of a particular division (e.g., an order, family, genus
or other such grouping of bioagents above the species level of
bioagents). In some embodiments, broad range survey intelligent
primers are capable of identification of bioagents at the species
or sub-species level. Examples of broad range survey primers
include, but are not limited to: primer pair numbers: 346 (SEQ ID
NOs: 202:1110), 347 (SEQ ID NOs: 560:1278), 348 SEQ ID NOs:
706:895), and 361 (SEQ ID NOs: 697:1398) which target DNA encoding
16S rRNA, and primer pair numbers 349 (SEQ ID NOs: 401:1156) and
360 (SEQ ID NOs: 409:1434) which target DNA encoding 23S rRNA.
[0297] In some embodiments, drill-down primers are designed with
the objective of identifying a bioagent at the sub-species level
(including strains, subtypes, variants and isolates) based on
sub-species characteristics which may, for example, include single
nucleotide polymorphisms (SNPs), variable number tandem repeats
(VNTRs), deletions, drug resistance mutations or any other
modification of a nucleic acid sequence of a bioagent relative to
other members of a species having different sub-species
characteristics. Drill-down intelligent primers are not always
required for identification at the sub-species level because broad
range survey intelligent primers may, in some cases provide
sufficient identification resolution to accomplishing this
identification objective. Examples of drill-down primers include,
but are not limited to: confirmation primer pairs such as primer
pair numbers 351 (SEQ ID NOs: 355:1423) and 353 (SEQ ID NOs:
220:1394), which target the pX01 virulence plasmid of Bacillus
anthracis. Other examples of drill-down primer pairs are found in
sets of triangulation genotyping primer pairs such as, for example,
the primer pair number 2146 (SEQ ID NOs: 437:1137) which targets
the arcC gene (encoding carmabate kinase) and is included in an 8
primer pair panel or kit for use in genotyping Staphylococcus
aureus, or in other panels or kits of primer pairs used for
determining drug-resistant bacterial strains, such as, for example,
primer pair number 2095 (SEQ ID NOs: 456:1261) which targets the
pv-luk gene (encoding Panton-Valentine leukocidin) and is included
in an 8 primer pair panel or kit for use in identification of drug
resistant strains of Staphylococcus aureus.
[0298] A representative process flow diagram used for primer
selection and validation process is outlined in FIG. 1. For each
group of organisms, candidate target sequences are identified (200)
from which nucleotide alignments are created (210) and analyzed
(220). Primers are then designed by selecting appropriate priming
regions (230) to facilitate the selection of candidate primer pairs
(240). The primer pairs are then subjected to in silico analysis by
electronic PCR (ePCR) (300) wherein bioagent identifying amplicons
are obtained from sequence databases such as GenBank or other
sequence collections (310) and checked for specificity in silico
(320). Bioagent identifying amplicons obtained from GenBank
sequences (310) can also be analyzed by a probability model which
predicts the capability of a given amplicon to identify unknown
bioagents such that the base compositions of amplicons with
favorable probability scores are then stored in a base composition
database (325). Alternatively, base compositions of the bioagent
identifying amplicons obtained from the primers and GenBank
sequences can be directly entered into the base composition
database (330). Candidate primer pairs (240) are validated by
testing their ability to hybridize to target nucleic acid by an in
vitro amplification by a method such as PCR analysis (400) of
nucleic acid from a collection of organisms (410). Amplification
products thus obtained are analyzed by gel electrophoresis or by
mass spectrometry to confirm the sensitivity, specificity and
reproducibility of the primers used to obtain the amplification
products (420).
[0299] Many of the important pathogens, including the organisms of
greatest concern as biowarfare agents, have been completely
sequenced. This effort has greatly facilitated the design of
primers for the detection of unknown bioagents. The combination of
broad-range priming with division-wide and drill-down priming has
been used very successfully in several applications of the
technology, including environmental surveillance for biowarfare
threat agents and clinical sample analysis for medically important
pathogens.
[0300] Synthesis of primers is well known and routine in the art.
The primers may be conveniently and routinely made through the
well-known technique of solid phase synthesis. Equipment for such
synthesis is sold by several vendors including, for example,
Applied Biosystems (Foster City, Calif.). Any other means for such
synthesis known in the art may additionally or alternatively be
employed.
[0301] In some embodiments primers are employed as compositions for
use in methods for identification of bacterial bioagents as
follows: a primer pair composition is contacted with nucleic acid
(such as, for example, bacterial DNA or DNA reverse transcribed
from the rRNA) of an unknown bacterial bioagent. The nucleic acid
is then amplified by a nucleic acid amplification technique, such
as PCR for example, to obtain an amplification product that
represents a bioagent identifying amplicon. The molecular mass of
each strand of the double-stranded amplification product is
determined by a molecular mass measurement technique such as mass
spectrometry for example, wherein the two strands of the
double-stranded amplification product are separated during the
ionization process. In some embodiments, the mass spectrometry is
electrospray Fourier transform ion cyclotron resonance mass
spectrometry (ESI-FTICR-MS) or electrospray time of flight mass
spectrometry (ESI-TOF-MS). A list of possible base compositions can
be generated for the molecular mass value obtained for each strand
and the choice of the correct base composition from the list is
facilitated by matching the base composition of one strand with a
complementary base composition of the other strand. The molecular
mass or base composition thus determined is then compared with a
database of molecular masses or base compositions of analogous
bioagent identifying amplicons for known viral bioagents. A match
between the molecular mass or base composition of the amplification
product and the molecular mass or base composition of an analogous
bioagent identifying amplicon for a known viral bioagent indicates
the identity of the unknown bioagent. In some embodiments, the
primer pair used is one of the primer pairs of Table 2. In some
embodiments, the method is repeated using one or more different
primer pairs to resolve possible ambiguities in the identification
process or to improve the confidence level for the identification
assignment.
[0302] In some embodiments, a bioagent identifying amplicon may be
produced using only a single primer (either the forward or reverse
primer of any given primer pair), provided an appropriate
amplification method is chosen, such as, for example, low
stringency single primer PCR (LSSP-PCR). Adaptation of this
amplification method in order to produce bioagent identifying
amplicons can be accomplished by one with ordinary skill in the art
without undue experimentation.
[0303] In some embodiments, the oligonucleotide primers are broad
range survey primers which hybridize to conserved regions of
nucleic acid encoding the hexon gene of all (or between 80% and
100%, between 85% and 100%, between 90% and 100% or between 95% and
100%) known bacteria and produce bacterial bioagent identifying
amplicons.
[0304] In some cases, the molecular mass or base composition of a
bacterial bioagent identifying amplicon defined by a broad range
survey primer pair does not provide enough resolution to
unambiguously identify a bacterial bioagent at or below the species
level. These cases benefit from further analysis of one or more
bacterial bioagent identifying amplicons generated from at least
one additional broad range survey primer pair or from at least one
additional division-wide primer pair. The employment of more than
one bioagent identifying amplicon for identification of a bioagent
is herein referred to as triangulation identification.
[0305] In other embodiments, the oligonucleotide primers are
division-wide primers which hybridize to nucleic acid encoding
genes of species within a genus of bacteria. In other embodiments,
the oligonucleotide primers are drill-down primers which enable the
identification of sub-species characteristics. Drill down primers
provide the functionality of producing bioagent identifying
amplicons for drill-down analyses such as strain typing when
contacted with nucleic acid under amplification conditions.
Identification of such sub-species characteristics is often
critical for determining proper clinical treatment of viral
infections. In some embodiments, sub-species characteristics are
identified using only broad range survey primers and division-wide
and drill-down primers are not used.
[0306] In some embodiments, the primers used for amplification
hybridize to and amplify genomic DNA, and DNA of bacterial
plasmids.
[0307] In some embodiments, various computer software programs may
be used to aid in design of primers for amplification reactions
such as Primer Premier 5 (Premier Biosoft, Palo Alto, Calif.) or
OLIGO Primer Analysis Software (Molecular Biology Insights,
Cascade, Colo.). These programs allow the user to input desired
hybridization conditions such as melting temperature of a
primer-template duplex for example. In some embodiments, an in
silico PCR search algorithm, such as (ePCR) is used to analyze
primer specificity across a plurality of template sequences which
can be readily obtained from public sequence databases such as
GenBank for example. An existing RNA structure search algorithm
(Macke et al., Nucl. Acids Res., 2001, 29, 4724-4735, which is
incorporated herein by reference in its entirety) has been modified
to include PCR parameters such as hybridization conditions,
mismatches, and thermodynamic calculations (SantaLucia, Proc. Natl.
Acad. Sci. U.S.A., 1998, 95, 1460-1465, which is incorporated
herein by reference in its entirety). This also provides
information on primer specificity of the selected primer pairs. In
some embodiments, the hybridization conditions applied to the
algorithm can limit the results of primer specificity obtained from
the algorithm. In some embodiments, the melting temperature
threshold for the primer template duplex is specified to be
35.degree. C. or a higher temperature. In some embodiments the
number of acceptable mismatches is specified to be seven mismatches
or less. In some embodiments, the buffer components and
concentrations and primer concentrations may be specified and
incorporated into the algorithm, for example, an appropriate primer
concentration is about 250 nM and appropriate buffer components are
50 mM sodium or potassium and 1.5 mM Mg.sup.2+.
[0308] One with ordinary skill in the art of design of
amplification primers will recognize that a given primer need not
hybridize with 100% complementarity in order to effectively prime
the synthesis of a complementary nucleic acid strand in an
amplification reaction. Moreover, a primer may hybridize over one
or more segments such that intervening or adjacent segments are not
involved in the hybridization event. (e.g., for example, a loop
structure or a hairpin structure). The primers of the present
invention may comprise at least 70%, at least 75%, at least 80%, at
least 85%, at least 90%, at least 95% or at least 99% sequence
identity with any of the primers listed in Table 2. Thus, in some
embodiments of the present invention, an extent of variation of 70%
to 100%, or any range therewithin, of the sequence identity is
possible relative to the specific primer sequences disclosed
herein. Determination of sequence identity is described in the
following example: a primer 20 nucleobases in length which is
identical to another 20 nucleobase primer having two non-identical
residues has 18 of 20 identical residues (18/20=0.9 or 90% sequence
identity). In another example, a primer 15 nucleobases in length
having all residues identical to a 15 nucleobase segment of primer
20 nucleobases in length would have 15/20=0.75 or 75% sequence
identity with the 20 nucleobase primer.
[0309] Percent homology, sequence identity or complementarity, can
be determined by, for example, the Gap program (Wisconsin Sequence
Analysis Package, Version 8 for UNIX, Genetics Computer Group,
University Research Park, Madison Wis.), using default settings,
which uses the algorithm of Smith and Waterman (Adv. Appl. Math.,
1981, 2, 482-489). In some embodiments, complementarity of primers
with respect to the conserved priming regions of viral nucleic acid
is between about 70% and about 75% 80%. In other embodiments,
homology, sequence identity or complementarity, is between about
75% and about 80%. In yet other embodiments, homology, sequence
identity or complementarity, is at least 85%, at least 90%, at
least 92%, at least 94%, at least 95%, at least 96%, at least 97%,
at least 98%, at least 99% or is 100%.
[0310] In some embodiments, the primers described herein comprise
at least 70%, at least 75%, at least 80%, at least 85%, at least
90%, at least 92%, at least 94%, at least 95%, at least 96%, at
least 98%, or at least 99%, or 100% (or any range therewithin)
sequence identity with the primer sequences specifically disclosed
herein.
[0311] One with ordinary skill is able to calculate percent
sequence identity or percent sequence homology and able to
determine, without undue experimentation, the effects of variation
of primer sequence identity on the function of the primer in its
role in priming synthesis of a complementary strand of nucleic acid
for production of an amplification product of a corresponding
bioagent identifying amplicon.
[0312] In one embodiment, the primers are at least 13 nucleobases
in length. In another embodiment, the primers are less than 36
nucleobases in length.
[0313] In some embodiments of the present invention, the
oligonucleotide primers are 13 to 35 nucleobases in length (13 to
35 linked nucleotide residues). These embodiments comprise
oligonucleotide primers 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleobases in
length, or any range therewithin. The present invention
contemplates using both longer and shorter primers. Furthermore,
the primers may also be linked to one or more other desired
moieties, including, but not limited to, affinity groups, ligands,
regions of nucleic acid that are not complementary to the nucleic
acid to be amplified, labels, etc. Primers may also form hairpin
structures. For example, hairpin primers may be used to amplify
short target nucleic acid molecules. The presence of the hairpin
may stabilize the amplification complex (see e.g., TAQMAN MicroRNA
Assays, Applied Biosystems, Foster City, Calif.).
[0314] In some embodiments, any oligonucleotide primer pair may
have one or both primers with less then 70% sequence homology with
a corresponding member of any of the primer pairs of Table 2 if the
primer pair has the capability of producing an amplification
product corresponding to a bioagent identifying amplicon. In other
embodiments, any oligonucleotide primer pair may have one or both
primers with a length greater than 35 nucleobases if the primer
pair has the capability of producing an amplification product
corresponding to a bioagent identifying amplicon.
[0315] In some embodiments, the function of a given primer may be
substituted by a combination of two or more primers segments that
hybridize adjacent to each other or that are linked by a nucleic
acid loop structure or linker which allows a polymerase to extend
the two or more primers in an amplification reaction.
[0316] In some embodiments, the primer pairs used for obtaining
bioagent identifying amplicons are the primer pairs of Table 2. In
other embodiments, other combinations of primer pairs are possible
by combining certain members of the forward primers with certain
members of the reverse primers. An example can be seen in Table 2
for two primer pair combinations of forward primer
16S_EC.sub.--789.sub.--810_F (SEQ ID NO:206), with the reverse
primers 16S_EC.sub.--880.sub.--894_R (SEQ ID NO: 796), or
16S_EC.sub.--882.sub.--899_R or (SEQ ID NO: 818). Arriving at a
favorable alternate combination of primers in a primer pair depends
upon the properties of the primer pair, most notably the size of
the bioagent identifying amplicon that would be produced by the
primer pair, which preferably is between about 45 to about 150
nucleobases in length. Alternatively, a bioagent identifying
amplicon longer than 150 nucleobases in length could be cleaved
into smaller segments by cleavage reagents such as chemical
reagents, or restriction enzymes, for example.
[0317] In some embodiments, the primers are configured to amplify
nucleic acid of a bioagent to produce amplification products that
can be measured by mass spectrometry and from whose molecular
masses candidate base compositions can be readily calculated.
[0318] In some embodiments, any given primer comprises a
modification comprising the addition of a non-templated T residue
to the 5' end of the primer (i.e., the added T residue does not
necessarily hybridize to the nucleic acid being amplified). The
addition of a non-templated T residue has an effect of minimizing
the addition of non-templated adenosine residues as a result of the
non-specific enzyme activity of Taq polymerase (Magnuson et al.,
Biotechniques, 1996, 21, 700-709), an occurrence which may lead to
ambiguous results arising from molecular mass analysis.
[0319] In some embodiments of the present invention, primers may
contain one or more universal bases. Because any variation (due to
codon wobble in the 3.sup.rd position) in the conserved regions
among species is likely to occur in the third position of a DNA (or
RNA) triplet, oligonucleotide primers can be designed such that the
nucleotide corresponding to this position is a base which can bind
to more than one nucleotide, referred to herein as a "universal
nucleobase." For example, under this "wobble" pairing, inosine (I)
binds to U, C or A; guanine (G) binds to U or C, and uridine (U)
binds to U or C. Other examples of universal nucleobases include
nitroindoles such as 5-nitroindole or 3-nitropyrrole (Loakes et
al., Nucleosides and Nucleotides, 1995, 14, 1001-1003), the
degenerate nucleotides dP or dK (Hill et al.), an acyclic
nucleoside analog containing 5-nitroindazole (Van Aerschot et al.,
Nucleosides and Nucleotides, 1995, 14, 1053-1056) or the purine
analog 1-(2-deoxy-.beta.-D-ribofuranosyl)-imidazole-4-carboxamide
(Sala et al., Nucl. Acids Res., 1996, 24, 3302-3306).
[0320] In some embodiments, to compensate for the somewhat weaker
binding by the wobble base, the oligonucleotide primers are
designed such that the first and second positions of each triplet
are occupied by nucleotide analogs that bind with greater affinity
than the unmodified nucleotide. Examples of these analogs include,
but are not limited to, 2,6-diaminopurine which binds to thymine,
5-propynyluracil (also known as propynylated thymine) which binds
to adenine and 5-propynylcytosine and phenoxazines, including
G-clamp, which binds to G. Propynylated pyrimidines are described
in U.S. Pat. Nos. 5,645,985, 5,830,653 and 5,484,908, each of which
is commonly owned and incorporated herein by reference in its
entirety. Propynylated primers are described in U.S Pre-Grant
Publication No. 2003-0170682, which is also commonly owned and
incorporated herein by reference in its entirety. Phenoxazines are
described in U.S. Pat. Nos. 5,502,177, 5,763,588, and 6,005,096,
each of which is incorporated herein by reference in its entirety.
G-clamps are described in U.S. Pat. Nos. 6,007,992 and 6,028,183,
each of which is incorporated herein by reference in its
entirety.
[0321] In some embodiments, primer hybridization is enhanced using
primers containing 5-propynyl deoxy-cytidine and deoxy-thymidine
nucleotides. These modified primers offer increased affinity and
base pairing selectivity.
[0322] In some embodiments, non-template primer tags are used to
increase the melting temperature (T.sub.m) of a primer-template
duplex in order to improve amplification efficiency. A non-template
tag is at least three consecutive A or T nucleotide residues on a
primer which are not complementary to the template. In any given
non-template tag, A can be replaced by C or G and T can also be
replaced by C or G. Although Watson-Crick hybridization is not
expected to occur for a non-template tag relative to the template,
the extra hydrogen bond in a G-C pair relative to an A-T pair
confers increased stability of the primer-template duplex and
improves amplification efficiency for subsequent cycles of
amplification when the primers hybridize to strands synthesized in
previous cycles.
[0323] In other embodiments, propynylated tags may be used in a
manner similar to that of the non-template tag, wherein two or more
5-propynylcytidine or 5-propynyluridine residues replace template
matching residues on a primer. In other embodiments, a primer
contains a modified internucleoside linkage such as a
phosphorothioate linkage, for example.
[0324] In some embodiments, the primers contain mass-modifying
tags. Reducing the total number of possible base compositions of a
nucleic acid of specific molecular weight provides a means of
avoiding a persistent source of ambiguity in determination of base
composition of amplification products. Addition of mass-modifying
tags to certain nucleobases of a given primer will result in
simplification of de novo determination of base composition of a
given bioagent identifying amplicon from its molecular mass.
[0325] In some embodiments of the present invention, the mass
modified nucleobase comprises one or more of the following: for
example, 7-deaza-2'-deoxyadenosine-5-triphosphate,
5-iodo-2'-deoxyuridine-5'-triphosphate,
5-bromo-2'-deoxyuridine-5'-triphosphate,
5-bromo-2'-deoxycytidine-5'-triphosphate,
5-iodo-2'-deoxycytidine-5'-triphosphate,
5-hydroxy-2'-deoxyuridine-5'-triphosphate,
4-thiothymidine-5'-triphosphate,
5-aza-2'-deoxyuridine-5'-triphosphate,
5-fluoro-2'-deoxyuridine-5'-triphosphate,
O6-methyl-2'-deoxyguanosine-5'-triphosphate,
N2-methyl-2'-deoxyguanosine-5'-triphosphate,
8-oxo-2'-deoxyguanosine-5'-triphosphate or
thiothymidine-5'-triphosphate. In some embodiments, the
mass-modified nucleobase comprises .sup.15N or .sup.13C or both
.sup.15N and .sup.13C.
[0326] In some embodiments, multiplex amplification is performed
where multiple bioagent identifying amplicons are amplified with a
plurality of primer pairs. The advantages of multiplexing are that
fewer reaction containers (for example, wells of a 96- or 384-well
plate) are needed for each molecular mass measurement, providing
time, resource and cost savings because additional bioagent
identification data can be obtained within a single analysis.
Multiplex amplification methods are well known to those with
ordinary skill and can be developed without undue experimentation.
However, in some embodiments, one useful and non-obvious step in
selecting a plurality candidate bioagent identifying amplicons for
multiplex amplification is to ensure that each strand of each
amplification product will be sufficiently different in molecular
mass that mass spectral signals will not overlap and lead to
ambiguous analysis results. In some embodiments, a 10 Da difference
in mass of two strands of one or more amplification products is
sufficient to avoid overlap of mass spectral peaks.
[0327] In some embodiments, as an alternative to multiplex
amplification, single amplification reactions can be pooled before
analysis by mass spectrometry. In these embodiments, as for
multiplex amplification embodiments, it is useful to select a
plurality of candidate bioagent identifying amplicons to ensure
that each strand of each amplification product will be sufficiently
different in molecular mass that mass spectral signals will not
overlap and lead to ambiguous analysis results.
C Determination of Molecular Mass of Bioagent Identifying
Amplicons
[0328] In some embodiments, the molecular mass of a given bioagent
identifying amplicon is determined by mass spectrometry. Mass
spectrometry has several advantages, not the least of which is high
bandwidth characterized by the ability to separate (and isolate)
many molecular peaks across a broad range of mass to charge ratio
(m/z). Thus mass spectrometry is intrinsically a parallel detection
scheme without the need for radioactive or fluorescent labels,
since every amplification product is identified by its molecular
mass. The current state of the art in mass spectrometry is such
that less than femtomole quantities of material can be readily
analyzed to afford information about the molecular contents of the
sample. An accurate assessment of the molecular mass of the
material can be quickly obtained, irrespective of whether the
molecular weight of the sample is several hundred, or in excess of
one hundred thousand atomic mass units (amu) or Daltons.
[0329] In some embodiments, intact molecular ions are generated
from amplification products using one of a variety of ionization
techniques to convert the sample to gas phase. These ionization
methods include, but are not limited to, electrospray ionization
(ES), matrix-assisted laser desorption ionization (MALDI) and fast
atom bombardment (FAB). Upon ionization, several peaks are observed
from one sample due to the formation of ions with different
charges. Averaging the multiple readings of molecular mass obtained
from a single mass spectrum affords an estimate of molecular mass
of the bioagent identifying amplicon. Electrospray ionization mass
spectrometry (ESI-MS) is particularly useful for very high
molecular weight polymers such as proteins and nucleic acids having
molecular weights greater than 10 kDa, since it yields a
distribution of multiply-charged molecules of the sample without
causing a significant amount of fragmentation.
[0330] The mass detectors used in the methods of the present
invention include, but are not limited to, Fourier transform ion
cyclotron resonance mass spectrometry (FT-ICR-MS), time of flight
(TOF), ion trap, quadrupole, magnetic sector, Q-TOF, and triple
quadrupole.
D. Base Compositions of Bioagent Identifying Amplicons
[0331] Although the molecular mass of amplification products
obtained using intelligent primers provides a means for
identification of bioagents, conversion of molecular mass data to a
base composition signature is useful for certain analyses. As used
herein, "base composition" is the exact number of each nucleobase
(A, T, C and G) determined from the molecular mass of a bioagent
identifying amplicon. In some embodiments, a base composition
provides an index of a specific organism. Base compositions can be
calculated from known sequences of known bioagent identifying
amplicons and can be experimentally determined by measuring the
molecular mass of a given bioagent identifying amplicon, followed
by determination of all possible base compositions which are
consistent with the measured molecular mass within acceptable
experimental error. The following example illustrates determination
of base composition from an experimentally obtained molecular mass
of a 46-mer amplification product originating at position 1337 of
the 16S rRNA of Bacillus anthracis. The forward and reverse strands
of the amplification product have measured molecular masses of
14208 and 14079 Da, respectively. The possible base compositions
derived from the molecular masses of the forward and reverse
strands for the B. anthracis products are listed in Table 1.
TABLE-US-00001 TABLE 1 Possible Base Compositions for B. anthracis
46mer Amplification Product Calc. Mass Mass Error Base Calc. Mass
Mass Error Base Forward Forward Composition of Reverse Reverse
Composition of Strand Strand Forward Strand Strand Strand Reverse
Strand 14208.2935 0.079520 A1 G17 C10 T18 14079.2624 0.080600 A0
G14 C13 T19 14208.3160 0.056980 A1 G20 C15 T10 14079.2849 0.058060
A0 G17 C18 T11 14208.3386 0.034440 A1 G23 C20 T2 14079.3075
0.035520 A0 G20 C23 T3 14208.3074 0.065560 A6 G11 C3 T26 14079.2538
0.089180 A5 G5 C1 T35 14208.3300 0.043020 A6 G14 C8 T18 14079.2764
0.066640 A5 G8 C6 T27 14208.3525 0.020480 A6 G17 C13 T10 14079.2989
0.044100 A5 G11 C11 T19 14208.3751 0.002060 A6 G20 C18 T2
14079.3214 0.021560 A5 G14 C16 T11 14208.3439 0.029060 A11 G8 C1
T26 14079.3440 0.000980 A5 G17 C21 T3 14208.3665 0.006520 A11 G11
C6 T18 14079.3129 0.030140 A10 G5 C4 T27 14208.3890 0.016020 A11
G14 C11 T10 14079.3354 0.007600 A10 G8 C9 T19 14208.4116 0.038560
A11 G17 C16 T2 14079.3579 0.014940 A10 G11 C14 T11 14208.4030
0.029980 A16 G8 C4 T18 14079.3805 0.037480 A10 G14 C19 T3
14208.4255 0.052520 A16 G11 C9 T10 14079.3494 0.006360 A15 G2 C2
T27 14208.4481 0.075060 A16 G14 C14 T2 14079.3719 0.028900 A15 G5
C7 T19 14208.4395 0.066480 A21 G5 C2 T18 14079.3944 0.051440 A15 G8
C12 T11 14208.4620 0.089020 A21 G8 C7 T10 14079.4170 0.073980 A15
G11 C17 T3 -- -- -- 14079.4084 0.065400 A20 G2 C5 T19 -- -- --
14079.4309 0.087940 A20 G5 C10 T13
[0332] Among the 16 possible base compositions for the forward
strand and the 18 possible base compositions for the reverse strand
that were calculated, only one pair (shown in bold) are
complementary base compositions, which indicates the true base
composition of the amplification product. It should be recognized
that this logic is applicable for determination of base
compositions of any bioagent identifying amplicon, regardless of
the class of bioagent from which the corresponding amplification
product was obtained.
[0333] In some embodiments, assignment of previously unobserved
base compositions (also known as "true unknown base compositions")
to a given phylogeny can be accomplished via the use of pattern
classifier model algorithms. Base compositions, like sequences,
vary slightly from strain to strain within species, for example. In
some embodiments, the pattern classifier model is the mutational
probability model. On other embodiments, the pattern classifier is
the polytope model. The mutational probability model and polytope
model are both commonly owned and described in U.S. patent
application Ser. No. 11/073,362 which is incorporated herein by
reference in entirety.
[0334] In one embodiment, it is possible to manage this diversity
by building "base composition probability clouds" around the
composition constraints for each species. This permits
identification of organisms in a fashion similar to sequence
analysis. A "pseudo four-dimensional plot" can be used to visualize
the concept of base composition probability clouds. Optimal primer
design requires optimal choice of bioagent identifying amplicons
and maximizes the separation between the base composition
signatures of individual bioagents. Areas where clouds overlap
indicate regions that may result in a misclassification, a problem
which is overcome by a triangulation identification process using
bioagent identifying amplicons not affected by overlap of base
composition probability clouds.
[0335] In some embodiments, base composition probability clouds
provide the means for screening potential primer pairs in order to
avoid potential misclassifications of base compositions. In other
embodiments, base composition probability clouds provide the means
for predicting the identity of a bioagent whose assigned base
composition was not previously observed and/or indexed in a
bioagent identifying amplicon base composition database due to
evolutionary transitions in its nucleic acid sequence. Thus, in
contrast to probe-based techniques, mass spectrometry determination
of base composition does not require prior knowledge of the
composition or sequence in order to make the measurement.
[0336] The present invention provides bioagent classifying
information similar to DNA sequencing and phylogenetic analysis at
a level sufficient to identify a given bioagent. Furthermore, the
process of determination of a previously unknown base composition
for a given bioagent (for example, in a case where sequence
information is unavailable) has downstream utility by providing
additional bioagent indexing information with which to populate
base composition databases. The process of future bioagent
identification is thus greatly improved as more BCS indexes become
available in base composition databases.
E. Triangulation Identification
[0337] In some cases, a molecular mass of a single bioagent
identifying amplicon alone does not provide enough resolution to
unambiguously identify a given bioagent. The employment of more
than one bioagent identifying amplicon for identification of a
bioagent is herein referred to as "triangulation identification."
Triangulation identification is pursued by determining the
molecular masses of a plurality of bioagent identifying amplicons
selected within a plurality of housekeeping genes. This process is
used to reduce false negative and false positive signals, and
enable reconstruction of the origin of hybrid or otherwise
engineered bioagents. For example, identification of the three part
toxin genes typical of B. anthracis (Bowen et al., J. Appl.
Microbiol., 1999, 87, 270-278) in the absence of the expected
signatures from the B. anthracis genome would suggest a genetic
engineering event.
[0338] In some embodiments, the triangulation identification
process can be pursued by characterization of bioagent identifying
amplicons in a massively parallel fashion using the polymerase
chain reaction (PCR), such as multiplex PCR where multiple primers
are employed in the same amplification reaction mixture, or PCR in
multi-well plate format wherein a different and unique pair of
primers is used in multiple wells containing otherwise identical
reaction mixtures. Such multiplex and multi-well PCR methods are
well known to those with ordinary skill in the arts of rapid
throughput amplification of nucleic acids. In other related
embodiments, one PCR reaction per well or container may be carried
out, followed by an amplicon pooling step wherein the amplification
products of different wells are combined in a single well or
container which is then subjected to molecular mass analysis. The
combination of pooled amplicons can be chosen such that the
expected ranges of molecular masses of individual amplicons are not
overlapping and thus will not complicate identification of
signals.
F. Codon Base Composition Analysis
[0339] In some embodiments of the present invention, one or more
nucleotide substitutions within a codon of a gene of an infectious
organism confer drug resistance upon an organism which can be
determined by codon base composition analysis. The organism can be
a bacterium, virus, fungus or protozoan.
[0340] In some embodiments, the amplification product containing
the codon being analyzed is of a length of about 35 to about 200
nucleobases. The primers employed in obtaining the amplification
product can hybridize to upstream and downstream sequences directly
adjacent to the codon, or can hybridize to upstream and downstream
sequences one or more sequence positions away from the codon. The
primers may have between about 70% to 100% sequence complementarity
with the sequence of the gene containing the codon being
analyzed.
[0341] In some embodiments, the codon base composition analysis is
undertaken
[0342] In some embodiments, the codon analysis is undertaken for
the purpose of investigating genetic disease in an individual. In
other embodiments, the codon analysis is undertaken for the purpose
of investigating a drug resistance mutation or any other
deleterious mutation in an infectious organism such as a bacterium,
virus, fungus or protozoan. In some embodiments, the bioagent is a
bacterium identified in a biological product.
[0343] In some embodiments, the molecular mass of an amplification
product containing the codon being analyzed is measured by mass
spectrometry. The mass spectrometry can be either electrospray
(ESI) mass spectrometry or matrix-assisted laser desorption
ionization (MALDI) mass spectrometry. Time-of-flight (TOF) is an
example of one mode of mass spectrometry compatible with the
analyses of the present invention.
[0344] The methods of the present invention can also be employed to
determine the relative abundance of drug resistant strains of the
organism being analyzed. Relative abundances can be calculated from
amplitudes of mass spectral signals with relation to internal
calibrants. In some embodiments, known quantities of internal
amplification calibrants can be included in the amplification
reactions and abundances of analyte amplification product estimated
in relation to the known quantities of the calibrants.
[0345] In some embodiments, upon identification of one or more
drug-resistant strains of an infectious organism infecting an
individual, one or more alternative treatments can be devised to
treat the individual.
G. Determination of the Quantity of a Bioagent
[0346] In some embodiments, the identity and quantity of an unknown
bioagent can be determined using the process illustrated in FIG. 2.
Primers (500) and a known quantity of a calibration polynucleotide
(505) are added to a sample containing nucleic acid of an unknown
bioagent. The total nucleic acid in the sample is then subjected to
an amplification reaction (510) to obtain amplification products.
The molecular masses of amplification products are determined (515)
from which are obtained molecular mass and abundance data. The
molecular mass of the bioagent identifying amplicon (520) provides
the means for its identification (525) and the molecular mass of
the calibration amplicon obtained from the calibration
polynucleotide (530) provides the means for its identification
(535). The abundance data of the bioagent identifying amplicon is
recorded (540) and the abundance data for the calibration data is
recorded (545), both of which are used in a calculation (550) which
determines the quantity of unknown bioagent in the sample.
[0347] A sample comprising an unknown bioagent is contacted with a
pair of primers that provide the means for amplification of nucleic
acid from the bioagent, and a known quantity of a polynucleotide
that comprises a calibration sequence. The nucleic acids of the
bioagent and of the calibration sequence are amplified and the rate
of amplification is reasonably assumed to be similar for the
nucleic acid of the bioagent and of the calibration sequence. The
amplification reaction then produces two amplification products: a
bioagent identifying amplicon and a calibration amplicon. The
bioagent identifying amplicon and the calibration amplicon should
be distinguishable by molecular mass while being amplified at
essentially the same rate. Effecting differential molecular masses
can be accomplished by choosing as a calibration sequence, a
representative bioagent identifying amplicon (from a specific
species of bioagent) and performing, for example, a 2-8 nucleobase
deletion or insertion within the variable region between the two
priming sites. The amplified sample containing the bioagent
identifying amplicon and the calibration amplicon is then subjected
to molecular mass analysis by mass spectrometry, for example. The
resulting molecular mass analysis of the nucleic acid of the
bioagent and of the calibration sequence provides molecular mass
data and abundance data for the nucleic acid of the bioagent and of
the calibration sequence. The molecular mass data obtained for the
nucleic acid of the bioagent enables identification of the unknown
bioagent and the abundance data enables calculation of the quantity
of the bioagent, based on the knowledge of the quantity of
calibration polynucleotide contacted with the sample.
[0348] In some embodiments, construction of a standard curve where
the amount of calibration polynucleotide spiked into the sample is
varied provides additional resolution and improved confidence for
the determination of the quantity of bioagent in the sample. The
use of standard curves for analytical determination of molecular
quantities is well known to one with ordinary skill and can be
performed without undue experimentation.
[0349] In some embodiments, multiplex amplification is performed
where multiple bioagent identifying amplicons are amplified with
multiple primer pairs which also amplify the corresponding standard
calibration sequences. In this or other embodiments, the standard
calibration sequences are optionally included within a single
vector which functions as the calibration polynucleotide. Multiplex
amplification methods are well known to those with ordinary skill
and can be performed without undue experimentation.
[0350] In some embodiments, the calibrant polynucleotide is used as
an internal positive control to confirm that amplification
conditions and subsequent analysis steps are successful in
producing a measurable amplicon. Even in the absence of copies of
the genome of a bioagent, the calibration polynucleotide should
give rise to a calibration amplicon. Failure to produce a
measurable calibration amplicon indicates a failure of
amplification or subsequent analysis step such as amplicon
purification or molecular mass determination. Reaching a conclusion
that such failures have occurred is in itself, a useful event.
[0351] In some embodiments, the calibration sequence is comprised
of DNA. In some embodiments, the calibration sequence is comprised
of RNA.
[0352] In some embodiments, the calibration sequence is inserted
into a vector that itself functions as the calibration
polynucleotide. In some embodiments, more than one calibration
sequence is inserted into the vector that functions as the
calibration polynucleotide. Such a calibration polynucleotide is
herein termed a "combination calibration polynucleotide." The
process of inserting polynucleotides into vectors is routine to
those skilled in the art and can be accomplished without undue
experimentation. Thus, it should be recognized that the calibration
method should not be limited to the embodiments described herein.
The calibration method can be applied for determination of the
quantity of any bioagent identifying amplicon when an appropriate
standard calibrant polynucleotide sequence is designed and used.
The process of choosing an appropriate vector for insertion of a
calibrant is also a routine operation that can be accomplished by
one with ordinary skill without undue experimentation.
H. Identification of Bacteria
[0353] In other embodiments of the present invention, the primer
pairs produce bioagent identifying amplicons within stable and
highly conserved regions of bacteria. The advantage to
characterization of an amplicon defined by priming regions that
fall within a highly conserved region is that there is a low
probability that the region will evolve past the point of primer
recognition, in which case, the primer hybridization of the
amplification step would fail. Such a primer set is thus useful as
a broad range survey-type primer. In another embodiment of the
present invention, the intelligent primers produce bioagent
identifying amplicons including a region which evolves more quickly
than the stable region described above. The advantage of
characterization bioagent identifying amplicon corresponding to an
evolving genomic region is that it is useful for distinguishing
emerging strain variants or the presence of virulence genes, drug
resistance genes, or codon mutations that induce drug
resistance.
[0354] The present invention also has significant advantages as a
platform for identification of diseases caused by emerging
bacterial strains such as, for example, drug-resistant strains of
Staphylococcus aureus. The present invention eliminates the need
for prior knowledge of bioagent sequence to generate hybridization
probes. This is possible because the methods are not confounded by
naturally occurring evolutionary variations occurring in the
sequence acting as the template for production of the bioagent
identifying amplicon. Measurement of molecular mass and
determination of base composition is accomplished in an unbiased
manner without sequence prejudice.
[0355] Another embodiment of the present invention also provides a
means of tracking the spread of a bacterium, such as a particular
drug-resistant strain when a plurality of samples obtained from
different locations are analyzed by the methods described above in
an epidemiological setting. In one embodiment, a plurality of
samples from a plurality of different locations is analyzed with
primer pairs which produce bioagent identifying amplicons, a subset
of which contains a specific drug-resistant bacterial strain. The
corresponding locations of the members of the drug-resistant strain
subset indicate the spread of the specific drug-resistant strain to
the corresponding locations.
I. Kits
[0356] The present invention also provides kits for carrying out
the methods described herein. In some embodiments, the kit may
comprise a sufficient quantity of one or more primer pairs to
perform an amplification reaction on a target polynucleotide from a
bioagent to form a bioagent identifying amplicon. In some
embodiments, the kit may comprise from one to fifty primer pairs,
from one to twenty primer pairs, from one to ten primer pairs, or
from two to five primer pairs. In some embodiments, the kit may
comprise one or more primer pairs recited in Table 2.
[0357] In some embodiments, the kit comprises one or more broad
range survey primer(s), division wide primer(s), or drill-down
primer(s), or any combination thereof. If a given problem involves
identification of a specific bioagent, the solution to the problem
may require the selection of a particular combination of primers to
provide the solution to the problem. A kit may be designed so as to
comprise particular primer pairs for identification of a particular
bioagent. A drill-down kit may be used, for example, to distinguish
different genotypes or strains, drug-resistant, or otherwise. In
some embodiments, the primer pair components of any of these kits
may be additionally combined to comprise additional combinations of
broad range survey primers and division-wide primers so as to be
able to identify a bacterium.
[0358] In some embodiments, the kit contains standardized
calibration polynucleotides for use as internal amplification
calibrants. Internal calibrants are described in commonly owned
U.S. Patent Application Ser. No. 60/545,425 which is incorporated
herein by reference in its entirety.
[0359] In some embodiments, the kit comprises a sufficient quantity
of reverse transcriptase (if RNA is to be analyzed for example), a
DNA polymerase, suitable nucleoside triphosphates (including
alternative dNTPs such as inosine or modified dNTPs such as the
5-propynyl pyrimidines or any dNTP containing molecular
mass-modifying tags such as those described above), a DNA ligase,
and/or reaction buffer, or any combination thereof, for the
amplification processes described above. A kit may further include
instructions pertinent for the particular embodiment of the kit,
such instructions describing the primer pairs and amplification
conditions for operation of the method. A kit may also comprise
amplification reaction containers such as microcentrifuge tubes and
the like. A kit may also comprise reagents or other materials for
isolating bioagent nucleic acid or bioagent identifying amplicons
from amplification, including, for example, detergents, solvents,
or ion exchange resins which may be linked to magnetic beads. A kit
may also comprise a table of measured or calculated molecular
masses and/or base compositions of bioagents using the primer pairs
of the kit.
[0360] Some embodiments are kits that contain one or more survey
bacterial primer pairs represented by primer pair compositions
wherein each member of each pair of primers has 70% to 100%
sequence identity with the corresponding member from the group of
primer pairs represented by any of the primer pairs of Table 5. The
survey primer pairs may include broad range primer pairs which
hybridize to ribosomal RNA, and may also include division-wide
primer pairs which hybridize to housekeeping genes such as rplB,
tufB, rpoB, rpoC, valS, and infB, for example.
[0361] In some embodiments, a kit may contain one or more survey
bacterial primer pairs and one or more triangulation genotyping
analysis primer pairs such as the primer pairs of Tables 8, 12, 14,
19, 21, 23, or 24. In some embodiments, the kit may represent a
less expansive genotyping analysis but include triangulation
genotyping analysis primer pairs for more than one genus or species
of bacteria. For example, a kit for surveying nosocomial infections
at a health care facility may include, for example, one or more
broad range survey primer pairs, one or more division wide primer
pairs, one or more Acinetobacter baumannii triangulation genotyping
analysis primer pairs and one or more Staphylococcus aureus
triangulation genotyping analysis primer pairs. One with ordinary
skill will be capable of analyzing in silico amplification data to
determine which primer pairs will be able to provide optimal
identification resolution for the bacterial bioagents of
interest.
[0362] In some embodiments, a kit may be assembled for
identification of strains of bacteria involved in contamination of
food. An example of such a kit embodiment is a kit comprising one
or more bacterial survey primer pairs of Table 5 with one or more
triangulation genotyping analysis primer pairs of Table 12 which
provide strain resolving capabilities for identification of
specific strains of Campylobacter jejuni.
[0363] Some embodiments of the kits are 96-well or 384-well plates
with a plurality of wells containing any or all of the following
components: dNTPs, buffer salts, Mg.sup.2+, betaine, and primer
pairs. In some embodiments, a polymerase is also included in the
plurality of wells of the 96-well or 384-well plates.
[0364] Some embodiments of the kit contain instructions for PCR and
mass spectrometry analysis of amplification products obtained using
the primer pairs of the kits.
[0365] Some embodiments of the kit include a barcode which uniquely
identifies the kit and the components contained therein according
to production lots and may also include any other information
relative to the components such as concentrations, storage
temperatures, etc. The barcode may also include analysis
information to be read by optical barcode readers and sent to a
computer controlling amplification, purification and mass
spectrometric measurements. In some embodiments, the barcode
provides access to a subset of base compositions in a base
composition database which is in digital communication with base
composition analysis software such that a base composition measured
with primer pairs from a given kit can be compared with known base
compositions of bioagent identifying amplicons defined by the
primer pairs of that kit.
[0366] In some embodiments, the kit contains a database of base
compositions of bioagent identifying amplicons defined by the
primer pairs of the kit. The database is stored on a convenient
computer readable medium such as a compact disk or USB drive, for
example.
[0367] In some embodiments, the kit includes a computer program
stored on a computer formatted medium (such as a compact disk or
portable USB disk drive, for example) comprising instructions which
direct a processor to analyze data obtained from the use of the
primer pairs of the present invention. The instructions of the
software transform data related to amplification products into a
molecular mass or base composition which is a useful concrete and
tangible result used in identification and/or classification of
bioagents. In some embodiments, the kits of the present invention
contain all of the reagents sufficient to carry out one or more of
the methods described herein.
[0368] While the present invention has been described with
specificity in accordance with certain of its embodiments, the
following examples serve only to illustrate the invention and are
not intended to limit the same. In order that the invention
disclosed herein may be more efficiently understood, examples are
provided below. It should be understood that these examples are for
illustrative purposes only and are not to be construed as limiting
the invention in any manner.
EXAMPLES
Example 1
Design and Validation of Primers that Define Bioagent Identifying
Amplicons for Identification of Bacteria
[0369] For design of primers that define bacterial bioagent
identifying amplicons, a series of bacterial genome segment
sequences were obtained, aligned and scanned for regions where
pairs of PCR primers would amplify products of about 45 to about
150 nucleotides in length and distinguish subgroups and/or
individual strains from each other by their molecular masses or
base compositions. A typical process shown in FIG. 1 is employed
for this type of analysis.
[0370] A database of expected base compositions for each primer
region was generated using an in silico PCR search algorithm, such
as (ePCR). An existing RNA structure search algorithm (Macke et
al., Nucl. Acids Res., 2001, 29, 4724-4735, which is incorporated
herein by reference in its entirety) has been modified to include
PCR parameters such as hybridization conditions, mismatches, and
thermodynamic calculations (SantaLucia, Proc. Natl. Acad. Sci.
U.S.A., 1998, 95, 1460-1465, which is incorporated herein by
reference in its entirety). This also provides information on
primer specificity of the selected primer pairs.
[0371] Table 2 represents a collection of primers (sorted by primer
pair number) designed to identify bacteria using the methods
described herein. The primer pair number is an in-house database
index number. Primer sites were identified on segments of genes,
such as, for example, the 16S rRNA gene. The forward or reverse
primer name shown in Table 2 indicates the gene region of the
bacterial genome to which the primer hybridizes relative to a
reference sequence. In Table 2, for example, the forward primer
name 16S_EC.sub.--1077.sub.--1106_F indicates that the forward
primer (_F) hybridizes to residues 1077-1106 of the reference
sequence represented by a sequence extraction of coordinates
4033120 . . . 4034661 from GenBank gi number 16127994 (as indicated
in Table 3). As an additional example: the forward primer name
BONTA_X52066.sub.--450.sub.--473 indicates that the primer
hybridizes to residues 450-437 of the gene encoding Clostridium
botulinum neurotoxin type A (BoNT/A) represented by GenBank
Accession No. X52066 (primer pair name codes appearing in Table 2
are defined in Table 3. One with ordinary skill knows how to obtain
individual gene sequences or portions thereof from genomic
sequences present in GenBank. In Table 2, Tp=5-propynyluracil;
Cp=5-propynylcytosine; *=phosphorothioate linkage; I=inosine. T.
GenBank Accession Numbers for reference sequences of bacteria are
shown in Table 3 (below). In some cases, the reference sequences
are extractions from bacterial genomic sequences or complements
thereof. TABLE-US-00002 TABLE 2 Primer Pairs for Identification of
Bacteria Primer Forward Forward Reverse Reverse Pair Primer Forward
SEQ ID Primer Reverse SEQ ID Number Name Sequence NO: Name Sequence
NO: 1 16S_EC_1077_1106_F GTGAGATGTTGGGTTAA 134 16S_EC_1175_1195_R
GACGTCATCCCCACCTT 809 GTCCCGTAACGAG CCTC 2 16S_EC_1082_1106_F
ATGTTGGGTTAAGTCCC 38 16S_EC_1175_1197_R TTGACGTCATCCCCACC 1398
GCAACGAG TTCCTC 3 16S_EC_1090_1111_F TTAAGTCCCGCAACGAT 651
16S_EC_1175_1196_R TGACGTCATCCCCACCT 1159 CGCAA TCCTC 4
16S_EC_1222_1241_F GCTACACACGTGCTACA 114 16S_EC_1303_1323_R
CGAGTTGCAGACTGCGA 787 ATG TCCG 5 16S_EC_1332_1353_F
AAGTCGGAATCGCTAGT 10 16S_EC_1389_1407_R GACGGGCGGTGTGTACA 806 AATCG
AG 6 16S_EC_30_54_F TGAACGCTGGTGGCATG 429 16S_EC_105_126_R
TACGCATTACTCACCCG 897 CTTAACAC TCCGC 7 16S_EC_38_64_F
GTGGCATGCCTAATACA 136 16S_EC_101_120_R TTACTCACCCGTCCGCC 1365
TGCAAGTCG GCT 8 16S_EC_49_68_F TAACACATGCAAGTCGA 152
16S_EC_104_120_R TTACTCACCCGTCCGCC 1364 ACG 9 16S_EC_683_700_F
GTGTAGCGGTGAAATGC 137 16S_EC_774_795_R GTATCTAATCCTGTTTG 839 G
CTCCC 10 16S_EC_713_732_F AGAACACCGATGGCGAA 21 16S_EC_789_809_R
CGTGGACTACCAGGGTA 798 GGC TCTA 11 16S_EC_785_806_F
GGATTAGAGACCCTGGT 118 16S_EC_880_897_R GGCCGTACTCCCCAGGC 830 AGTCC
G 12 16S_EC_785_810_F GGATTAGATACCCTGGT 119 16S_EC_880_897_2_R
GGCCGTACTCCCCAGGC 830 AGTCCACGC G 13 16S_EC_789_810_F
TAGATACCCTGGTAGTC 206 16S_EC_880_894_R CGTACTCCCCAGGCG 796 CACGC 14
16S_EC_960_981_F TTCGATGCAACGCGAAG 672 16S_EC_1054_1073_R
ACGAGCTGACGACAGCC 735 AACCT ATG 15 16S_EC_969_985_F
ACGCGAAGAACCTTACC 19 16S_EC_1061_1078_R ACGACACGAGCTGACGA 734 C 16
23S_EC_1826_1843_F CTGACACCTGCCCGGTG 80 23S_EC_1906_1924_R
GACCGTTATAGTTACGG 805 C CC 17 23S_EC_2645_2669_F TCTGTCCCTAGTACGAG
408 23S_EC_2744_2761_R TGCTTAGATGCTTTCAG 1252 AGGACCGG C 18
23S_EC_2645_2669_ CTGTCCCTAGTACGAGA 83 23S_EC_2751_2767_R
GTTTCATGCTTAGATGC 846 2_F GGACCGG TTTCAGC 19 23S_EC_493_518_F
GGGGAGTGAAAGAGATC 125 23S_EC_551_571_R ACAAAAGGTACGCCGTC 717
CTGAAACCG ACCC 20 23S_EC_493_518_2_F GGGGAGTGAAAGAGATC 125
23S_EC_551_571_2_R ACAAAAGGCACGCCATC 716 CTGAAACCG ACCC 21
23S_EC_971_992_F CGAGAGGGAAACAACCC 66 23S_EC_1059_1077_R
TGGCTGCTTCTAAGCCA 1282 AGACC AC 22 CAPC_BA_104_131_F
GTTATTTAGCACTCGTT 139 CAPC_BA_180_205_R TGAATCTTGAAACACCA 1150
TTTAATCAGCC TACGTAACG 23 CAPC_BA_114_133_F ACTCGTTTTTAATCAGC 20
CAPC_BA_185_205_R TGAATCTTGAAACACCA 1149 CCG TACG 24
CAPC_BA_274_303_F GATTATTGTTATCCTGT 109 CAPC_BA_349_376_R
GTAACCCTTGTCTTTGA 837 TATGCCATTTGAG ATTGTATTTGC 25
CAPC_BA_276_296_F TTATTGTTATCCTGTTA 663 CAPC_BA_358_377_R
GGTAACCCTTGTCTTTG 834 TGCC AAT 26 CAPC_BA_281_301_F
GTTATCCTGTTATGCCA 138 CAPC_BA_361_378_R TGGTAACCCTTGTCTTT 1298 TTTG
G 27 CAPC_BA_315_334_F CCGTGGTATTGGAGTTA 59 CAPC_BA_361_378_R
TGGTAACCCTTGTCTTT 1298 TTG G 28 CYA_BA_1055_1072_F
GAAAGAGTTCGGATTGG 92 CYA_BA_1112_1130_R TGTTGACCATGCTTCTT 1352 G AG
29 CYA_BA_1349_1370_F ACAACGAAGTACAATAC 12 CYA_BA_1447_1426_R
CTTCTACATTTTTAGCC 800 AAGAC ATCAC 30 CYA_BA_1353_1379_F
CGAAGTACAATACAAGA 64 CYA_BA_1448_1467_R TGTTAACGGCTTCAAGA 1342
CAAAAGAAGG CCC 31 CYA_BA_1359_1379_F ACAATACAAGACAAAAG 13
CYA_BA_1447_1461_R CGGCTTCAAGACCCC 794 AAGG 32 CYA_BA_914_937_F
CAGGTTTAGTACCAGAA 53 CYA_BA_999_1026_R ACCACTTTTAATAAGGT 728
CATGCAG TTGTAGCTAAC 33 CYA_BA_916_935_F GGTTTAGTACCAGAACA 131
CYA_BA_1003_1025_R CCACTTTTAATAAGGTT 768 TGC TGTAGC 34
INFB_EC_1365_1393_ TGCTCGTGGTGCACAAG 524 INFB_EC_1439_1467_R
TGCTGCTTTCGCATGGT 1248 F TAACGGATATTA TAATTGCTTCAA 35
LEF_BA_1033_1052_F TCAAGAAGAAAAAGAGC 254 LEF_BA_1119_1135_R
GAATATCAATTTGTAGC 803 36 LEF_BA_1036_1066_F CAAGAAGAAAAAGAGCT 44
LEF_BA_1119_1149_R AGATAAAGAATCACGAA 745 TCTAAAAAGAATAC
TATCAATTTGTAGC 37 LEF_BA_756_781_F AGCTTTTGCATATTATA 26
LEF_BA_843_872_R TCTTCCAAGGATAGATT 1135 TCGAGCCAC TATTTCTTGTTCG 38
LEF_BA_758_778_F CTTTTGCATATTATATC 90 LEF_BA_843_865_R
AGGATAGATTTATTTCT 748 GAGC TGTTCG 39 LEF_BA_795_813_F
TTTACAGCTTTATGCAC 700 LEF_BA_883_900_R TCTTGACAGCATCCGTT 1140 CG G
40 LEF_BA_883_899_F CAACGGATGCTGGCAAG 43 LEF_BA_939_958_R
CAGATAAAGAATCGCTC 762 CAG 41 PAG_BA_122_142_F CAGAATCAAGTTCCCAG 49
PAG_BA_190_209_R CCTGTAGTAGAAGAGGT 781 GGG AAC 42 PAG_BA_123_145_F
AGAATCAAGTTCCCAGG 22 PAG_BA_187_210_R CCCTGTAGTAGAAGAGG 774 GGTTAC
TAACCAC 43 PAG_BA_269_287_F AATCTGCTATTTGGTCA 11 PAG_BA_326_344_R
TGATTATCAGCGGAAGT 1186 GG AG 44 PAG_BA_655_675_F GAAGGATATACGGTTGA
93 PAG_BA_755_772_R CCGTGCTCCATTTTTCA 778 TGTC G 45
PAG_BA_753_772_F TCCTGAAAAATGGAGCA 341 PAG_BA_849_868_R
TCGGATAAGCTGCCACA 1089 CGG AGG 46 PAG_BA_763_781_F
TGGAGCACGGCTTCTGA 552 PAG_BA_849_868_R TCGGATAAGCTGCCACA 1089 TC
AGG 47 RPOC_EC_1018_1045_ CAAAACTTATTAGGTAA 39 RPOC_EC_1095_1124_R
TCAAGCGCCATTTCTTT 959 F GCGTGTTGACT TGGTAAACCACAT 48
RPOC_EC_1018_1045_ CAAAACTTATTAGGTAA 39 RPOC_EC_1095_1124_2_R
TCAAGCGCCATCTCTTT 958 F GCGTGTTGACT CGGTAATCCACAT 49
RPOC_EC_114_140_F TAAGAAGCCGGAAACCA 158 RPOC_EC_213_232_R
GGCGCTTGTACTTACCG 831 TCAACTACCG CAC 50 RPOC_EC_2178_2196_
TGATTCTGGTGCCCGTG 478 RPOC_EC_2225_2246_R TTGGCCATCAGGCCACG 1414 F
GT CATAC 51 RPOC_EC_2178_2196_ TGATTCCGGTGCCCGTG 477
RPOC_EC_2225_2246_2_R TTGGCCATCAGACCACG 1413 2_F GT CATAC 52
RPOC_EC_2218_2241_ CTGGCAGGTATGCGTGG 81 RPOC_EC_2313_2337_R
CGCACCGTGGGTTGAGA 790 F TCTGATG TGAAGTAC 53 RPOC_EC_2218_2241_
CTTGCTGGTATGCGTGG 86 RPOC_EC_2313_2337_2_R CGCACCATGCGTAGAGA 789
2_F TCTGATG TGAAGTAC 54 RPOC_EC_808_833_F CGTCGGGTGATTAACCG 75
RPOC_EC_865_889_R GTTTTTCGTTGCGTACG 847 TAACAACCG ATGATGTC 55
RPOC_EC_808_833_2_ CGTCGTGTAATTAACCG 76 RPOC_EC_865_891_R
ACGTTTTTCGTTTTGAA 741 F TAACAACCG CGATAATGCT 56 RPOC_EC_993_1019_F
CAAAGGTAAGCAAGGTC 41 RPOC_EC_1036_1059_R
CGAACGGCCTGAGTAGT 785 GTTTCCGTCA CAACACG 57 RPOC_EC_993_1019_
CAAAGGTAAGCAAGGAC 40 RPOC_EC_1036_1059_2_R CGAACGGCCAGAGTAGT 784
2_F GTTTCCGTCA CAACACG 58 SSPE_BA_115_137_F CAAGCAAACGCACAATC 45
SSPE_BA_197_222_R TGCACGTCTGTTTCAGT 1201 AGAAGC TGCAAATTC 59
TUFB_EC_239_259_F TAGACTGCCCAGGACAC 204 TUFB_EC_283_303_R
GCCGTCCATCTGAGCAG 815 GCTG CACC 60 TUFB_EC_239_259_2_
TTGACTGCCCAGGTCAC 678 TUFB_EC_283_303_2_R GCCGTCCATTTGAGCAG 816 F
GCTG CACC 61 TUFB_EC_976_1000_F AACTACCGTCCGCAGTT 4
TUFB_EC_1045_1068_R GTTGTCGCCAGGCATAA 845 CTACTTCC CCATTTC 62
TUFB_EC_976_1000_ AACTACCGTCCTCAGTT 5 TUFB_EC_1045_1068_2_R
GTTGTCACCAGGCATTA 844 2_F CTACTTCC CCATTTC 63 TUFB_EC_985_1012_F
CCACAGTTCTACTTCCG 56 TUFB_EC_1033_1062_R TCCAGGCATTACCATTT 1006
TACTACTGACG CTACTCCTTCTGG 66 RPLB_EC_650_679_F GACCTACAGTAAGAGGT 98
RPLB_EC_739_762_R TCCAAGTGCTGGTTTAC 999 TCTGTAATGAACC CCCATGG 67
RPLB_EC_688_710_F CATCCACACGGTGGTGG 54 RPLB_EC_736_757_R
GTGCTGGTTTACCCCAT 842 TGAAGG GGAGT 68 RPOC_EC_1036_1060_
CGTGTTGACTATTCGGG 78 RPOC_EC_1097_1126_R ATTCAAGAGCCATTTCT 754 F
GCGTTCAG TTTGGTAAACCAC 69 RPOB_EC_3762_3790_ TCAACAACCTCTTGGAG 248
RPOB_EC_3836_3865_R TTTCTTGAAGAGTATGA 1435 F GTAAAGCTCAGT
GCTGCTCCGTAAG 70 RPLB_EC_688_710_F CATCCACACGGTGGTGG 54
RPLB_EC_743_771_R TGTTTTGTATCCAAGTG 1356 TGAAGG CTGGTTTACCCC 71
VALS_EC_1105_1124_ CGTGGCGGCGTGGTTAT 77 VALS_EC_1195_1218_R
CGGTACGAACTGGATGT 795 F CGA CGCCGTT 72 RPOB_EC_1845_1866_
TATCGCTCAGGCGAACT 233 RPOB_EC_1909_1929_R GCTGGATTCGCCTTTGC 825 F
CCAAC TACG 73 RPLB_EC_669_698_F TGTAATGAACCCTAATG 623
RPLB_EC_735_761_R CCAAGTGCTGGTTTACC 767 ACCATCCACACGG CCATGGAGTA 74
RPLB_EC_671_700_F TAATGAACCCTAATGAC 169 RPLB_EC_737_762_R
TCCAAGTGCTGGTTTAC 1000 CATCCACACGGTG CCCATGGAG 75
SP101_SPET11_1_29_ AACCTTAATTGGAAAGA 2 SP101_SPET11_92_116_R
CCTACCCAACGTTCACC 779 F AACCCAAGAAGT AAGGGCAG 76 SP101_SPET11_118_
GCTGGTGAAAATAACCC 115 SP101_SPET11_213_238_R TGTGGCCGATTTCACCA 1340
147_F AGATGTCGTCTTC CCTGCTCCT 77 SP101_SPET11_216_
AGCAGGTGGTGAAATCG 24 SP101_SPET11_308_333_R TGCCACTTTGACAACTC 1209
243_F GCCACATGATT CTGTTGCTG 78 SP101_SPET11_266_ CTTGTACTTGTGGCTCA
89 SP101_SPET11_355_380_R GCTGCTTTGATGGCTGA 824 295_F CACGGCTGTTTGG
ATCCCCTTC 79 SP101_SPET11_322_ GTCAAAGTGGCACGTTT 132
SP101_SPET11_423_441_R ATCCCCTGCTTCTGCTG 753 344_F ACTGGC CC 80
SP101_SPET11_358_ GGGGATTCAGCCATCAA 126 SP101_SPET11_448_473_R
CCAACCTTTTCCACAAC 766 387_F AGCAGCTATTGAC AGAATCAGC 81
SP101_SPET11_600_ CCTTACTTCGAACTATG 62 SP101_SPET11_686_714_R
CCCATTTTTTCACGCAT 772 629_F AATCTTTTGGAAG GCTGAAAATATC 82
SP101_SPET11_658_ GGGGATTGATATCACCG 127 SP101_SPET11_756_784_R
GATTGGCGATAAAGTGA 813 684_F ATAAGAAGAA TATTTTCTAAAA 83
SP101_SPET11_776_ TCGCCAATCAAAACTAA 364 SP101_SPET11_871_896_R
GCCCACCAGAAAGACTA 814 801_F GGGAATGGC GCAGGATAA 84
SP101_SPET11_893_ GGGCAACAGCAGCGGAT 123 SP101_SPET11_988_1012_R
CATGACAGCCAAGACCT 763 921_F TGCGATTGCGCG CACCCACC 85
SP101_SPET11_1154_ CAATACCGCAACAGCGG 47 SP101_SPET11_1251_1277_R
GACCCCAACCTGGCCTT 804 1179_F TGGCTTGGG TTGTCGTTGA 86
SP101_SPET11_1314_ CGCAAAAAAATCCAGCT 68 SP101_SPET11_1403_1431_R
AAACTATTTTTTTAGCT 711 1336_F ATTAGC ATACTCGAACAC 87
SP101_SPET11_1408_ CGAGTATAGCTAAAAAA 67 SP101_SPET11_1486_1515_R
GGATAATTGGTCGTAAC 828 1437_F ATAGTTTATGACA AAGGGATAGTGAG 88
SP101_SPET11_1688_ CCTATATTAATCGTTTA 60 SP101_SPET11_1783_1808_R
ATATGATTATCATTGAA 752 1716_F CAGAAACTGGCT CTGCGGCCG 89
SP101_SPET11_1711_ CTGGCTAAAACTTTGGC 82 SP101_SPET11_1808_1835_R
GCGTGACGACCTTCTTG 821 1733_F AACGGT AATTGTAATCA 90
SP101_SPET11_1807_ ATGATTACAATTCAAGA 33 SP101_SPET11_1901_1927_R
TTGGACCTGTAATCAGC 1412 1835_F AGGTCGTCACGC TGAATACTGG 91
SP101_SPET11_1967_ TAACGGTTATCATGGCC 155 SP101_SPET11_2062_2083_R
ATTGCCCAGAAATCAAA 755 1991_F CAGATGGG TCATC 92 SP101_SPET11_2260_
CAGAGACCGTTTTATCC 50 SP101_SPET11_2375_2397_R TCTGGGTGACCTGGTGT
1131 2283_F TATCAGC TTTAGA 93 SP101_SPET11_2375_ TCTAAAACACCAGGTCA
390 SP101_SPET11_2470_2497_R AGCTGCTAGATGAGCTT 747 2399_F CCCAGAAG
CTGCCATGGCC 94 SP101_SPET11_2468_ ATGGCCATGGCAGAAGC 35
SP101_SPET11_2543_2570_R CCATAAGGTCACCGTCA 770 2487_F TCA
CCATTCAAAGC 95 SP101_SPET11_2961_ ACCATGACAGAAGGCAT 15
SP101_SPET11_3023_3045_R GGAATTTACCAGCGATA 827 2984_F TTTGACA
GACACC 96 SP101_SPET11_3075_ GATGACTTTTTAGCTAA 108
SP101_SPET11_3168_3196_R AATCGACGACCATCTTG 715 3103_F TGGTCAGGCAGC
GAAAGATTTCTC 97 SP101_SPET11_3386_ AGCGTAAAGGTGAACCT 25
SP101_SPET11_3480_3506_R CCAGCAGTTACTGTCCC 769 3403_F T CTCATCTTTG
98 SP101_SPET11_3511_ GCTTCAGGAATCAATGA 116
SP101_SPET11_3605_3629_R GGGTCTACACCTGCACT 832 3535_F TGGAGCAG
TGCATAAC 111 RPOB_EC_3775_3803_ CTTGGAGGTAAGTCTCA 87
RPOB_EC_3829_3858_R CGTATAAGCTGCACCAT 797 F TTTTGGTGGGCA
AAGCTTGTAATGC 112 VALS_EC_1833_1850_ CGACGCGCTGCGCTTCA 65
VALS_EC_1920_1943_R GCGTTCCACAGCTTGTT 822 F C GCAGAAG 113
RPOB_EC_1336_1353_ GACCACCTCGGCAACCG 97 RPOB_EC_1438_1455_R
TTCGCTCTCGGCCTGGC 1386 F T C 114 TUFB_EC_225_251_F
GCACTATGCACACGTAG 111 TUFB_EC_284_309_R TATAGCACCATCCATCT 930
ATTGTCCTGG GAGCGGCAC 115 DNAK_EC_428_449_F CGGCGTACTTCAACGAC 72
DNAK_EC_503_522_R CGCGGTCGGCTCGTTGA 792 AGCCA TGA 116
VALS_EC_1920_1943_ CTTCTGCAACAAGCTGT 85 VALS_EC_1948_1970_R
TCGCAGTTCATCAGCAC 1075 F GGAACGC GAAGCG 117 TUFB_EC_757_774_F
AAGACGACCTGCACGGG 6 TUFB_EC_849_867_R GCGCTCCACGTCTTCAC 819 C GC
118 23S_EC_2646_2667_ CTGTTCTTAGTACGAGA 84 23S_EC_2745_2765_R
TTCGTGCTTAGATGCTT 1389 F GGACC TCAG 119 16S_EC_969_985_1P_
ACGCGAAGAACCTTACp 19 16S_EC_1061_1078_2P_R ACGACACGAGCpTpGAC 733 F
C GAC 120 16S_EC_972_985_2P_ CGAAGAACpCpTTACC 63
16S_EC_1064_1075_2P_R ACACGAGCpTpGAC 727 F 121 16S_EC_972_985_F
CGAAGAACCTTACC 63 16S_EC_1064_1075_R ACACGAGCTGAC 727 122 TRNA_ILE-
CCTGATAAGGGTGAGGT 61 23S_EC_40_59_R ACGTCCTTCATCGCCTC 740
RRNH_EC_32_50.2_F CG TGA 123 23S_EC_-7_15_F GTTGTGAGGTTAAGCGA 140
23S_EC_430_450_R CTATCGGTCAGTCAGGA 799 CTAAG GTAT 124
23S_EC_-7_15_F GTTGTGAGGTTAAGCGA 141 23S_EC_891_910_R
TTGCATCGGGTTGGTAA 1403 CTAAG GTC 125 23S_EC_430_450_F
ATACTCCTGACTGACCG 30 23S_EC_1424_1442_R AACATAGCCTTCTCCGT 712 ATAG
CC 126 23S_EC_891_910_F GACTTACCAACCCGATG 100 23S_EC_1908_1931_R
TACCTTAGGACCGTTAT 893 CAA AGTTACG 127 23S_EC_1424_1442_F
GGACGGAGAAGGCTATG 117 23S_EC_2475_2494_R CCAAACACCGCCGTCGA 765 TT
TAT 128 23S_EC_1908_1931_F CGTAACTATAACGGTCC 73 23S_EC_2833_2852_R
GCTTACACACCCGGCCT 826 TAAGGTA ATC 129 23S_EC_2475_2494_F
ATATCGACGGCGGTGTT 31 TRNA_ASP- GCGTGACAGGCAGGTAT 820 TGG
RRNH_EC_23_41.2_R TC 131 16S_EC_-60_-39_F AGTCTCAAGAGTGAACA 28
16S_EC_508_525_R GCTGCTGGCACGGAGTT 823 CGTAA A 132 16S_EC_326_345_F
GACACGGTCCAGACTCC 95 16S_EC_1041_1058_R CCATGCAGCACCTGTCT 771 TAC C
133 16S_EC_705_724_F GATCTGGAGGAATACCG 107 16S_EC_1493_1512_R
ACGGTTACCTTGTTACG 739 GTG ACT 134 16S_EC_1268_1287_F
GAGAGCAAGCGGACCTC 101 TRNA_ALA- CCTCCTGCGTGCAAAGC 780
ATA RRNH_EC_30_46.2_R 135 16S_EC_969_985_F ACGCGAAGAACCTTACC 19
16S_EC_1061_1078.2_R ACAACACGAGCTGACGA 719 C 137 16S_EC_969_985_F
ACGCGAAGAACCTTACC 19 16S_EC_1061_1078.2_I14_R ACAACACGAGCTGICGA 721
C 138 16S_EC_969_985_F ACGCGAAGAACCTTACC 19
16S_EC_1061_1078.2_I12_R ACAACACGAGCIGACGA 718 C 139
16S_EC_969_985_F ACGCGAAGAACCTTACC 19 16S_EC_1061_1078.2_I11_R
ACAACACGAGITGACGA 722 C 140 16S_EC_969_985_F ACGCGAAGAACCTTACC 19
16S_EC_1061_1078.2_I16_R ACAACACGAGCTGACIA 720 C 141
16S_EC_969_985_F ACGCGAAGAACCTTACC 19 16S_EC_1061_1078.2_2I_R
ACAACACGAICTIACGA 723 C 142 16S_EC_969_985_F ACGCGAAGAACCTTACC 19
16S_EC_1061_1078.2_3I_R ACAACACIAICTIACGA 724 C 143
16S_EC_969_985_F ACGCGAAGAACCTTACC 19 16S_EC_1061_1078.2_4I_R
ACAACACIAICTIACIA 725 C 147 23S_EC_2652_2669_ CTAGTACGAGAGGACCG 79
23S_EC_2741_2760_R ACTTAGATGCTTTCAGC 743 F G GGT 158
16S_EC_683_700_F GTGTAGCGGTGAAATGC 137 16S_EC_880_894_R
CGTACTCCCCAGGCG 796 G 159 16S_EC_1100_1116_F CAACGAGCGCAACCCTT 42
16S_EC_1174_1188_R TCCCCACCTTCCTCC 1019 215 SSPE_BA_121_137_F
AACGCACAATCAGAAGC 3 SSPE_BA_197_216_R TCTGTTTCAGTTGCAAA 1132 TTC
220 GROL_EC_941_959_F TGGAAGATCTGGGTCAG 544 GROL_EC_1039_1060_R
CAATCTGCTGACGGATC 759 GC TGAGC 221 INFB_EC_1103_1124_
GTCGTGAAAACGAGCTG 133 INFB_EC_1174_1191_R CATGATGGTCACAACCG 764 F
GAAGA G 222 HFLB_EC_1082_1102_ TGGCGAACCTGGTGAAC 569
HFLB_EC_1144_1168_R CTTTCGCTTTCTCGAAC 802 F GAAGC TCAACCAT 223
INFB_EC_1969_1994_ CGTCAGGGTAAATTCCG 74 INFB_EC_2038_2058_R
AACTTCGCCTTCGGTCA 713 F TGAAGTTAA TGTT 224 GROL_EC_219_242_F
GGTGAAAGAAGTTGCCT 128 GROL_EC_328_350_R TTCAGGTCCATCGGGTT 1377
CTAAAGC CATGCC 225 VALS_EC_1105_1124_ CGTGGCGGCGTGGTTAT 77
VALS_EC_1195_1214_R ACGAACTGGATGTCGCC 732 F CGA GTT 226
16S_EC_556_575_F CGGAATTACTGGGCGTA 70 16S_EC_683_700_R
CGCATTTCACCGCTACA 791 AAG C 227 RPOC_EC_1256_1277_
ACCCAGTGCTGCTGAAC 16 RPOC_EC_1295_1315_R GTTCAAATGCCTGGATA 843 F
CGTGC CCCA 228 16S_EC_774_795_F GGGAGCAAACAGGATTA 122
16S_EC_880_894_R CGTACTCCCCAGGCG 796 GATAC 229 RPOC_EC_1584_1604_
TGGCCCGAAAGAAGCTG 567 RPOC_EC_1623_1643_R ACGCGGGCATGCAGAGA 737 F
AGCG TGCC 230 16S_EC_1082_1100_F ATGTTGGGTTAAGTCCC 37
16S_EC_1177_1196_R TGACGTCATCCCCACCT 1158 GC TCC 231
16S_EC_1389_1407_F CTTGTACACACCGCCCG 88 16S_EC_1525_1541_R
AAGGAGGTGATCCAGCC 714 TC 232 16S_EC_1303_1323_F CGGATTGGAGTCTGCAA
71 16S_EC_1389_1407_R GACGGGCGGTGTGTACA 808 CTCG AG 233
23S_EC_23_37_F GGTGGATGCCTTGGC 129 23S_EC_115_130_R
GGGTTTCCCCATTCGG 833 234 23S_EC_187_207_F GGGAACTGAAACATCTA 121
23S_EC_242_256_R TTCGCTCGCCGCTAC 1385 AGTA 235 23S_EC_1602_1620_F
TACCCCAAACCGACACA 184 23S_EC_1686_1703_R CCTTCTCCCGAAGTTACG 782 GG
236 23S_EC_1685_1703_F CCGTAACTTCGGGAGAA 58 23S_EC_1828_1842_R
CACCGGGCAGGCGTC 760 GG 237 23S_EC_1827_1843_F GACGCCTGCCCGGTGC 99
23S_EC_1929_1949_R CCGACAAGGAATTTCGC 775 TACC 238
23S_EC_2434_2456_F AAGGTACTCCGGGGATA 9 23S_EC_2490_2511_R
AGCCGACATCGAGGTGC 746 ACAGGC CAAAC 239 23S_EC_2599_2616_F
GACAGTTCGGTCCCTAT 96 23S_EC_2653_2669_R CCGGTCCTCTCGTACTA 777 C 240
23S_EC_2653_2669_F TAGTACGAGAGGACCGG 227 23S_EC_2737_2758_R
TTAGATGCTTTCAGCAC 1369 TTATC 241 23S_BS_-68_-44_F AAACTAGATAACAGTAG
1 23S_BS_5_21_R GTGCGCCCTTTCTAACT 841 ACATCAC T 242 16S_EC_8_27_F
AGAGTTTGATCATGGCT 23 16S_EC_342_358_R ACTGCTGCCTCCCGTAG 742 CAG 243
16S_EC_314_332_F CACTGGAACTGAGACAC 48 16S_EC_556_575_R
CTTTACGCCCAGTAATT 801 GG CCG 244 16S_EC_518_536_F CCAGCAGCCGCGGTAAT
57 16S_EC_774_795_R GTATCTAATCCTGTTTG 839 AC CTCCC 245
16S_EC_683_700_F GTGTAGCGGTGAAATGC 137 16S_EC_967_985_R
GGTAAGGTTCTTCGCGT 835 G TG 246 16S_EC_937_954_F AAGCGGTGGAGCATGTG 7
16S_EC_1220_1240_R ATTGTAGCACGTGTGTA 757 G GCCC 247
16S_EC_1195_1213_F CAAGTCATCATGGCCCT 46 16S_EC_1525_1541_R
AAGGAGGTGATCCAGCC 714 TA 248 16S_EC_8_27_F AGAGTTTGATCATGGCT 23
16S_EC_1525_1541_R AAGGAGGTGATCCAGCC 714 CAG 249 23S_EC_1831_1849_F
ACCTGCCCAGTGCTGGA 18 23S_EC_1919_1936_R TCGCTACCTTAGGACCG 1080 AG T
250 16S_EC_1387_1407_F GCCTTGTACACACCTCC 112 16S_EC_1494_1513_R
CACGGCTACCTTGTTAC 761 CGTC GAC 251 16S_EC_1390_1411_F
TTGTACACACCGCCCGT 693 16S_EC_1486_1505_R CCTTGTTACGACTTCAC 783
CATAC CCC 252 16S_EC_1367_1387_F TACGGTGAATACGTTCC 191
16S_EC_1485_1506_R ACCTTGTTACGACTTCA 731 CGGG CCCCA 253
16S_EC_804_822_F ACCACGCCGTAAACGAT 14 16S_EC_909_929_R
CCCCCGTCAATTCCTTT 773 GA GAGT 254 16S_EC_791_812_F
GATACCCTGGTAGTCCA 106 16S_EC_886_904_R GCCTTGCGACCGTACTC 817 CACCG
CC 255 16S_EC_789_810_F TAGATACCCTGGTAGTC 206 16S_EC_882_899_R
GCGACCGTACTCCCCAG 818 CACGC G 256 16S_EC_1092_1109_F
TAGTCCCGCAACGAGCG 228 168_EC_1174_1195_R GACGTCATCCCCACCTT 810 C
CCTCC 257 23S_EC_2586_2607_F TAGAACGTCGCGAGACA 203
23S_EC_2658_2677_R AGTCCATCCCGGTCCTC 749 GTTCG TCG 258
RNASEP_SA_31_49_F GAGGAAAGTCCATGCTC 103 RNASEP_SA_358_379_R
ATAAGCCATGTTCTGTT 750 AC CCATC 258 RNASEP_SA_31_49_F
GAGGAAAGTCCATGCTC 103 RNASEP_EC_345_362_R ATAAGCCGGGTTCTGTC 751 AC
G 258 RNASEP_SA_31_49_F GAGGAAAGTCCATGCTC 103 RNASEP_BS_363_384_R
GTAAGCCATGTTTTGTT 838 AC CCATC 258 RNASEP_BS_43_61_F
GAGGAAAGTCCATGCTC 104 RNASEP_SA_358_379_R ATAAGCCATGTTCTGTT 750 GC
CCATC 258 RNASEP_BS_43_61_F GAGGAAAGTCCATGCTC 104
RNASEP_EC_345_362_R ATAAGCCGGGTTCTGTC 751 GC G 258
RNASEP_BS_43_61_F GAGGAAAGTCCATGCTC 104 RNASEP_BS_363_384_R
GTAAGCCATGTTTTGTT 838 GC CCATC 258 RNASEP_EC_61_77_F
GAGGAAAGTCCGGGCTC 105 RNASEP_SA_358_379_R ATAAGCCATGTTCTGTT 750
CCATC 258 RNASEP_EC_61_77_F GAGGAAAGTCCGGGCTC 105
RNASEP_EC_345_362_R ATAAGCCGGGTTCTGTC 751 G 258 RNASEP_EC_61_77_F
GAGGAAAGTCCGGGCTC 105 RNASEP_BS_363_384_R GTAAGCCATGTTTTGTT 838
CCATC 259 RNASEP_BS_43_61_F GAGGAAAGTCCATGCTC 104
RNASEP_BS_363_384_R GTAAGCCATGTTTTGTT 838 GC CCATC 260
RNASEP_EC_61_77_F GAGGAAAGTCCGGGCTC 105 RNASEP_EC_345_362_R
ATAAGCCGGGTTCTGTC 751 G 262 RNASEP_SA_31_49_F GAGGAAAGTCCATGCTC 103
RNASEP_SA_358_379_R ATAAGCCATGTTCTGTT 750 AC CCATC 263
16S_EC_1082_1100_F ATGTTGGGTTAAGTCCC 37 16S_EC_1525_1541_R
AAGGAGGTGATCCAGCC 714 GC
264 16S_EC_556_575_F CGGAATTACTGGGCGTA 70 16S_EC_774_795_R
GTATCTAATCCTGTTTG 839 AAG CTCCC 265 16S_EC_1082_1100_F
ATGTTGGGTTAAGTCCC 37 16S_EC_1177_1196_10G_R TGACGTCATGCCCACCT 1160
GC TCC 266 16S_EC_1082_1100_F ATGTTGGGTTAAGTCCC 37
16S_EC_1177_1196_10G_ TGACGTCATGGCCACCT 1161 GC 11G_R TCC 268
YAED_EC_513_532_F_ GGTGTTAAATAGCCTGG 130 TRNA_ALA-
AGACCTCCTGCGTGCAA 744 MOD CAG RRNH_EC_30_49_F_MOD AGC 269
16S_EC_1082_1100_ ATGTTGGGTTAAGTCCC 37 16S_EC_1177_1196_R_MOD
TGACGTCATCCCCACCT 1158 F_MOD GC TCC 270 23S_EC_2586_2607_
TAGAACGTCGCGAGACA 203 23S_EC_2658_2677_R_MOD AGTCCATCCCGGTCCTC 749
F_MOD GTTCG TCG 272 16S_EC_969_985_F ACGCGAAGAACCTTACC 19
16S_EC_1389_1407_R GACGGGCGGTGTGTACA 807 AG 273 16S_EC_683_700_F
GTGTAGCGGTGAAATGC 137 16S_EC_1303_1323_R CGAGTTGCAGACTGCGA 788 G
TCCG 274 16S_EC_49_68_F TAACACATGCAAGTCGA 152 16S_EC_880_894_R
CGTACTCCCCAGGCG 796 ACG 275 16S_EC_49_68_F TAACACATGCAAGTCGA 152
16S_EC_1061_1078_R ACGACACGAGCTGACGA 734 ACG C 277
CYA_BA_1349_1370_F ACAACGAAGTACAATAC 12 CYA_BA_1426_1447_R
CTTCTACATTTTTAGCC 800 AAGAC ATCAC 278 16S_EC_1090_1111_
TTAAGTCCCGCAACGAG 650 16S_EC_1175_1196_R TGACGTCATCCCCACCT 1159 2_F
CGCAA TCCTC 279 16S_EC_405_432_F TGAGTGATGAAGGCCTT 464
16S_EC_507_527_R CGGCTGCTGGCACGAAG 793 AGGGTTGTAAA TTAG 280
GROL_EC_496_518_F ATGGACAAGGTTGGCAA 34 GROL_EC_577_596_R
TAGCCGCGGTCGAATTG 914 GGAAGG CAT 281 GROL_EC_511_536_F
AAGGAAGGCGTGATCAC 8 GROL_EC_571_593_R CCGCGGTCGAATTGCAT 776
CGTTGAAGA GCCTTC 288 RPOB_EC_3802_3821_ CAGCGTTTCGGCGAAAT 51
RPOB_EC_3862_3885_R CGACTTGACGGTTAACA 786 F GGA TTTCCTG 289
RPOB_EC_3799_3821_ GGGCAGCGTTTCGGCGA 124 RPOB_EC_3862_3888_R
GTCCGACTTGACGGTCA 840 F AATGGA ACATTTCCTG 290 RPOC_EC_2146_2174_
CAGGAGTCGTTCAACTC 52 RPOC_EC_2227_2245_R ACGCCATCAGGCCACGC 736 F
GATCTACATGAT AT 291 ASPS_EC_405_422_F GCACAACCTGCGGCTGC 110
ASPS_EC_521_538_R ACGGCACGAGGTAGTCG 738 G C 292 RPOC_EC_1374_1393_
CGCCGACTTCGACGGTG 69 RPOC_EC_1437_1455_R GAGCATCAGCGTGCGTG 811 F
ACC CT 293 TUFB_EC_957_979_F CCACACGCCGTTCTTCA 55
TUFB_EC_1034_1058_R GGCATCACCATTTCCTT 829 ACAACT GTCCTTCG 294
16S_EC_7_33_F GAGAGTTTGATCCTGGC 102 16S_EC_101_122_R
TGTTACTCACCCGTCTG 1345 TCAGAACGAA CCACT 295 VALS_EC_610_649_F
ACCGAGCAAGGAGACCA 17 VALS_EC_705_727_R TATAACGCACATCGTCA 929 GC
GGGTGA 344 16S_EC_971_990_F GCGAAGAACCTTACCAG 113
16S_EC_1043_1062_R ACAACCATGCACCACCT 726 GTC GTC 346
16S_EC_713_732_ TAGAACACCGATGGCGA 202 16S_EC_789_809_TMOD_R
TCGTGGACTACCAGGGT 1110 TMOD_F AGGC ATCTA 347 16S_EC_785_806_
TGGATTAGAGACCCTGG 560 16S_EC_880_897_TMOD_R TGGCCGTACTCCCCAGG 1278
TMOD_F TAGTCC CG 348 16S_EC_960_981_ TTTCGATGCAACGCGAA 706
16S_EC_1054_1073_TMOD_R TACGAGCTGACGACAGC 895 TMOD_F GAACCT CATG
349 23S_EC_1826_1843_ TCTGACACCTGCCCGGT 401 23S_EC_1906_1924_TMOD_R
TGACCGTTATAGTTACG 1156 TMOD_F GC GCC 350 CAPC_BA_274_303_
TGATTATTGTTATCCTG 476 CAPC_BA_349_376_TMOD_R TGTAACCCTTGTCTTTG 1314
TMOD_F TTATGCCATTTGAG AATTGTATTTGC 351 CYA_BA_1353_1379_
TCGAAGTACAATACAAG 355 CYA_BA_1448_1467_TMOD_R TTGTTAACGGCTTCAAG
1423 TMOD_F ACAAAAGAAGG ACCC 352 INFB_EC_1365_1393_
TTGCTCGTGGTGCACAA 687 INFB_EC_1439_1467_TMOD_R TTGCTGCTTTCGCATGG
1411 TMOD_F GTAACGGATATTA TTAATTGCTTCAA 353 LEF_BA_756_781_
TAGCTTTTGCATATTAT 220 LEF_BA_843_872_TMOD_R TTCTTCCAAGGATAGAT 1394
TMOD_F ATCGAGCCAC TTATTTCTTGTTCG 354 RPOC_EC_2218_2241_
TCTGGCAGGTATGCGTG 405 RPOC_EC_2313_2337_TMOD_R TCGCACCGTGGGTTGAG
1072 TMOD_F GTCTGATG ATGAAGTAC 355 SSPE_BA_115_137_
TCAAGCAAACGCACAAT 255 SSPE_BA_197_222_TMOD_R TTGCACGTCTGTTTCAG 1402
TMOD_F CAGAAGC TTGCAAATTC 356 RPLB_EC_650_679_ TGACCTACAGTAAGAGG
448 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGGTTTA 1380 TMOD_F
TTCTGTAATGAACC CCCCATGG 357 RPLB_EC_688_710_ TCATCCACACGGTGGTG 296
RPLB_EC_736_757_TMOD_R TGTGCTGGTTTACCCCA 1337 TMOD_F GTGAAGG TGGAGT
358 VALS_EC_1105_1124_ TCGTGGCGGCGTGGTTA 385
VALS_EC_1195_1218_TMOD_R TCGGTACGAACTGGATG 1093 TMOD_F TCGA
TCGCCGTT 359 RPOB_EC_1845_1866_ TTATCGCTCAGGCGAAC 659
RPOB_EC_1909_1929_TMOD_R TGCTGGATTCGCCTTTG 1250 TMOD_F TCCAAC CTACG
360 23S_EC_2646_2667_ TCTGTTCTTAGTACGAG 409 23S_EC_2745_2765_TMOD_R
TTTCGTGCTTAGATGCT 1434 TMOD_F AGGACC TTCAG 361 16S_EC_1090_1111_
TTTAAGTCCCGCAACGA 697 16S_EC_1175_1196_TMOD_R TTGACGTCATCCCCACC
1398 2_TMOD_F GCGCAA TTCCTC 362 RPOB_EC_3799_3821_
TGGGCAGCGTTTCGGCG 581 RPOB_EC_3862_3888_TMOD_R TGTCCGACTTGACGGTC
1325 TMOD_F AAATGGA AACATTTCCTG 363 RPOC_EC_2146_2174_
TCAGGAGTCGTTCAACT 284 RPOC_EC_2227_2245_TMOD_R TACGCCATCAGGCCACG
898 TMOD_F CGATCTACATGAT CAT 364 RPOC_EC_1374_1393_
TCGCCGACTTCGACGGT 367 RPOC_EC_1437_1455_TMOD_R TGAGCATCAGCGTGCGT
1166 TMOD_F GACC GCT 367 TUFB_EC_957_979_ TCCACACGCCGTTCTTC 308
TUFB_EC_1034_1058_TMOD_R TGGCATCACCATTTCCT 1276 TMOD_F AACAACT
TGTCCTTCG 423 SP101_SPET11_893_ TGGGCAACAGCAGCGGA 580
SP101_SPET11_988_1012_ TCATGACAGCCAAGACC 990 921_TMOD_F
TTGCGATTGCGCG TMOD_R TCACCCACC 424 SP101_SPET11_1154_
TCAATACCGCAACAGCG 258 SP101_SPET11_1251_1277_ TGACCCCAACCTGGCCT
1155 1179_TMOD_F GTGGCTTGGG TMOD_R TTTGTCGTTGA 425
SP101_SPET11_118_ TGCTGGTGAAAATAACC 528 SP101_SPET11_213_238_
TTGTGGCCGATTTCACC 1422 147_TMOD_F CAGATGTCGTCTTC TMOD_R ACCTGCTCCT
426 SP101_SPET11_1314_ TCGCAAAAAAATCCAGC 363
SP101_SPET11_1403_1431_ TAAACTATTTTTTTAGC 849 1336_TMOD_F TATTAGC
TMOD_R TATACTCGAACAC 427 SP101_SPET11_1408_ TCGAGTATAGCTAAAAA 359
SP101_SPET11_1486_1515_ TGGATAATTGGTCGTAA 1268 1437_TMOD_F
AATAGTTTATGACA TMOD_R CAAGGGATAGTGAG 428 SP101_SPET11_1688_
TCCTATATTAATCGTTT 334 SP101_SPET11_1783_1808_ TATATGATTATCATTGA 932
1716_TMOD_F ACAGAAACTGGCT TMOD_R ACTGCGGCCG 429 SP101_SPET11_1711_
TCTGGCTAAAACTTTGG 406 SP101_SPET11_1808_1835_ TGCGTGACGACCTTCTT
1239 1733_TMOD_F CAACGGT TMOD_R GAATTGTAATCA 430 SP101_SPET11_1807_
TATGATTACAATTCAAG 235 SP101_SPET11_1901_1927_ TTTGGACCTGTAATCAG
1439 1835_TMOD_F AAGGTCGTCACGC TMOD_R CTGAATACTGG 431
SP101_SPET11_1967_ TTAACGGTTATCATGGC 649 SP101_SPET11_2062_2083_
TATTGCCCAGAAATCAA 940 1991_TMOD_F CCAGATGGG TMOD_R ATCATC 432
SP101_SPET11_216_ TAGCAGGTGGTGAAATC 210 SP101_SPET11_308_333_
TTGCCACTTTGACAACT 1404 243_TMOD_F GGCCACATGATT TMOD_R CCTGTTGCTG
433 SP101_SPET11_2260_ TCAGAGACCGTTTTATC 272
SP101_SPET11_2375_2397_ TTCTGGGTGACCTGGTG 1393 2283_TMOD_F CTATCAGC
TMOD_R TTTTAGA 434 SP101_SPET11_2375_ TTCTAAAACACCAGGTC 675
SP101_SPET11_2470_2497_ TAGCTGCTAGATGAGCT 918 2399_TMOD_F ACCCAGAAG
TMOD_R TCTGCCATGGCC 435 SP101_SPET11_2468_ TATGGCCATGGCAGAAG 238
SP101_SPET11_2543_2570_ TCCATAAGGTCACCGTC 1007 2487_TMOD_F CTCA
TMOD_R ACCATTCAAAGC 436 SP101_SPET11_266_ TCTTGTACTTGTGGCTC 417
SP101_SPET11_355_380_ TGCTGCTTTGATGGCTG 1249 295_TMOD_F
ACACGGCTGTTTGG TMOD_R AATCCCCTTC 437 SP101_SPET11_2961_
TACCATGACAGAAGGCA 183 SP101_SPET11_3023_3045_ TGGAATTTACCAGCGAT
1264 2984_TMOD_F TTTTGACA TMOD_R AGACACC 438 SP101_SPET11_3075_
TGATCACTTTTTAGCTA 473 SP101_SPET11_3168_3196_ TAATCGACGACCATCTT 875
3103_TMOD_F ATGGTCAGGCAGC TMOD_R GGAAAGATTTCTC 439
SP101_SPET11_322_ TGTCAAAGTGGCACGTT 631 SP101_SPET11_423_441_
TATCCCCTGCTTCTGCT 934 344_TMOD_F TACTGGC TMOD_R GCC 440
SP101_SPET11_3386_ TAGCGTAAAGGTGAACC 215 SP101_SPET11_3480_3506_
TCCAGCAGTTACTGTCC 1005 3403_TMOD_F TT TMOD_R CCTCATCTTTG 441
SP101_SPET11_3511_ TGCTTCAGGAATCAATG 531 SP101_SPET11_3605_3629_
TGGGTCTACACCTGCAC 1294
3535_TMOD_F ATGGAGCAG TMOD_R TTGCATAAC 442 SP101_SPET11_358_
TGGGGATTCAGCCATCA 588 SP101_SPET11_448_473_ TCCAACCTTTTCCACAA 998
387_TMOD_F AAGCAGCTATTGAC TMOD_R CAGAATCAGC 443 SP101_SPET11_600_
TCCTTACTTCGAACTAT 348 SP101_SPET11_686_714_ TCCCATTTTTTCACGCA 1018
629_TMOD_F GAATCTTTTGGAAG TMOD_R TGCTGAAAATATC 444
SP101_SPET11_658_ TGGGGATTGATATCACC 589 SP101_SPET11_756_784_
TGATTGGCGATAAAGTG 1189 684_TMOD_F GATAAGAAGAA TMOD_R ATATTTTCTAAAA
445 SP101_SPET11_776_ TTCGCCAATCAAAACTA 673 SP101_SPET11_871_896_
TGCCCACCAGAAAGACT 1217 801_TMOD_F AGGGAATGGC TMOD_R AGCAGGATAA 446
SP101_SPET11_1_29_ TAACCTTAATTGGAAAG 154 SP101_SPET11_92_116_
TCCTACCCAACGTTCAC 1044 TMOD_F AAACCCAAGAAGT TMOD_R CAAGGGCAG 447
SP101_SPET11_364_ TCAGCCATCAAAGCAGC 276 SP101_SPET11_448_471_R
TACCTTTTCCACAACAG 894 385_F TATTG AATCAGC 448 SP101_SPET11_3085_
TAGCTAATGGTCAGGCA 216 SP101_SPET11_3170_3194_R TCGACGACCATCTTGGA
1066 3104_F GCC AAGATTTC 449 RPLB_EC_690_710_F TCCACACGGTGGTGGTG
309 RPLB_EC_737_758_R TGTGCTGGTTTACCCCA 1336 AAGG TGGAG 481
BONTA_X52066_538_ TATGGCTCTACTCAA 239 BONTA_X52066_647_660_R
TGTTACTGCTGGAT 1346 552_F 482 BONTA_X52066_538_ TA*TpGGC*Tp*Cp*Tp
143 BONTA_X52066_647_660P_R TG*Tp*TpA*Cp*TpG* 1146 552P_F
A*Cp*Tp*CpAA Cp*TpGGAT 483 BONTA_X52066_701_ GAATAGCAATTAATCCA 94
BONTA_X52066_759_775_R TTACTTCTAACCCACTC 1367 720_F AAT 484
BONTA_X52066_701_ GAA*TpAG*CpAA*Tp* 91 BONTA_X52066_759_775P_R
TTA*Cp*Tp*Tp*Cp*T 1359 720P_F TpAA*Tp*Cp*CpAAAT
pAA*Cp*Cp*CpA*Cp*TpC 485 BONTA_X52066_450_ TCTAGTAATAATAGGAC 393
BONTA_X52066_517_539_R TAACCATTTCGCGTAAG 859 473_F CCTCAGC ATTCAA
486 BONTA_X52066_450_ T*Cp*TpAGTAATAATA 142 BONTA_X52066_517_539P_R
TAACCA*Tp*Tp*Tp* 857 473P_F GGA*Cp*Cp*Cp*Tp* CpGCGTAAGA*Tp*Tp*
CpAGC CpAA 487 BONTA_X52066_591_ TGAGTCACTTGAAGTTG 463
BONTA_X52066_644_671_R TCATGTGCTAATGTTAC 992 620_F ATACAAATCCTCT
TGCTGGATCTG 608 SSPE_BA_156_168P_F TGGTpGCpTpAGCpATT 616
SSPE_BA_243_255P_R TGCpAGCpTGATpTpGT 1241 609 SSPE_BA_75_89P_F
TACpAGAGTpTpTpGCp 192 SSPE_BA_163_177P_R TGTGCTpTpTpGAATpG 1338 GAC
CpT 610 SSPE_BA_150_168P_F TGCTTCTGGTpGCpTpA 533 SSPE_BA_243_264P_R
TGATTGTTTTGCpAGCp 1191 GCpATT TGATpTpGT 611 SSPE_BA_72_89P_F
TGGTACpAGAGTpTpTp 602 SSPE_BA_163_182P_R TCATTTGTGCTpTpTpG 995
GCpGAC AATpGCpT 612 SSPE_BA_114_137P_F TCAAGCAAACGCACAAT 255
SSPE_BA_196_222P_R TTGCACGTCpTpGTTTC 1401 pCpAGAAGC AGTTGCAAATTC
699 SSPE_BA_123_153_F TGCACAATCAGAAGCTA 488 SSPE_BA_202_231_R
TTTCACAGCATGCACGT 1431 AGAAAGCGCAAGCT CTGTTTCAGTTGC 700
SSPE_BA_156_168_F TGGTGCTAGCATT 612 SSPE_BA_243_255_R TGCAGCTCATTGT
1202 701 SSPE_BA_75_89_F TACAGAGTTTGCGAC 179 SSPE_BA_163_177_R
TGTGCTTTGAATGCT 1338 702 SSPE_BA_150_168_F TGCTTCTGGTGCTAGCA 533
SSPE_BA_243_264_R TGATTGTTTTGCAGCTG 1190 TT ATTGT 703
SSPE_BA_72_89_F TGGTACAGAGTTTGCGA 600 SSPE_BA_163_182_R
TCATTTGTGCTTTGAAT 995 C GCT 704 SSPE_BA_146_168_F TGCAAGCTTCTGGTGCT
484 SSPE_BA_242_267_R TTGTGATTGTTTTGCAG 1421 AGCATT CTGATTGTG 705
SSPE_BA_63_89_F TGCTAGTTATGGTACAG 518 SSPE_BA_163_191_R
TCATAACTAGCATTTGT 986 AGTTTGCGAC GCTTTGAATGCT 706 SSPE_BA_114_137_F
TCAAGCAAACGCACAAT 255 SSPE_BA_196_222_R TTGCACGTCTGTTTCAG 1402
CAGAAGC TTGCAAATTC 770 PLA_AF053945_7377_ TGACATCCGGCTCACGT 442
PLA_AF053945_7434_7462_R TGTAAATTCCGCAAAGA 1313 7402_F TATTATGGT
CTTTGGCATTAG 771 PLA_AF053945_7382_ TCCGGCTCACGTTATTA 327
PLA_AF053945_7482_7502_R TGGTCTGAGTACCTCCT 1304 7404_F TGGTAC TTGC
772 PLA_AF053945_7481_ TGCAAAGGAGGTACTCA 481
PLA_AF053945_7539_7562_R TATTGGAAATACCGGCA 943 7503_F GACCAT
GCATCTC 773 PLA_AF053945_7186_ TTATACCGGAAACTTCC 657
PLA_AF053945_7257_7280_R TAATGCGATACTGGCCT 879 7211_F CGAAAGGAG
GCAAGTC 774 CAF1_AF053947_ TCAGTTCCGTTATCGCC 292
CAF1_AF053947_33494_ TGCGGGCTGGTTCAACA 1235 33407_33430_F ATTGCAT
33514_R AGAG 775 CAF1_AF053947_ TCACTCTTACATATAAG 270
CAF1_AF053947_33595_ TCCTGTTTTATAGCCGC 1053 33515_33541_F
GAAGGCGCTC 33621_R CAAGAGTAAG 776 CAF1_AF053947_ TGGAACTATTGCAACTG
542 CAF1_AF053947_33499_ TGATGCGGGCTGGTTCA 1183 33435_33457_F
CTAATG 33517_R AC 777 CAF1_AF053947_ TCAGGATGGAAATAACC 286
CAF1_AF053947_33755_ TCAAGGTTCTCACCGTT 962 33687_33716_F
ACCAATTCACTAC 33782_R TACCTTAGGAG 778 INV_U22457_515_
TGGCTCCTTGGTATGAC 573 INV_U22457_571_598_R TGTTAAGTGTGTTGCGG 1343
539_F TCTGCTTC CTGTCTTTATT 779 INV_U22457_699_ TGCTGAGGCCTGGACCG
525 INV_U22457_753_776_R TCACGCGACGAGTGCCA 976 724_F ATTATTTAC
TCCATTG 780 INV_U22457_834_ TTATTTACCTGCACTCC 664
INV_U22457_942_966_R TGACCCAAAGCTGAAAG 1154 858_F CACAACTG CTTTACTG
781 INV_U22457_1558_ TGGTAACAGAGCCTTAT 597 INV_U22457_1619_1643_R
TTGCGTTGCAGATTATC 1408 1581_F AGGCGCA TTTACCAA 782 LL_NC003143_
TGTAGCCGCTAAGCACT 627 LL_NC003143_2367073_ TCTCATCCCGATATTAC 1123
2366996_2367019_F ACCATCC 2367097_R CGCCATGA 783 LL_NC003143_
TGGACGGCATCACGATT 550 LL_NC003143_2367249_ TGGCAACAGCTCAACAC 1272
2367172_2367194_F CTCTAC 2367271_R CTTTGG 874 RPLB_EC_649_679_F
TGICCIACIGTIIGIGG 620 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGGTTTA 1380
TTCTGTAATGAACC CCCCATGG 875 RPLB_EC_642_679P_F TpCpCpTpTpGITpGIC
646 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGGTTTA 1380 CIACIGTIIGIGGTTCT
CCCCATGG GTAATGAACC 876 MECIA_Y14051_3315_ TTACACATATCGTGAGC 653
MECIA_Y14051_3367_3393_R TGTGATATGGAGGTGTA 1333 3341_F AATGAACTGA
GAAGGTGTTA 877 MECA_Y14051_3774_ TAAAACAAACTACGGTA 144
MECA_Y14051_3828_3854_R TCCCAATCTAACTTCCA 1015 3802_F ACATTGATCGCA
CATACCATCT 878 MECA_Y14051_3645_ TGAAGTAGAAATGACTG 434
MECA_Y14051_3690_3719_R TGATCCTGAATGTTTAT 1181 3670_F AACGTCCGA
ATCTTTAACGCCT 879 MECA_Y14051_4507_ TCAGGTACTGCTATCCA 288
MECA_Y14051_4555_4581_R TGGATAGACGTCATATG 1269 4530_F CCCTCAA
AAGGTGTGCT 880 MECA_Y14051_4510_ TGTACTGCTATCCACCC 626
MECA_Y14051_4586_4610_R TATTCTTCGTTACTCAT 939 4530_F TCAA GCCATACA
881 MECA_Y14051_4669_ TCACCAGGTTCAACTCA 262 MECA_Y14051_4765_4793_R
TAACCACCCCAAGATTT 858 4698_F AAAAATATTAACA ATCTTTTTGCCA 882
MECA_Y14051_4520_ TCpCpACpCpCpTpCpA 389 MECA_Y14051_4590_4600P_R
TpACpTpCpATpGCpCp 1357 4530P_F A A 883 MECA_Y14051_4520_
TCpCpACpCpCpTpCpA 389 MECA_Y14051_4600_4610P_R TpATpTpCpTpTpCpGT
1358 4530P_F A pT 902 TRPE_AY094355_ ATGTCGATTGCAATCCG 36
TRPE_AY094355_1569_ TGCGCGAGCTTTTATTT 1231 1467_1491_F TACTTGTG
1592_R GGGTTTC 903 TRPE_AY094355_ TGGATGGCATGGTGAAA 557
TRPE_AY094355_1551_ TATTTGGGTTTCATTCC 944 1445_1471_F TGGATATGTC
1580_R ACTCAGATTCTGG 904 TRPE_AY094355_ TCAAATGTACAAGGTGA 247
TRPE_AY094355_1392_ TCCTCTTTTCACAGGCT 1048 1278_1303_F AGTGCGTGA
1418_R CTACTTCATC 905 TRPE_AY094355_ TCGACCTTTGGCAGGAA 357
TRPE_AY094355_1171_ TACATCGTTTCGCCCAA 885 1064_1086_F CTAGAC 1196_R
GATCAATCA 906 TRPE_AY094355_666_ GTGCATGCGGATACAGA 135
TRPE_AY094355_769_791_R TTCAAAATGCGGAGGCG 1372 688_F GCAGAG TATGTG
907 TRPE_AY094355_757_ TGCAAGCGCGACCACAT 483
TRPE_AY094355_864_883_R TGCCCAGGTACAACCTG 1218 776_F ACG CAT 908
RECA_AF251469_43_ TGGTACATGTGCCTTCA 601 RECA_AF251469_140_163_R
TTCAAGTGCTTGCTCAC 1375 68_F TTGATGCTG CATTGTC 909
RECA_AF251469_169_ TGACATGCTTGTCCGTT 446 RECA_AF251469_277_300_R
TGGCTCATAAGACGCGC 1280 190_F CAGGC TTGTAGA 910 PARC_X95819_87_
TGGTGACTCGGCATGTT 609 PARC_X95819_201_222_R TTCGGTATAACGCATCG 1387
110_F ATGAAGC CAGCA 911 PARC_X95819_87_ TGGTGACTCGGCATGTT 609
PARC_X95819_192_219_R GGTATAACGCATCGCAG 836 110_F ATGAAGC
CAAAAGATTTA 912 PARC_X95819_123_ GGCTCAGCCATTTAGTT 120
PARC_X95819_232_260_R TCGCTCAGCAATAATTC 1081
147_F ACCGCTAT ACTATAAGCCGA 913 PARC_X95819_43_ TCAGCGCGTACAGTGGG
277 PARC_X95819_143_170_R TTCCCCTGACCTTCGAT 1383 63_F TGAT
TAAAGGATAGC 914 OMPA_AY485227_272_ TTACTCCATTATTGCTT 655
OMPA_AY485227_364_388_R GAGCTGCGCCAACGAAT 812 301_F GGTTACACTTTCC
AAATCGTC 915 OMPA_AY485227_379_ TGCGCAGCTCTTGGTAT 509
OMPA_AY485227_492_519_R TGCCGTAACATAGAAGT 1223 401_F CGAGTT
TACCGTTGATT 916 OMPA_AY485227_311_ TACACAACAATGGCGGT 178
OMPA_AY485227_424_453_R TACGTCGCCTTTAACTT 901 335_F AAAGATGG
GGTTATATTCAGC 917 OMPA_AY485227_415_ TGCCTCGAAGCTGAATA 506
OMPA_AY485227_514_546_R TCGGGCGTAGTTTTTAG 1092 441_F TAACCAAGTT
TAATTAAATCAGAAGT 918 OMPA_AY485227_494_ TCAACGGTAACTTCTAT 252
OMPA_AY485227_569_596_R TCGTCGTATTTATAGTG 1108 520_F GTTACTTCTG
ACCAGCACCTA 919 OMPA_AY485227_551_ TCAAGCCGTACGTATTA 257
OMPA_AY485227_658_680_R TTTAAGCGCCAGAAAGC 1425 577_F TTAGGTGCTG
ACCAAC 920 OMPA_AY485227_555_ TCCGTACGTATTATTAG 328
OMPA_AY485227_635_662_R TCAACACCAGCGTTACC 954 581_F GTGCTGGTCA
TAAAGTACCTT 921 OMPA_AY485227_556_ TCGTACGTATTATTAGG 379
OMPA_AY485227_659_683_R TCGTTTAAGCGCCAGAA 1114 583_F TGCTGGTCACT
AGCACCAA 922 OMPA_AY485227_657_ TGTTGGTGCTTTCTGGC 645
OMPA_AY485227_739_765_R TAAGCCAGCAAGAGCTG 871 679_F GCTTAA
TATAGTTCCA 923 OMPA_AY485227_660_ TGGTGCTTTCTGGCGCT 613
OMPA_AY485227_786_807_R TACAGGAGCAGCAGGCT 884 683_F TAAACGA TCAAG
924 GYRA_AF100557_4_ TCTGCCCGTGTCGTTGG 402 GYRA_AF100557_119_142_R
TCGAACCGAAGTTACCC 1063 23_F TGA TGACCAT 925 GYRA_AF100557_70_
TCCATTGTTCGTATGGC 316 GYRA_AF100557_178_201_R TGCCAGCTTAGTCATAC
1211 94_F TCAAGACT GGACTTC 926 GYRB_AB008700_19_ TCAGGTGGCTTACACGG
289 GYRB_AB008700_111_140_R TATTGCGGATCACCATG 941 40_F CGTAG
ATGATATTCTTGC 927 GYRB_AB008700_265_ TCTTTCTTGAATGCTGG 420
GYRB_AB008700_369_395_R TCGTTGAGATGGTTTTT 1113 292_F TGTACGTATCG
ACCTTCGTTG 928 GYRB_AB008700_368_ TCAACGAAGGTAAAAAC 251
GYRB_AB008700_466_494_R TTTGTGAAACAGCGAAC 1440 394_F CATCTCAACG
ATTTTCTTGGTA 929 GYRB_AB008700_477_ TGTTCGCTGTTTCACAA 641
GYRB_AB008700_611_632_R TCACGCGCATCATCACC 977 504_F ACAACATTCCA
AGTCA 930 GYRB_AB008700_760_ TACTTACTTGAGAATCC 198
GYRB_AB008700_862_888_R ACCTGCAATATCTAATG 729 787_F ACAAGCTGCAA
CACTCTTACG 931 WAAA_Z96925_2_29_F TCTTGCTCTTTCGTGAG 416
WAAA_Z96925_115_138_R CAAGCGGTTTGCCTCAA 758 TTCAGTAAATG ATAGTCA 932
WAAA_Z96925_286_ TCGATCTGGTTTCATGC 360 WAAA_Z96925_394_412_R
TGGCACGAGCCTGACCT 1274 311_F TGTTTCAGT GT 939 RPOB_EC_3798_3821_
TGGGCAGCGTTTCGGCG 581 RPOB_EC_3862_3889_R TGTCCGACTTGACGGTC 1326 F
AAATGGA AGCATTTCCTG 940 RPOB_EC_3798_3821_ TGGGCAGCGTTTCGGCG 581
RPOB_EC_3862_3889_2_R TGTCCGACTTGACGGTT 1327 F AAATGGA AGCATTTCCTG
941 TUFB_EC_275_299_F TGATCACTGGTGCTGCT 468 TUFB_EC_337_362_R
TGGATGTGCTCACGAGT 1271 CAGATGGA CTGTGGCAT 942 TUFB_EC_251_278_F
TGCACGCCGACTATGTT 493 TUFB_EC_337_360_R TATGTGCTCACGAGTTT 937
AAGAACATGAT GCGGCAT 949 GYRB_AB008700_760_ TACTTACTTGAGAATCC 198
GYRB_AB008700_862_888_ TCCTGCAATATCTAATG 1050 787_F ACAAGCTGCAA 2_R
CACTCTTACG 958 RPOC_EC_2223_2243_ TGGTATGCGTGGTCTGA 605
RPOC_EC_2329_2352_R TGCTAGACCTTTACGTG 1243 F TGGC CACCGTG 959
RPOC_EC_918_938_F TCTGGATAACGGTCGTC 404 RPOC_EC_1009_1031_R
TCCAGCAGGTTCTGACG 1004 GCGG GAAACG 960 RPOC_EC_2334_2357_
TGCTCGTAAGGGTCTGG 523 RPOC_EC_2380_2403_R TACTAGACGACGGGTCA 905 F
CGGATAC GGTAACC 961 RPOC_EC_917_938_F TATTGGACAACGGTCGT 242
RPOC_EC_1009_1034_R TTACCGAGCAGGTTCTG 1362 CGCGG ACGGAAACG 962
RPOB_EC_2005_2027_ TCGTTCCTGGAACACGA 387 RPOB_EC_2041_2064_R
TTGACGTTGCATGTTCG 1399 F TGACGC AGCCCAT 963 RPOB_EC_1527_1549_
TCAGCTGTCGCAGTTCA 282 RPOB_EC_1630_1649_R TCGTCGCGGACTTCGAA 1104 F
TGGACC GCC 964 INFB_EC_1347_1367_ TGCGTTTACCGCAATGC 515
INFB_EC_1414_1432_R TCGGCATCACGCCGTCG 1090 F GTGC TC 965
VALS_EC_1128_1151_ TATGCTGACCGACCAGT 237 VALS_EC_1231_1257_R
TTCGCGCATCCAGGAGA 1384 F GGTACGT AGTACATGTT 978 RPOC_EC_2145_2175_
TCAGGAGTCGTTCAACT 285 RPOC_EC_2228_2247_R TTACGCCATCAGGCCAC 1363 F
CGATCTACATGATG GCA 1045 CJST_CJ_1668_ TGCTCGAGTGATTGACT 522
CJST_CJ_1774_1799_R TGAGCGTGTGGAAAAGG 1170 1700_F TTGCTAAATTTAGAGA
ACTTGGATG 1046 CJST_CJ_2171_ TCGTTTGGTGGTGGTAG 388
CJST_CJ_2283_2313_R TCTCTTTCAAAGCACCA 1126 2197_F ATGAAAAAGG
TTGCTCATTATAGT 1047 CJST_CJ_584_616_F TCCAGGACAAATGTATG 315
CJST_CJ_663_692_R TTCATTTTCTGGTCCAA 1379 AAAAATGTCCAAGAAC
AGTAAGCAGTATC 1048 CJST_CJ_360_394_F TCCTGTTATCCCTGAAG 346
CJST_CJ_442_476_R TCAACTGGTTCAAAAAC 955 TAGTTAATCAAGTTTGT
ATTAAGTTGTAATTGTC T C 1049 CJST_CJ_2636_ TGCCTAGAAGATCTTAA 504
CJST_CJ_2753_2777_R TTGCTGCCATAGCAAAG 1409 2668_F AAATTTCCGCCAACTT
CCTACAGC 1050 CJST_CJ_1290_ TGGCTTATCCAAATTTA 575
CJST_CJ_1406_1433_R TTTGCTCATGATCTGCA 1437 1320_F GATCGTGGTTTTAC
TGAAGCATAAA 1051 CJST_CJ_3267_ TTTGATTTTACGCCGTC 707
CJST_CJ_3356_3385_R TCAAAGAACCCGCACCT 951 3293_F CTCCAGGTCG
AATTCATCATTTA 1052 CJST_CJ_5_39_F TAGGCGAAGATATACAA 222
CJST_CJ_104_137_R TCCCTTATTTTTCTTTC 1029 AGAGTATTAGAAGCTAG
TACTACCTTCGGATAAT A 1053 CJST_CJ_1080_ TTGAGGGTATGCACCGT 681
CJST_CJ_1166_1198_R TCCCCTCATGTTTAAAT 1022 1110_F CTTTTTGATTCTTT
GATCAGGATAAAAAGC 1054 CJST_CJ_2060_ TCCCGGACTTAATATCA 323
CJST_CJ_2148_2174_R TCGATCCGCATCACCAT 1068 2090_F ATGAAAATTGTGGA
CAAAAGCAAA 1055 CJST_CJ_2869_ TGAAGCTTGTTCTTTAG 432
CJST_CJ_2979_3007_R TCCTCCTTGTGCCTCAA 1045 2895_F CAGGACTTCA
AACGCATTTTTA 1056 CJST_CJ_1880_ TCCCAATTAATTCTGCC 317
CJST_CJ_1981_2011_R TGGTTCTTACTTGCTTT 1309 1910_F ATTTTTCCAGGTAT
GCATAAACTTTCCA 1057 CJST_CJ_2185_ TAGATGAAAAGGGCGAA 208
CJST_CJ_2283_2316_R TGAATTCTTTCAAAGCA 1152 2212_F GTGGCTAATGG
CCATTGCTCATTATAGT 1058 CJST_CJ_1643_ TTATCGTTTGTGGAGCT 660
CJST_CJ_1724_1752_R TGCAATGTGTGCTATGT 1198 1670_F AGTGCTTATGC
CAGCAAAAAGAT 1059 CJST_CJ_2165_ TGCGGATCGTTTGGTGG 511
CJST_CJ_2247_2278_R TCCACACTGGATTGTAA 1002 2194_F TTGTAGATGAAAA
TTTACCTTGTTCTTT 1060 CJST_CJ_599_632_F TGAAAAATGTCCAAGAA 424
CJST_CJ_711_743_R TCCCGAACAATGAGTTG 1024 GCATAGCAAAAAAAGCA
TATCAACTATTTTTAC 1061 CJST_CJ_360_393_F TCCTGTTATCCCTGAAG 345
CJST_CJ_443_477_R TACAACTGGTTCAAAAA 882 TAGTTAATCAAGTTTGT
CATTAAGCTGTAATTGT C 1062 CJST_CJ_2678_ TCCCCAGGACACCCTGA 321
CJST_CJ_2760_2787_R TGTGCTTTTTTTGCTGC 1339 2703_F AATTTCAAC
CATAGCAAAGC 1063 CJST_CJ_1268_ AGTTATAAACACGGCTT 29
CJST_CJ_1349_1379_R TCGGTTTAAGCTCTACA 1096 1299_F TCCTATGGCTTATCC
TGATCGTAAGGATA 1064 CJST_CJ_1680_ TGATTTTGCTAAATTTA 479
CJST_CJ_1795_1822_R TATGTGTAGTTGAGCTT 938 1713_F GAGAAATTGCGGATGAA
ACTACATGAGC 1065 CJST_CJ_2857_ TGGCATTTCTTATGAAG 565
CJST_CJ_2965_2998_R TGCTTCAAAACGCATTT 1253 2887_F CTTGTTCTTTAGCA
TTACATTTTCGTTAAAG 1070 RNASEP_BKM_580_ TGCGGGTAGGGAGCTTG 512
RNASEP_BKM_665_686_R TCCGATAAGCCGGATTC 1034 599_F AGC TGTGC 1071
RNASEP_BKM_616_ TCCTAGAGGAATGGCTG 333 RNASEP_BKM_665_687_R
TGCCGATAAGCCGGATT 1222 637_F CCACG CTGTGC 1072 RNASEP_BDP_574_
TGGCACGGCCATCTCCG 561 RNASEP_BDP_616_635_R TCGTTTCACCCTGTCAT 1115
592_F TG GCCG 1073 23S_BRM_1110_1129_ TGCGCGGAAGATGTAAC 510
23S_BRM_1176_1201_R TCGCAGGCTTACAGAAC 1074 F GGG GCTCTCCTA 1074
23S_BRM_515_536_F TGCATACAAACAGTCGG 496 23S_BRM_616_635_R
TCGGACTCGCTTTCGCT 1088 AGCCT ACG 1075 RNASEP_CLB_459_
TAAGGATAGTGCAACAG 162 RNASEP_CLB_498_526_R TGCTCTTACCTCACCGT 1247
487_F AGATATACCGCC TCCACCCTTACC 1076 RNASEP_CLB_459_
TAAGGATAGTGCAACAG 162 RNASEP_CLB_498_522_R TTTACCTCGCCTTTCCA
1426
487_F AGATATACCGCC CCCTTACC 1077 ICD_CXB_93_120_F TCCTGACCGACCCATTA
343 ICD_CXB_172_194_R TAGGATTTTTCCACGGC 921 TTCCCTTTATC GGCATC 1078
ICD_CXB_92_120_F TTCCTGACCGACCCATT 671 ICD_CXB_172_194_R
TAGGATTTTTCCACGGC 921 ATTCCCTTTATC GGCATC 1079 ICD_CXB_176_198_F
TCGCCGTGGAAAAATCC 369 ICD_CXB_224_247_R TAGCCTTTTCTCCGGCG 916
TACGCT TAGATCT 1080 IS1111A_NC002971_ TCAGTATGTATCCACCG 290
IS1111A_NC002971_6928_ TAAACGTCCGATACCAA 848 6866_6891_F TAGCCAGTC
6954_R TGGTTCGCTC 1081 IS1111A_NC002971_ TGGGTGACATTCATCAA 594
IS1111A_NC002971_7529_ TCAACAACACCTCCTTA 952 7456_7483_F
TTTCATCGTTC 7554_R TTCCCACTC 1082 RNASEP_RKP_419_ TGGTAAGAGCGCACCGG
599 RNASEP_RKP_542_565_R TCAAGCGATCTACCCGC 957 448_F TAAGTTGGTAACA
ATTACAA 1083 RNASEP_RKP_422_ TAAGAGCGCACCGGTAA 159
RNASEP_RKP_542_565_R TCAAGCGATCTACCCGC 957 443_F GTTGG ATTACAA 1084
RNASEP_RKP_466_ TCCACCAAGAGCAAGAT 310 RNASEP_RKP_542_565_R
TCAAGCGATCTACCCGC 957 491_F CAAATAGGC ATTACAA 1085 RNASEP_RKP_264_
TCTAAATGGTCGTGCAG 391 RNASEP_RKP_295_321_R TCTATAGAGTCCGGACT 1119
287_F TTGCGTG TTCCTCGTGA 1086 RNASEP_RKP_426_ TGCATACCGGTAAGTTG 497
RNASEP_RKP_542_565_R TCAAGCGATCTACCCGC 957 448_F GCAACA ATTACAA
1087 OMPB_RKP_860_890_F TTACAGGAAGTTTAGGT 654 OMPB_RKP_972_996_R
TCCTGCAGCTCTACCTG 1051 GGTAATCTAAAAGG CTCCATTA 1088 OMPB_RKP_1192_
TCTACTGATTTTGGTAA 392 OMPB_RKP_1288_1315_R TAGCAgCAAAAGTTATC 910
1221_F TCTTGCAGCACAG ACACCTGCAGT 1089 OMPB_RKP_3417_
TGCAAGTGGTACTTCAA 485 OMPB_RKP_3520_3550_R TGGTTGTAGTTCCTGTA 1310
3440_F CATGGGG GTTGTTGCATTAAC 1090 GLTA_RKP_1043_ TGGGACTTGAAGCTATC
576 GLTA_RKP_1138_1162_R TGAACATTTGCGACGGT 1147 1072_F
GCTCTTAAAGATG ATACCCAT 1091 GLTA_RKP_400_428_F TCTTCTCATCCTATGGC
413 GLTA_RKP_499_529_R TGGTGGGTATCTTAGCA 1305 TATTATGCTTGC
ATCATTCTAATAGC 1092 GLTA_RKP_1023_ TCCGTTCTTACAAATAG 330
GLTA_RKP_1129_1156_R TTGGCGACGGTATACCC 1415 1055_F CAATAGAACTTGAAGC
ATAGCTTTATA 1093 GLTA_RKP_1043_ TGGAGCTTGAAGCTATC 553
GLTA_RKP_1138_1162_R TGAACATTTGCGACGGT 1147 1072_2_F GCTCTTAAAGATG
ATACCCAT 1094 GLTA_RKP_1043_ TGGAACTTGAAGCTCTC 543
GLTA_RKP_1138_1164 R TGTGAACATTTGCGACG 1330 1072_3_F GCTCTTAAAGATG
GTATACCCAT 1095 GLTA_RKP_400_428_F TCTTCTCATCCTATGGC 413
GLTA_RKP_505_534_R TGCGATGGTAGGTATCT 1230 TATTATGCTTGC
TAGCAATCATTCT 1096 CTXA_VBC_117_142_F TCTTATGCCAAGAGGAC 410
CTXA_VBC_194_218_R TGCCTAACAAATCCCGT 1226 AGAGTGAGT CTGAGTTC 1097
CTXA_VBC_351_377_F TGTATTAGGGGCATACA 630 CTXA_VBC_441_466_R
TGTCATCAAGCACCCCA 1324 GTCCTCATCC AAATGAACT 1098 RNASEP_VBC_331_
TCCGCGGAGTTGACTGG 325 RNASEP_VBC_388_414_R TGACTTTCCTCCCCCTT 1163
349_F GT ATCAGTCTCC 1099 TOXR_VBC_135_158_F TCGATTAGGCAGCAACG 362
TOXR_VBC_221_246_R TTCAAAACCTTGCTCTC 1370 AAAGCCG GCCAAACAA 1100
ASD_FRT_1_29_F TTGCTTAAAGTTGGTTT 690 ASD_FRT_86_116_R
TGAGATGTCGAAAAAAA 1164 TATTGGTTGGCG CGTTGGCAAAATAC 1101
ASD_FRT_43_76_F TCAGTTTTAATGTCTCG 295 ASD_FRT_129_156_R
TCCATATTGTTGCATAA 1009 TATGATCGAATCAAAAG AACCTGTTGGC 1102
GALE_FRT_168_199_F TTATCAGCTAGACCTTT 658 GALE_FRT_241_269_R
TCACCTACAGCTTTAAA 973 TAGGTAAAGCTAAGC GCCAGCAAAATG 1103
GALE_FRT_834_865_F TCAAAAAGCCCTAGGTA 245 GALE_FRT_901_925_R
TAGCCTTGGCAACATCA 915 AAGAGATTCCATATC GCAAAACT 1104
GALE_FRT_308_339_F TCCAAGGTACACTAAAC 306 GALE_FRT_390_422_R
TCTTCTGTAAAGGGTGG 1136 TTACTTGAGCTAATG TTTATTATTCATCCCA 1105
IPAH_SGF_258_277_F TGAGGACCGTGTCGCGC 458 IPAH_SGF_301_327_R
TCCTTCTGATGCCTGAT 1055 TCA GGACCAGGAG 1106 IPAH_SGF_113_134_F
TCCTTGACCGCCTTTCC 350 IPAH_SGF_172_191_R TTTTCCAGCCATGCAGC 1441
GATAC GAC 1107 IPAH_SGF_462_486_F TCAGACCATGCTCGCAG 271
IPAH_SGF_522_540_R TGTCACTCCCGACACGC 1322 AGAAACTT CA 1111
RNASEP_BRM_461_ TAAACCCCATCGGGAGC 147 RNASEP_BRM_542_561_R
TGCCTCGCGCAACCTAC 1227 488_F AAGACCGAATA CCG 1112 RNASEP_BRM_325_
TACCCCAGGGAAAGTGC 185 RNASEP_BRM_402_428_R TCTCTTACCCCACCCTT 1125
347_F CACAGA TCACCCTTAC 1128 HUPB_CJ_113_134_F TAGTTGCTCAAACAGCT
230 HUPB_CJ_157_188_R TCCCTAATAGTAGAAAT 1028 GGGCT AACTGCATCAGTAGC
1129 HUPB_CJ_76_102_F TCCCGGAGCTTTTATGA 324 HUPB_CJ_157_188_R
TCCCTAATAGTAGAAAT 1028 CTAAAGCAGAT AACTGCATCAGTAGC 1130
HUPB_CJ_76_102_F TCCCGGAGCTTTTATGA 324 HUPB_CJ_114_135_R
TAGCCCAGCTGTTTGAG 913 CTAAAGCAGAT CAACT 1151 AS_MLST-11-
TGAGATTGCTGAACATT 454 AB_MLST-11- TTGTACATTTGAAACAA 1418
OIF007_62_91_F TAATGCTGATTGA OIF007_169_203_R TATGCATGACATGTGAA T
1152 AB_MLST-11- TATTGTTTCAAATGTAC 243 AB_MLST-11-
TCACAGGTTCTACTTCA 969 OIF007_185_214_F AAGGTGAAGTGCG
OIF007_291_324_R TCAATAATTTCCATTGC 1153 AB_MLST-11-
TGGAACGTTATCAGGTG 541 AB_MLST-11- TTGCAATCGACATATCC 1400
OIF007_260_289_F CCCCAAAAATTCG OIF007_364_393_R ATTTCACCATGCC 1154
AB_MLST-11- TGAAGTGCGTGATGATA 436 AB_MLST-11- TCCGCCAAAAACTCCCC
1036 OIF007_206_239_F TCGATGCACTTGATGTA OIF007_318_344_R TTTTCACAGG
1155 AB_MLST-11- TCGGTTTAGTAAAAGAA 378 AB_MLST-11-
TTCTGCTTGAGGAATAG 1392 OIF007_522_552_F CGTATTGCTCAACC
OIF007_587_610_R TGCGTGG 1156 AB_MLST-11- TCAACCTGACTGCGTGA 250
AB_MLST-11- TACGTTCTACGATTTCT 902 OIF007_547_571_F ATGGTTGT
OIF007_656_686_R TCATCAGGTACATC 1157 AB_MLST-11- TCAAGCAGAAGCTTTGG
256 AB_MLST-11- TACAACGTGATAAACAC 881 OIF007_601_627_F AAGAAGAAGG
OIF007_710_736_R GACCAGAAGC 1158 AB_MLST-11- TCGTGCCCGCAATTTGC 384
AB_MLST-11- TAATGCCGGGTAGTGCA 878 OIF007_1202_1225_F ATAAAGC
OIF007_1266_1296_R ATCCATTCTTCTAG 1159 AB_MLST-11-
TCGTGCCCGCAATTTGC 384 AB_MLST-11- TGCACCTGCGGTCGAGC 1199
OIF007_1202_1225_F ATAAAGC OIF007_1299_1316_R G 1160 AB_MLST-11-
TTGTAGCACAGCAAGGC 694 AB_MLST-11- TGCCATCCATAATCACG 1215
OIF007_1234_1264_F AAATTTCCTGAAAC OIF007_1335_1362_R CCATACTGACG
1161 AB_MLST-11- TAGGTTTACGTCAGTAT 225 AB_MLST-11-
TGCCAGTTTCCACATTT 1212 OIF007_1327_1356_F GGCGTGATTATGG
OIF007_1422_1448_R CACGTTCGTG 1162 AB_MLST-11- TCGTGATTATGGATGGC
383 AB_MLST-11- TCGCTTGAGTGTAGTCA 1083 OIF007_1345_1369_F AACGTGAA
OIF007_1470_1494_R TGATTGCG 1163 AB_MLST-11- TTATGGATGGCAACGTG 662
AB_MLST-11- TCGCTTGAGTGTAGTCA 1083 OIF007_1351_1375_F AAACGCGT
OIF007_1470_1494_R TGATTGCG 1164 AB_MLST-11- TCTTTGCCATTGAAGAT 422
AB_MLST-11- TCGCTTGAGTGTAGTCA 1083 OIF007_1387_1412_F GACTTAAGC
OIF007_1470_1494_R TGATTGCG 1165 AB_MLST-11- TACTAGCGGTAAGCTTA 194
AB_MLST-11- TGAGTCGGGTTCACTTT 1173 OIF007_1542_1569_F AACAAGATTGC
OIF007_1656_1680_R ACCTGGCA 1166 AB_MLST-11- TTGCCAATGATATTCGT 684
AB_MLST-11- TGAGTCGGGTTCACTTT 1173 OIF007_1566_1593_F TGGTTAGCAAG
OIF007_1656_1680_R ACCTGGCA 1167 AB_MLST-11- TCGGCGAAATCCGTATT 375
AB_MLST-11- TACCGGAAGCACCAGCG 890 OIF007_1611_1638_F CCTGAAAATGA
OIF007_1731_1757_R ACATTAATAG 1168 AB_MLST-11- TACCACTATTAATGTCG
182 AB_MLST-11- TGCAACTGAATAGATTG 1195 OIF007_1726_1752_F
CTGGTGCTTC OIF007_1790_1821_R CAGTAAGTTATAAGC 1169 AB_MLST-11-
TTATAACTTACTGCAAT 656 AB_MLST-11- TGAATTATGCAAGAAGT 1151
OIF007_1792_1826_F CTATTCAGTTGCTTGGT OIF007_1876_1909_R
GATCAATTTTCTCACGA G 1170 AB_MLST-11- TTATAACTTACTGCAAT 656
AB_MLST-11- TGCCGTAACTAACATAA 1224 OIF007_1792_1826_F
CTATTCAGTTGCTTGGT OIF007_1895_1927_R GAGAATTATGCAAGAA G 1171
AB_MLST-11- TGGTTATGTACCAAATA 618 AB_MLST-11- TGACGGCATCGATACCA
1157 OIF007_1970_2002_F CTTTGTCTGAAGATGG OIF007_2097_2118_R CCGTC
1172 RNASEP_BRM_461_ TAAACCCCATCGGGAGC 147 RNASEP_BRM_542_561_2_R
TGCCTCGTGCAACCCAC 1228 488_F AAGACCGAATA CCG 2000 CTXB_NC002505_46_
TCAGCGTATGCACATGG 278 CTXB_NC002505_132_162_R TCCGGCTAGAGATTCTG
1039 70_F AACTCCTC TATACGACAATATC 2001 FUR_NC002505_87_
TGAGTGCCAACATATCA 465 FUR_NC002505_205_228_R TCCGCCTTCAAAATGGT 1037
113_F GTGCTGAAGA GGCGAGT 2002 FUR_NC002505_87_ TGAGTGCCAACATATCA
465 FUR_NC002505_178_205_R TCACGATACCTGCATCA 974 113_F GTGCTGAAGA
TCAAATTGGTT 2003 GAPA_NC002505_533_ TCGACAACACCATTATC 356
GAPA_NC002505_646_671_R TCAGAATCGATGCCAAA 980 560_F TATGGTGTGAA
TGCGTCATC 2004 GAPA_NC002505_694_ TCAATGAACGACCAACA 259
GAPA_NC002505_769_798_R TCCTCTATGCAACTTAG 1046 721_F AGTGATTGATG
TATCAACAGGAAT 2005 GAPA_NC002505_753_ TGCTAGTCAATCTATCA 517
GAPA_NC0002505_856_881_R TCCATCGCAGTCACGTT 1011 782_F TTCCGGTTGATAC
TACTGTTGG 2006 GYRB_NC002505_2_ TGCCGGACAATTACGAT 501
GYRB_NC002505_109_134_R TCCACCACCTCAAAGAC 1003 32_F TCATCGAGTATTAA
CATGTGGTG 2007 GYRB_NC002505_123_ TGAGGTGGTGGATAACT 460
GYRB_NC002505_199_225_R TCCGTCATCGCTGACAG 1042 152_F CAATTGATGAAGC
AAACTGAGTT 2008 GYRB_NC002505_768_ TATGCAGTGGAACGATG 236
GYRB_NC002505_832_860_R
TGGAAACCGGCTAAGTG 1262 794_F GTTTCCAAGA AGTACCACCATC 2009
GYRB_NC002505_837_ TGGTACTCACTTAGCGG 603 GYRB_NC002505_937_957_R
TCCTTCACGCGCATCAT 1054 860_F GTTTCCG CACC 2010 GYRB_NC002505_934_
TCGGGTGATGATGCGCG 377 GYRB_NC002505_982_1007_R TGGCTTGAGAATTTAGG
1283 956_F TGAAGG ATCCGGCAC 2011 GYRB_NC002505_ TAAAGCCCGTGAAATGA
148 GYRB_NC002505_1255_ TGAGTCACCCTCCACAA 1172 1161_1190_F
CTCGTCGTAAAGG 1284_R TGTATAGTTCAGA 2012 OMPU_NC002505_85_
TACGCTGACGGAATCAA 190 OMPU_NC002505_154_180_R TGCTTCAGCACGGCCAC
1254 110_F CCAAAGCGG CAACTTCTAG 2013 OMPU_NC002505_258_
TGACGGCCTATACGGTG 451 OMPU_NC002505_346_369_R TCCGAGACCAGCGTAGG
1033 283_F TTGGTTTCT TGTAACG 2014 OMPU_NC002505_431_
TCACCGATATCATGGCT 266 OMPU_NC002505_544_567_R TCGGTCAGCAAAACGGT
1094 455_F TACCACGG AGCTTGC 2015 OMPU_NC002505_ TAGGCGTGAAAGCAAGC
223 OMPU_NC002505_625_651_R TAGAGAGTAGCCATCTT 908 533_557_F
TACCGTTT CACCGTTGTC 2016 OMPU_NC002505_689_ TAGGTGCTGGTTACGCA 224
OMPU_NC002505_725_751_R TGGGGTAAGACGCGGCT 1291 713_F GATCAAGA
AGCATGTATT 2017 OMPU_NC002505_727_ TACATGCTAGCCGCGTC 181
OMPU_NC002505_811_835_R TAGCAGCTAGCTCGTAA 911 747_F TTAC CCAGTGTA
2018 OMPU_NC002505_931_ TACTACTTCAAGCCGAA 193 OMPU_NC002505_1033_
TTAGAAGTCGTAACGTG 1368 953_F CTTCCG 1053_R GACC 2019
OMPU_NC002505_927_ TACTTACTACTTCAAGC 197 OMPU_NC002505_1033_
TGGTTAGAAGTCGTAAC 1307 953_F CGAACTTCCG 1054_R GTGGACC 2020
TCPA_NC002505_48_ TCACGATAAGAAAACCG 269 TCPA_NC002505_148_170_R
TTCTGCGAATCAATCGC 1391 73_F GTCAAGAGG ACGCTG 2021 TDH_NC004605_265_
TGGCTGACATCCTACAT 574 TDH_NC004605_357_386_R TGTTGAAGCTGTACTTG 1351
289_F GACTGTGA ACCTGATTTTACG 2022 VVHA_NC004460_772_
TCTTATTCCAACTTCAA 412 VVHA_NC004460_862_886_R TACCAAAGCGTGCACGA 887
802_F ACCGAACTATGACG TAGTTGAG 2023 23S_EC_2643_2667_F
TGCCTGTTCTTAGTACG 508 23S_EC_2746_2770_R TGGGTTTCGCGCTTAGA 1297
AGAGGACC TGCTTTCA 2024 16S_EC_713_732_ TAGAACACCGATGGCGA 202
16S_EC_789_811_R TGCGTGGACTACCAGGG 1240 TMOD_F AGGC TATCTA 2025
16S_EC_784_806_F TGGATTAGAGACCCTGG 560 16S_EC_880_897_TMOD_R
TGGCCGTACTCCCCAGG 1278 TAGTCC CG 2026 16S_EC_959_981_F
TGTCGATGCAACGCGAA 634 16S_EC_1052_1074_R TACGAGCTGACGACAGC 896
GAACCT CATGCA 2027 TUFB_EC_956_979_F TGCACACGCCGTTCTTC 489
TUFB_EC_1034_1058_2_R TGCATCACCATTTCCTT 1204 AACAACT GTCCTTCG 2028
RPOC_EC_2146_2174_ TCAGGAGTCGTTCAACT 284 RPOC_EC_2227_2249_R
TGCTAGGCCATCAGGCC 1244 TMOD_F CGATCTACATGAT ACGCAT 2029
RPOB_EC_1841_1866_ TGGTTATCGCTCAGGCG 617 RPOB_EC_1909_1929_TMOD_R
TGCTGGATTCGCCTTTG 1250 F AACTCCAAC CTACG 2030 RPLB_EC_650_679_
TGACCTACAGTAAGAGG 449 RPLB_EC_739_763_R TGCCAAGTGCTGGTTTA 1208
TMOD_F TTCTGTAATGAACC CCCCATGG 2031 RPLB_EC_690_710_F
TCCACACGGTGGTGGTG 309 RPLB_EC_737_760_R TGGGTGCTGGTTTACCC 1295 AAGG
CATGGAG 2032 INFB_EC_1366_1393_ TCTCGTGGTGCACAAGT 397
INFB_EC_1439_1469_R TGTGCTGCTTTCGCATG 1335 F AACGGATATTA
GTTAATTGCTTCAA 2033 VALS_EC_1105_1124_ TCGTGGCGGCGTGGTTA 385
VALS_EC_1195_1219_R TGGGTACGAACTGGATG 1292 TMOD_F TCGA TCGCCGTT
2034 SSPE_BA_113_137_F TGCAAGCAAACGCACAA 482 SSPE_BA_197_222_TMOD_R
TTGCACGTCTGTTTCAG 1402 TCAGAAGC TTGCAAATTC 2035 RPOC_EC_2218_2241_
TCTGGCAGGTATGCGTG 405 RPOC_EC_2313_2338_R TGGCACCGTGGGTTGAG 1273
TMOD_F GTCTGATG ATGAAGTAC 2056 MECI-R_NC003923- TTTACACATATCGTGAG
698 MECI-R_NC003923-41798- TTGTGATATGGAGGTGT 1420
41798-41609_33_60_ CAATGAACTGA 41609_86_113_R AGAAGGTGTTA F 2057
AGR-III_NC003923- TCACCAGTTTGCCACGT 263 AGR-III_NC003923-
ACCTGCATCCCTAAACG 730 2108074- ATCTTCAA 2108074-2109507_56_79_R
TACTTGC 2109507_1_23_F 2058 AGR-III_NC003923- TGAGCTTTTAGTTGACT 457
AGR-III_NC003923- TACTTCAGCTTCGTCCA 906 2108074- TTTTCAACAGC
2108074-2109507_622_ ATAAAAAATCACAAT 2109507_569_596_F 653_R 2059
AGR-III_NC003923- TTTCACACAGCGTGTTT 701 AGR-III_NC003923-
TGTAGGCAAGTGCATAA 1319 2108074-2109507_ ATAGTTCTACCA
2108074-2109507_1070_ GAAATTGATACA 1024_1052_F 1098_R 2060
AGR-I_AJ617706_ TGGTGACTTCATAATGG 610 AGR-I_AJ617706_694_726_R
TCCCCATTTAATAATTC 1021 622_651_F ATGAAGTTGAAGT CACCTACTATCACACT
2061 AGR-I_AJ617706_ TGGCATTTTAAAAAACA 579 AGR-I_AJ617706_626_655_R
TGGTACTTCAACTTCAT 1302 580_611_F TTGGTAACATCGCAC CCATTATGAAGTC 2062
AGR-II_NC002745- TCTTGCAGCAGTTTATT 415 AGR-II_NC002745-2079448-
TTGTTTATTGTTTCCAT 1424 2079448-2080879_ TGATGAACCTAAAGT
2080879_700_731_R ATGCTACACACTTTC 620_651_F 2063 AGR-II_NC002745-
TGTACCCGCTGAATTAA 624 AGR-II_NC002745-2079448- TCGCCATAGCTAAGTTG
1077 2079448-2080879_ CGAATTTATACGAC 2080879_715_745_R
TTTATTGTTTCCAT 649_679_F 2064 AGR-IV_AJ617711_ TGGTATTCTATTTTGCT
606 AGR-IV_AJ617711_1004_ TGCGCTATCAACGATTT 1233 931_961_F
GATAATGACCTCGC 1035_R TGACAATATATGTGA 2065 AGR-IV_AJ617711_
TGGCACTCTTGCCTTTA 562 AGR-IV_AJ617711_309_ TCCCATACCTATGGCGA 1017
250_283_F ATATTAGTAAACTATCA 335_R TAACTGTCAT 2066 BLAZ_NC002952
TCCACTTATCGCAAATG 312 BLAZ_NC002952 TGGCCACTTTTATCAGC 1277 (1913827
. . . GAAAATTAAGCAA (1913827 . . . 1914672)_ AACCTTACAGTC
1914672)_68_68_F 68_68_R 2067 BLAZ_NC002952 TGCACTTATCGCAAATG 494
BLAZ_NC002952 TAGTCTTTTGGAACACC 926 (1913827 . . . GAAAATTAAGCAA
(1913827 . . . 1914672)_ GTCTTTAATTAAAGT 1914672)_68_68_2_F
68_68_2_R 2068 BLAZ_NC002952 TGATACTTCAACGCCTG 467 BLAZ_NC002952
TGGAACACCGTCTTTAA 1263 (1913827 . . . CTGCTTTC (1913827 . . .
1914672)_ TTAAAGTATCTCC 1914672)_68_68_3_F 68_68_3_R 2069
BLAZ_NC002952 TATACTTCAACGCCTGC 232 BLAZ_NC002952 TCTTTTCTTTGCTTAAT
1145 (1913827 . . . TGCTTTC (1913827 . . . 1914672)_ TTTCCATTTGCGAT
1914672)_68_68_4_F 68_68_4_R 2070 BLAZ_NC002952 TGCAATTGCTTTAGTTT
487 BLAZ_NC0002952 TTACTTCCTTACCACTT 1366 (1913827 . . .
TAAGTGCATGTAATTC (1913827 . . . 1914672)_ TTAGTATCTAAAGCATA
1914672)_1_33_F 34_67_R 2071 BLAZ_NC002952 TCCTTGCTTTAGTTTTA 351
BLAZ_NC0002952 TGGGGACTTCCTTACCA 1289 (1913827 . . .
AGTGCATGTAATTCAA (1913827 . . . 1914672)_ CTTTTAGTATCTAA
1914672)_3_34_F 40_68_R 2072 BSA-A_NC003923- TAGCGAATGTGGCTTTA 214
BSA-A_NC003923-1304065- TGCAAGGGAAACCTAGA 1197 1304065- CTTCACAATT
1303589_165_193_R ATTACAAACCCT 1303589_99_125_F 2073
BSA-A_NC003923- ATCAATTTGGTGGCCAA 32 BSA-A_NC003923-1304065-
TGCATAGGGAAGGTAAC 1203 1304065- GAACCTGG 1303589_253_278_R
ACCATAGTT 1303589_194_218_F 2074 BSA-A_NC003923- TTGACTGCGGCACAACA
679 BSA-A_NC003923-1304065- TAACAACGTTACCTTCG 856 1304065- CGGAT
1303589_388_415_R CGATCCACTAA 1303589_328_349_F 2075
BSA-A_NC003923- TGCTATGGTGTTACCTT 519 BSA-A_NC003923-1304065-
TGTTGTGCCGCAGTCAA 1353 1304065- CCCTATGCA 1303589_317_344_R
ATATCTAAATA 1303589_253_278_F 2076 BSA-B_NC003923-
TAGCAACAAATATATCT 209 BSA-B_NC003923-1917149- TGTGAAGAACTTTCAAA
1331 1917149- GAAGCAGCGTACT 1914156_1011_1039_R TCTGTGAATCCA
1914156_953_982_F 2077 BSA-B_NC003923- TGAAAAGTATGGATTTG 426
BSA-B_NC003923-1917149- TCTTCTTGAAAAATTGT 1138 1917149-
AACAACTCGTGAATA 1914156_1109_1136_R TGTCCCGAAAC 1914156_1050_1081_
F 2078 BSA-B_NC003923- TCATTATCATGCGCCAA 300
BSA-B_NC003923-1917149- TGGACTAATAACAATGA 1267 1917149- TGAGTGCAGA
1914156_1323_1353_R GCTCATTGTACTGA 1914156_1260_1286_ F 2079
BSA-B_NC003923- TTTCATCTTATCGAGGA 703 BSA-B_NC003923-1917149-
TGAATATGTAATGCAAA 1148 1917149- CCCGAAATCGA 1914156_2186_2216_R
CCAGTCTTTGTCAT 1914156_2126_2153_ F 2080 ERMA_NC002952-
TCGCTATCTTATCGTTG 372 ERMA_NC002952-55890- TGAGTCTACACTTGGCT 1174
55890- AGAAGGGATT 56621_487_513_R TAGGATGAAA 56621_366_392_F 2081
ERMA_NC002952- TAGCTATCTTATCGTTG 217 ERMA_NC002952-55890-
TGAGCATTTTTATATCC 1167 55890- AGAAGGGATTTGC 56621_438_465_R
ATCTCCACCAT 56621_366_395_F 2082 ERMA_NC002952- TGATCGTTGAGAAGGGA
470 ERMA_NC002952-55890- TCTTGGCTTAGGATGAA 1143 55890- TTTGCGAAAAGA
56621_473_504_R AATATAGTGGTGGTA 56621_374_402_F 2083 ERMA_NC002952-
TGCAAAATCTGCAACGA 480 ERMA_NC002952-55890- TCAATACAGAGTCTACA 964
55890- GCTTTGG 56621_491_520_R CTTGGCTTAGGAT 56621_404_427_F
2084 ERMA_NC002952- TCATCCTAAGCCAAGTG 297 ERMA_NC002952-55890-
TGGACGATATTCACGGT 1266 55890- TAGACTCTGTA 56621_586_615_R
TTACCCACTTATA 56621_489_516_F 2085 ERMA_NC002952- TATAAGTGGGTAAACCG
231 ERMA_NC002952-55890- TTGACATTTGCATGCTT 1397 55890- TGAATATCGTGT
56621_640_665_R CAAAGCCTG 56621_586_614_F 2086 ERMC_NC005908-
TCTGAACATGATAATAT 399 ERMC_NC005908-2004- TCCGTAGTTTTGCATAA 1041
2004-2738_85_116_F CTTTGAAATCGGCTC 2738_173_206_R TTTATGGTCTATTTCAA
2087 ERMC_NC005908- TCATGATAATATCTTTG 298 ERMC_NC005908-2004-
TTTATGGTCTATTTCAA 1429 2004-2738_90_120_F AAATCGGCTCAGGA
2738_160_189_R TGGCAGTTACGAA 2088 ERMC_NC005908- TCAGGAAAAGGGCATTT
283 ERMC_NC005908-2004- TATGGTCTATTTCAATG 936 2004-2738_115_139_
TACCCTTG 2738_161_187_R GCAGTTACGA F 2089 ERMC_NC005908-
TAATCGTGGAATACGGG 168 ERMC_NC005908-2004- TCAACTTCTGCCATTAA 956
2004-2738_374_397_ TTTGCTA 2738_425_452_R AAGTAATGCCA F 2090
ERMC_NC005908- TCTTTGAAATCGGCTCA 421 ERMC_NC005908-2004-
TGATGGTCTATTTCAAT 1185 2004-2738_101_125_ GGAAAAGG 2738_159_188_R
GGCAGTTACGAAA F 2091 ERMB_Y13600-625- TGTTGGGAGTATTCCTT 644
ERMB_Y13600-625- TCAACAATCAGATAGAT 953 1362_291_321_F
ACCATTTAAGCACA 1362_352_380_R GTCAGACGCATG 2092 ERMB_Y13600-625-
TGGAAAGCCATGCGTCT 536 ERMB_Y13600-625- TGCAAGAGCAACCCTAG 1196
1362_344_367_F GACATCT 1362_415_437_R TGTTCG 2093 ERMB_Y13600-625-
TGGATATTCACCGAACA 556 ERMB_Y13600-625- TAGGATGAAAGCATTCC 919
1362_404_429_F CTAGGGTTG 1362_471_493_R GCTGGC 2094
ERMB_Y13600-625- TAAGCTGCCAGCGGAAT 161 ERMB_Y13600-625-
TCATCTGTGGTATGGCG 989 1362_465_487_F GCTTTC 1362_521_545_R GGTAAGTT
2095 PVLUK_NC003923- TGAGCTGCATCAACTGT 456 PVLUK_NC003923-1529595-
TGGAAAACTCATGAAAT 1261 1529595- ATTGGATAG 1531285_775_804_R
TAAAGTGAAAGGA 1531285_688_713_F 2096 PVLUK_NC003923-
TGGAACAAAATAGTCTC 539 PVLUK_NC003923-1529595- TCATTAGGTAAAATGTC 993
1529595- TCGGATTTTGACT 1531285_1095_1125_R TGGACATGATCCAA
1531285_1039_1068_ F 2097 PVLUK_NC003923- TGAGTAACATCCATATT 461
PVLUK_NC003923-1529595- TCTCATGAAAAAGGCTC 1124 1529595-
TCTGCCATACGT 1531285_950_978_R AGGAGATACAAG 1531285_908_936_F 2098
PVLUK_NC003923- TCGGAATCTGATGTTGC 373 PVLUK_NC003923-1529595-
TCACACCTGTAAGTGAG 968 1529595- AGTTGTT 1531285_654_682_R
AAAAAGGTTGAT 1531285_610_633_F 2099 SA442_NC003923-
TGTCGGTACACGATATT 635 SA442_NC003923-2538576- TTTCCGATGCAACGTAA
1433 2538576- CTTCACGA 2538831_98_124_R TGAGATTTCA 2538831_11_35_F
2100 SA442_NC003923- TGAAATCTCATTACGTT 427 SA442_NC003923-2538576-
TCGTATGACCAGCTTCG 1098 2538576- GCATCGGAAA 2538831_163_188_R
GTACTACTA 2538831_98_124_F 2101 SA442_NC003923- TCTCATTACGTTGCATC
395 SA442_NC003923-2538576- TTTATGACCAGCTTCGG 1428 2538576- GGAAACA
2538831_161_187_R TACTACTAAA 2538831_103_126_F 2102 SA442_NC003923-
TAGTACCGAAGCTGGTC 226 SA442_NC003923-2538576- TGATAATGAAGGGAAAC
1179 2538576- ATACGA 2538831_231_257_R CTTTTTCACG 2538831_166_188_F
2103 SEA_NC003923- TGCAGGGAACAGCTTTA 495 SEA_NC003923-2052219-
TCGATCGTGACTCTCTT 1070 2052219- GGCA 2051456_173_200_R TATTTTCAGTT
2051456_115_135_F 2104 SEA_NC003923- TAACTCTGATGTTTTTG 156
SEA_NC003923-2052219- TGTAATTAACCGAAGGT 1315 2052219- ATGGGAAGGT
2051456_621_651_R TCTGTAGAAGTATG 2051456_572_598_F 2105
SEA_NC003923- TGTATGGTGGTGTAACG 629 SEA_NC003923-2052219-
TAACCGTTTCCAAAGGT 861 2052219- TTACATGATAATAATC 2051456_464_492_R
ACTGTATTTTGT 2051456_382_414_F 2106 SEA_NC003923- TTGTATGTATGGTGGTG
695 SEA_NC003923-2052219- TAACCGTTTCCAAAGGT 862 2052219-
TAACGTTACATGA 2051456_459_492_R ACTGTATTTTGTTTACC 2051456_377_406_F
2107 SEB_NC002758- TTTCACATGTAATTTTG 702 SEB_NC002758-2135540-
TCATCTGGTTTAGGATC 988 2135540- ATATTCGCACTGA 2135140_273_298_R
TGGTTGACT 2135140_208_237_F 2108 SEB_NC002758- TATTTCACATGTAATTT
244 SEB_NC002758-2135540- TGCAACTCATCTGGTTT 1194 2135540-
TGATATTCGCACT 2135140_281_304_R AGGATCT 2135140_206_235_F 2109
SEB_NC002758- TAACAACTCGCCTTATG 151 SEB_NC002758-2135540-
TGTGCAGGCATCATGTC 1334 2135540- AAACGGGATATA 2135140_402_402_R
ATACCAA 2135140_402_402_F 2110 SEB_NC002758- TTGTATGTATGGTGGTG 696
SEB_NC002758-2135540- TTACCATCTTCAAATAC 1361 2135540- TAACTGAGCA
2135140_402_402_2_R CCGAACAGTAA 2135140_402_402_2_F 2111
SEC_NC003923- TTAACATGAAGGAAACC 648 SEC_NC003923-651678-
TGAGTTTGCACTTCAAA 1177 851678- ACTTTGATAATGG 852768_620_647_R
AGAAATTGTGT 852768_546_575_F 2112 SEC_NC003923- TGGAATAACAAAACATG
546 SEC_NC003923-851678- TCAGTTTGCACTTCAAA 985 851678-
AAGGAAACCACTT 852768_619_647_R AGAAATTGTGTT 852768_537_566_F 2113
SEC_NC003923- TGAGTTTAACAGTTCAC 466 SEC_NC003923-851678-
TCGCCTGGTGCAGGCAT 1078 851678- CATATGAAACAGG 852768_794_815_R CATAT
852768_720_749_F 2114 SEC_NC003923- TGGTATGATATGATGCC 604
SEC_NC003923-851678- TCTTCACACTTTTAGAA 1133 851678- TGCACCA
852768_853_886_R TCAACCGTTTTATTGTC 852768_787_810_F 2115
SED_M28521_657_ TGGTGGTGAAATAGATA 615 SED_M28521_741_770_R
TGTACACCATTTATCCA 1318 682_F GGACTGCTT CAAATTGATTGGT 2116
SED_M28521_690_ TGGAGGTGTCACTCCAC 554 SED_M28521_739_770_R
TGGGCACCATTTATCCA 1288 711_F ACGAA CAAATTGATTGGTAT 2117
SED_M28521_833_ TTGCACAAGCAAGGCGC 683 SED_M28521_888_911_R
TCGCGCTGTATTTTTCC 1079 854_F TATTT TCCGAGA 2118 SED_M28521_962_
TGGATGTTAAGGGTGAT 559 SED_M28521_1022_1048_R TGTCAATATGAAGGTGC 1320
987_F TTTCCCGAA TCTGTGGATA 2119 SEA-SEE_NC002952- TTTACACTACTTTTATT
699 SEA-SEE_NC002952- TCATTTATTTCTTCGCT 994 2131289- CATTGCCCTAACG
2131289-2130703_71_98_R TTTCTCGCTAC 2130703_16_45_F 2120
SEA-SEE_NC002952- TGATCATCCGTGGTATA 469 SEA-SEE_NC002952-
TAAGCACCATATAAGTC 870 2131289- ACGATTTATTAGT 2131289-2130703_314_
TACTTTTTTCCCTT 2130703_249_278_F 344_R 2121 SEE_NC002952-
TGACATGATAATAACCG 445 SEE_NC002952-2131289- TCTATAGGTACTGTAGT 1120
2131289- ATTGACCGAAGA 2130703_465_494_R TTGTTTTCCGTCT
2130703_409_437_F 2122 SEE_NC002952- TGTTCAAGAGCTAGATC 640
SEE_NC002952-2131289- TTTGCACCTTACCGCCA 1436 2131289- TTCAGGCAA
2130703_586_586_R AAGCT 2130703_525_550_F 2123 SEE_NC002952-
TGTTCAAGAGCTAGATC 639 SEE_NC002952-2131289- TACCTTACCGCCAAAGC 892
2131289- TTCAGGCA 2130703_586_586_2_R TGTCT 2130703_525_549_F 2124
SEE_NC002952- TCTGGAGGCACACCAAA 403 SEE_NC002952-2131289-
TCCGTCTATCCACAAGT 1043 2131289- TAAAACA 2130703_444_471_R
TAATTGGTACT 2130703_361_384_F 2125 SEG_NC002758- TGCTCAACCCGATCCTA
520 SEG_NC002758-1955100- TAACTCCTCTTCCTTCA 863 1955100- AATTAGACGA
1954171_321_346_R ACAGGTGGA 1954171_225_251_F 2126 SEG_NC002758-
TGGACAATAGACAATCA 548 SEG_NC002758-1955100- TGCTTTGTAATCTAGTT 1260
1955100- CTTGGATTTACA 1954171_671_702_R CCTGAATAGTAACCA
1954171_623_651_F 2127 SEG_NC002758- TGGAGGTTGTTGTATGT 555
SEG_NC002758-1955100- TGTCTATTGTCGATTGT 1329 1955100- ATGGTGGT
1954171_607_635_R TACCTGTACAGT 1954171_540_564_F 2128 SEG_NC002758-
TACAAAGCAAGACACTG 173 SEG_NC002758-1955100- TGATTCAAATGCAGAAC 1187
1955100- GCTCACTA 1954171_735_762_R CATCAAACTCG 1954171_694_718_F
2129 SEH_NC002953- TTGCAACTGCTGATTTA 682 SEH_NC002953-60024-
TAGTGTTGTACCTCCAT 927 60024- GCTCAGA 60977_547_576_R ATAGACATTCAGA
60977_449_472_F 2130 SEH_NC002953- TAGAAATCAAGGTGATA 201
SEH_NC002953-60024- TTCTGAGCTAAATCAGC 1390 60024- GTGGCAATGA
60977_450_473_R AGTTGCA 60977_408_434_F 2131 SEH_NC002953-
TCTGAATGTCTATATGG 400 SEH_NC002953-60024- TACCATCTACCCAAACA 888
60024- AGGTACAACACTA 60977_608_634_R TTAGCACCAA 60977_547_576_F
2132 SEH_NC002953- TTCTGAATGTCTATATG 677 SEH_NC002953-60024-
TAGCACCAATCACCCTT 909 60024- GAGGTACAACACT 60977_594_616_R TCCTGT
60977_546_575_F 2133 SEI_NC002758- TCAACTCGAATTTTCAA 253
SEI_NC002758-1957830- TCACAAGGACCATTATA 966 1957830- CAGGTACCA
1956949_419_446_R ATCAATGCCAA 1956949_324_349_F 2134 SEI_NC002758-
TTCAACAGGTACCAATG 666 SEI_NC002758-1957830- TGTACAAGGACCATTAT 1316
1957830- ATTTGATCTCA 1956949_420_447_R AATCAATGCCA
1956949_336_363_F 2135 SEI_NC002758- TGATCTCAGAATCTAAT 471
SEI_NC002758-1957830- TCTGGCCCCTCCATACA 1129 1957830- AATTGGGACGAA
1956949_449_474_R TGTATTTAG 1956949_356_384_F
2136 SEI_NC002758- TCTCAAGGTGATATTGG 394 SEI_NC002758-1957830-
TGGGTAGGTTTTTATCT 1293 1957830- TGTAGGTAACTTAA 1956949_290_316_R
GTGACGCCTT 1956949_223_253_F 2137 SEJ_AF053140_1307_
TGTGGAGTAACACTGCA 637 SEJ_AF053140_1381_1404_R TCTAGCGGAACAACAGT
1118 1332_F TGAAAACAA TCTGATG 2138 SEJ_AF053140_1378_
TAGCATCAGAACTGTTG 211 SEJ_AF053140_1429_1458_R TCCTGAAGATCTAGTTC
1049 1403_F TTCCGCTAG TTGAATGGTTACT 2139 SEJ_AF053140_1431_
TAACCATTCAAGAACTA 153 SEJ_AF053140_1500_1531_R TAGTCCTTTCTGAATTT
925 1459_F GATCTTCAGGCA TACCATCAAAGGTAC 2140 SEJ_AF053140_1434_
TCATTCAAGAACTAGAT 301 SEJ_AF053140_1521_1549_R TCAGGTATGAAACACGA
984 1461_F CTTCAGGCAAG TTAGTCCTTTCT 2141 TSST_NC002758-
TGGTTTAGATAATTCCT 619 TSST_NC002758-2137564- TGTAAAAGCAGGGCTAT 1312
2137564- TAGGATCTATGCGT 2138293_278_305_R AATAAGGACTC
2138293_206_236_F 2142 TSST_NC002758- TGCGTATAAAAAACACA 514
TSST_NC002758-2137564- TGCCCTTTTGTAAAAGC 1221 2137564- GATGGCAGCA
2138293_289_313_R AGGGCTAT 2138293_232_258_F 2143 TSST_NC002758-
TCCAAATAAGTGGCGTT 304 TSST_NC002758-2137564- TACTTTAAGGGGCTATC 907
2137564- ACAAATACTGAA 2138293_448_478_R TTTACCATGAACCT
2138293_382_410_F 2144 TSST_NC002758- TCTTTTACAAAAGGGGA 423
TSST_NC002758-2137564- TAAGTTCCTTCGCTAGT 874 2137564- AAAAGTTGACTT
2138293_347_373_R ATGTTGGCTT 2138293_297_325_F 2145 ARCC_NC003923-
TCGCCGGCAATGCCATT 368 ARCC_NC003923-2725050- TGAGTTAAAATGCGATT 1175
2725050- GGATA 2724595_97_128_R GATTTCAGTTTCCAA 2724595_37_58_F
2146 ARCC_NC003923- TGAATAGTGATAGAACT 437 ARCC_NC003923-2725050-
TCTTCTTCTTTCGTATA 1137 2725050- GTAGGCACAATCGT 2724595_214_245_R
AAAAGGACCAATTGG 2724595_131_161_F 2147 ARCC_NC003923-
TTGGTCCTTTTTATACG 691 ARCC_NC003923-2725050- TGGTGTTCTAGTATAGA 1306
2725050- AAAGAAGAAGTTGAA 2724595_322_353_R TTGAGGTAGTGGTGA
2724595_218_249_F 2148 AROE_NC003923- TTGCGAATAGAACGATG 686
AROE_NC003923-1674726- TCGAATTCAGCTAAATA 1064 1674726- GCTCGT
1674277_435_464_R CTTTTCAGCATCT 1674277_371_393_F 2149
AROE_NC003923- TGGGGCTTTAAATATTC 590 AROE_NC003923-1674726-
TACCTGCATTAATCGCT 891 1674726- CAATTGAAGATTTTCA 1674277_155_181_R
TGTTCATCAA 1674277_30_62_F 2150 AROE_NC003923- TGATGGCAAGTGGATAG
474 AR0E_NC003923-1674726- TAAGCAATACCTTTACT 869 1674726-
GGTATAATACAG 1674277_308_335_R TGCACCACCTG 1674277_204_232_F 2151
GLPF_NC003923- TGCACCGGCTATTAAGA 491 GLPF_NC003923-1296927-
TGCAACAATTAATGCTC 1193 1296927- ATTACTTTGCCAACT 1297391_382_414_R
CGACAATTAAAGGATT 1297391_270_301_F 2152 GLPF_NC003923-
TGGATGGGGATTAGCGG 558 GLPF_NC003923-1296927- TAAAGACACCGCTGGGT 850
1296927- TTACAATG 1297391_81_108_R TTAAATGTGCA 1297391_27_51_F 2153
GLPF_NC003923- TAGCTGGCGCGAAATTA 218 GLPF_NC003923-1296927-
TCACCGATAAATAAAAT 972 1296927- GGTGT 1297391_323_359_R
ACCTAAAGTTAATGCCA 1297391_239_260_F TTG 2154 GMK_NC003923-
TACTTTTTTAAAACTAG 200 GMK_NC003923-1190906- TGATATTGAACTGGTGT 1180
1190906- GGATGCGTTTGAAGC 1191334_166_197_R ACCATAATAGTTGCC
1191334_91_122_F 2155 GMK_NC003923- TGAAGTAGAAGGTGCAA 435
GMK_NC003923-1190906- TCGCTCTCTCAAGTGAT 1082 1190906- AGCAAGTTAGA
1191334_305_333_R CTAAACTTGGAG 1191334_240_267_F 2156 GMK_NC003923-
TCACCTCCAAGTTTAGA 268 GMK_NC003923-1190906- TGGGACGTAATCGTATA 1284
1190906- TCACTTGAGAGA 1191334_403_432_R AATTCATCATTTC
1191334_301_329_F 2157 PTA_NC003923- TCTTGTTTATGCTGGTA 418
PTA_NC003923-628885- TGGTACACCTGGTTTCG 1301 628885- AAGCAGATGG
629355_314_345_R TTTTGATGATTTGTA 629355_237_263_F 2158
PTA_NC003923- TGAATTAGTTCAATCAT 439 PTA_NC003923-628885-
TGCATTGTACCGAAGTA 1207 628885- TTGTTGAACGACGT 629355_211_239_R
GTTCACATTGTT 629355_141_171_F 2159 PTA_NC003923- TCCAAACCAGGTGTATC
303 PTA_NC003923-628885- TGTTCTGGATTGATTGC 1349 628885-
AAGAACATCAGG 629355_393_422_R ACAATCACCAAAG 629355_328_356_F 2160
TPI_NC003923- TGCAAGTTAAGAAAGCT 486 TPI_NC003923-830671-
TGAGATGTTGATGATTT 1165 830671- GTTGCAGGTTTAT 831072_209_239_R
ACCAGTTCCGATTG 831072_131_160_F 2161 TPI_NC003923-
TCCCACGAAACAGATGA 318 TPI_NC003923-830671- TGGTACAACATCGTTAG 1300
830671- AGAAATTAACAAAAAAG 831072_97_129_R CTTTACCACTTTCACG
831072_1_34_F 2162 TPI_NC003923- TCAAACTGGGCAATCGG 246
TPI_NC003923-830671- TGGCAGCAATAGTTTGA 1275 830671- AACTGGTAAATC
831072_253_286_R CGTACAAATGCACACAT 831072_199_227_F 2163
YQI_NC003923- TGAATTGCTGCTATGAA 440 YQI_NC003923-378916-
TCGCCAGCTAGCACGAT 1076 378916- AGGTGGCTT 379431_259_284_R GTCATTTTC
379431_142_167_F 2164 YQI_NC003923- TACAACATATTATTAAA 175
YQI_NC003923-378916- TTCGTGCTGGATTTTGT 1388 378916-
GAGACGGGTTTGAATCC 379431_120_145_R CCTTGTCCT 379431_44_77_F 2165
YQI_NC003923- TCCAGCACGAATTGCTG 314 YQI_NC003923-378916-
TCCAACCCAGAACCACA 997 378916- CTATGAAAG 379431_193_221_R
TACTTTATTCAC 379431_135_160_F 2166 YQI_NC003923- TAGCTGGCGGTATGGAG
219 YQI_NC003923-378916- TCCATCTGTTAAACCAT 1013 378916- AATATGTCT
379431_364_396_R CATATACCATGCTATC 379431_275_300_F 2167 BLAZ_
TCCACTTATCGCAAATG 312 BLAZ_ TGGCCACTTTTATCAGC 1277 (1913827 . . .
GAAAATTAAGCAA (1913827 . . . 1914672)_ AACCTTACAGTC
1914672)_546_575_F 655_683_R 2168 BLAZ_ TGCACTTATCGCAAATG 494 BLAZ_
TAGTCTTTTGGAACACC 926 (1913827 . . . GAAAATTAAGCAA (1913827 . . .
1914672)_ GTCTTTAATTAAAGT 1914672)_546_575.sub.-- 628_659_R 2_F
2169 BLAZ_ TGATACTTCAACGCCTG 467 BLAZ_ TGGAACACCGTCTTTAA 1263
(1913827 . . . CTGCTTTC (1913827 . . . 1914672)_ TTAAAGTATCTCC
1914672)_507_531_F 622_651_R 2170 BLAZ_ TATACTTCAACGCCTGC 232 BLAZ_
TCTTTTCTTTGCTTAAT 1145 (1913827 . . . TGCTTTC (1913827 . . .
1914672)_ TTTCCATTTGCGAT 1914672)_508_531_F 553_583_R 2171 BLAZ_
TGCAATTGCTTTAGTTT 487 BLAZ_ TTACTTCCTTACCACTT 1366 (1913827 . . .
TAAGTGCATGTAATTC (1913827 . . . 1914672)_ TTAGTATCTAAAGCATA
1914672)_24_56_F 121_154_R 2172 BLAZ_ TCCTTGCTTTAGTTTTA 351 BLAZ_
TGGGGACTTCCTTACCA 1289 (1913827 . . . AGTGCATGTAATTCAA (1913827 . .
. 1914672)_ CTTTTAGTATCTAA 1914672)_26_58_F 127_157_R 2173
BLAZ_NC002952- TCCACTTATCGCAAATG 312 BLAZ_NC002952-1913827-
TGGCCACTTTTATCAGC 1277 1913827- GAAAATTAAGCAA 1914672_655_683_R
AACCTTACAGTC 1914672_546_575_F 2174 BLAZ_NC002952-
TGCACTTATCGCAAATG 494 BLAZ_NC002952-1913827- TAGTCTTTTGGAACACC 926
1913827- GAAAATTAAGCAA 1914672_628_659_R GTCTTTAATTAAAGT
1914672_546_575_ 2_F 2175 BLAZ_NC002952- TGATACTTCAACGCCTG 467
BLAZ_NC002952-1913827- TGGAACACCGTCTTTAA 1263 1913827- CTGCTTTC
1914672_622_651_R TTAAAGTATCTCC 1914672_507_531_F 2176
BLAZ_NC002952- TATACTTCAACGCCTGC 232 BLAZ_NC002952-1913827-
TCTTTTCTTTGCTTAAT 1145 1913827- TGCTTTC 1914672_553_583_R
TTTCCATTTGCGAT 1914672_508_531_F 2177 BLAZ_NC002952-
TGCAATTGCTTTAGTTT 487 BLAZ_NC002952-1913827- TTACTTCCTTACCACTT 1366
1913827- TAAGTGCATGTAATTC 1914672_121_154_R TTAGTATCTAAAGCATA
1914672_24_56_F 2178 BLAZ_NC002952- TCCTTGCTTTAGTTTTA 351
BLAZ_NC002952-1913827- TGGGGACTTCCTTACCA 1289 1913827-
AGTGCATGTAATTCAA 1914672_127_157_R CTTTTAGTATCTAA 1914672_26_58_F
2247 TUFB_NC002758- TGTTGAACGTGGTCAAA 643 TUFB_NC002758-615038-
TGTCACCAGCTTCAGCG 1321 615038- TCAAAGTTGGTG 616222_793_820_R
TAGTCTAATAA 616222_693_721_F 2248 TUFB_NC002758- TCGTGTTGAACGTGGTC
386 TUFB_NC002758-615038- TGTCACCAGCTTCAGCG 1321 615038- AAATCAAAGT
616222_793_820_R TAGTCTAATAA 616222_690_716_F 2249 TUFB_NC002758-
TGAACGTGGTCAAATCA 430 TUFB_NC002758-615038- TGTCACCAGCTTCAGCG 1321
615038- AAGTTGGTGAAGA 616222_793_820_R TAGTCTAATAA 616222_696_725_F
2250 TUFB_NC002758- TCCCAGGTGACGATGTA 320 TUFB_NC002758-615038-
TGGTTTGTCAGAATCAC 1311 615038- CCTGTAATC 616222_601_630_R
GTTCTGGAGTTGG 616222_488_513_F 2251 TUFB_NC002758-
TGAAGGTGGACGTCACA 433 TUFB_NC002758-615038- TAGGCATAACCATTTCA 922
615038- CTCCATTCTTC 616222_1030_1060_R GTACCTTCTGGTAA
616222_945_972_F 2252 TUFB_NC002758- TCCAATGCCACAAACTC 307
TUFB_NC002758-615038- TTCCATTTCAACTAATT 1382 615038- GTGAACA
616222_424_459_R CTAATAATTCTTCATCG 616222_333_356_F TC 2253
NUC_NC002758- TCCTGAAGCAAGTGCAT 342 NUC_NC002758-894288-
TACGCTAAGCCACGTCC 899 894288- TTACGA 894974_483_509_R ATATTTATCA
894974_402_424_F 2254 NUC_NC002758- TCCTTATAGGGATGGCT 349
NUC_NC002758-894288- TGTTTGTGATGCATTTG 1354 894288- ATCAGTAATGTT
894974_165_189_R CTGAGCTA 894974_53_81_F 2255 NUC_NC002758-
TCAGCAAATGCATCACA 273 NUC_NC002758-894288- TAGTTGAAGTTGCACTA 928
894288- AACAGATAA 894974_222_250_R TATACTGTTGGA
894974_169_194_F 2256 NUC_NC002758- TACAAAGGTCAACCAAT 174
NUC_NC002758-894288- TAAATGCACTTGCTTCA 853 894288- GACATTCAGACTA
894974_396_421_R GGGCCATAT 894974_316_345_F 2270 RPOB_EC_3798_3821_
TGGCCAGCGCTTCGGTG 566 RPOB_EC_3868_3895_R TCACGTCGTCCGACTTC 979 1_F
AAATGGA ACGGTCAGCAT 2271 RPOB_EC_3789_3812_ TCAGTTCGGCGGTCAGC 294
RPOB_EC_3860_3890_R TCGTCGGACTTAACGGT 1107 F GCTTCGG CAGCATTTCCTGCA
2272 RPOB_EC_3789_3812_ TCAGTTCGGCGGTCAGC 294 RPOB_EC_3860_3890_2_R
TCGTCCGACTTAACGGT 1102 F GCTTCGG CAGCATTTCCTGCA 2273
RPOB_EC_3789_3812_ TCAGTTCGGCGGTCAGC 294 RPOB_EC_3862_3890_R
TCGTCGGACTTAACGGT 1106 F GCTTCGG CAGCATTTCCTG 2274
RPOB_EC_3789_3812_ TCAGTTCGGCGGTCAGC 294 RPOB_EC_3862_3890_2_R
TCGTCCGACTTAACGGT 1101 F GCTTCGG CAGCATTTCCTG 2275
RPOB_EC_3793_3812_ TTCGGCGGTCAGCGCTT 674 RPOB_EC_3865_3890_R
TCGTCGGACTTAACGGT 1105 F CGG CAGCATTTC 2276 RPOB_EC_3793_3812_
TTCGGCGGTCAGCGCTT 674 RPOB_EC_3865_3890_2_R TCGTCCGACTTAACGGT 1100
F CGG CAGCATTTC 2309 MUPR_X75439_1658_ TCCTTTGATATATTATG 352
MUPR_X75439_1744_1773_R TCCCTTCCTTAATATGA 1030 1689_F
CGATGGAAGGTTGGT GAAGGAAACCACT 2310 MUPR_X75439_1330_
TTCCTCCTTTTGAAAGC 669 MUPR_X75439_1413_1441_R TGAGCTGGTGCTATATG
1171 1353_F GACGGTT AACAATACCAGT 2312 MUPR_X75439_1314_
TTTCCTCCTTTTGAAAG 704 MUPR_X75439_1381_1409_R TATATGAACAATACCAG 931
1338_F CGACGGTT TTCCTTCTGAGT 2313 MUPR_X75439_2486_
TAATTGGGCTCTTTCTC 172 MUPR_X75439_2548_2574_R TTAATCTGGCTGCGGAA
1360 2516_F GCTTAAACACCTTA GTGAAATCGT 2314 MUPR_X75439_2547_
TACGATTTCACTTCCGC 188 MUPR_X75439_2605_2630_R TCGTCCTCTCGAATCTC
1103 2572_F AGCCAGATT CGATATACC 2315 MUPR_X75439_2666_
TGCGTACAATACGCTTT 513 MUPR_X75439_2711_2740_R TCAGATATAAATGGAAC 981
2696_F ATGAAATTTTAACA AAATGGAGCCACT 2316 MUPR_X75439_2813_
TAATCAAGCATTGGAAG 165 MUPR_X75439_2867_2890_R TCTGCATTTTTGCGAGC
1127 2843_F ATGAAATGCATACC CTGTCTA 2317 MUPR_X75439_884_
TGACATGGACTCCCCCT 447 MUPR_X75439_977_1007_R TGTACAATAAGGAGTCA 1317
914_F ATATAACTCTTGAG CCTTATGTCCCTTA 2318 CTXA_NC002505-
TGGTCTTATGCCAAGAG 608 CTXA_NC002505-1568114- TCGTGCCTAACAAATCC 1109
1568114- GACAGAGTGAGT 1567341_194_221_R CGTCTGAGTTC
1567341_114_142_F 2319 CTXA_NC002505- TCTTATGCCAAGAGGAC 411
CTXA_NC002505-1568114- TCGTGCCTAACAAATCC 1109 1568114- AGAGTGAGTACT
1567341_194_221_R CGTCTGAGTTC 1567341_117_145_F 2320 CTXA_NC002505-
TGGTCTTATGCCAAGAG 608 CTXA_NC002505-1568114- TAACAAATCCCGTCTGA 855
1568114- GACAGAGTGAGT 1567341_186_214_R GTTCCTCTTGCA
1567341_114_142_F 2321 CTXA_NC002505- TCTTATGCCAAGAGGAC 411
CTXA_NC002505-1568114- TAACAAATCCCGTCTGA 855 1568114- AGAGTGAGTACT
1567341_186_214_R GTTCCTCTTGCA 1567341_117_145_F 2322
CTXA_NC002505- AGGACAGAGTGAGTACT 27 CTXA_NC002505-1568114-
TCCCGTCTGAGTTCCTC 1027 1568114- TTGACCGAGGT 1567341_180_207_R
TTGCATGATCA 1567341_129_156_F 2323 CTXA_NC002505- TGCCAAGAGGACAGAGT
500 CTXA_NC002505-1568114- TAACAAATCCCGTCTGA 855 1568114-
GAGTACTTTGA 1567341_186_214_R GTTCCTCTTGCA 1567341_122_149_F 2324
INV_U22457-74- TGCTTATTTACCTGCAC 530 INV_U22457-74-
TGACCCAAAGCTGAAAG 1154 3772_831_858_F TCCCACAACTG 3772_942_966_R
CTTTACTG 2325 INV_U22457-74- TGAATGCTTATTTACCT 438 INV_U22457-74-
TAACTGACCCAAAGCTG 864 3772_827_857_F GCACTCCCACAACT 3772_942_970_R
AAAGCTTTACTG 2326 INV_U22457-74- TGCTGGTAACAGAGCCT 526
INV_U22457-74- TGGGTTGCGTTGCAGAT 1296 3772_1555_1581_F TATAGGCGCA
3772_1619_1647_R TATCTTTACCAA 2327 INV_U22457-74- TGGTAACAGAGCCTTAT
598 INV_U22457-74- TCATAAGGGTTGCGTTG 987 3772_1558_1585_F
AGGCGCATATG 3772_1622_1652_R CAGATTATCTTTAC 2328 ASD_NC006570-
TGAGGGTTTTATGCTTA 459 ASD_NC006570-439714- TGATTCGATCATACGAG 1188
439714- AAGTTGGTTTTATTGGT 438608_54_84_R ACATTAAAACTGAG
438608_3_37_F T 2329 ASD_NC006570- TAAAGTTGGTTTTATTG 149
ASD_NC006570-439714- TCAAAATCTTTTGATTC 948 439714- GTTGGCGCGGA
438608_66_95_R GATCATACGAGAC 438608_18_45_F 2330 ASD_NC006570-
TTAAAGTTGGTTTTATT 647 ASD_NC006570-439714- TCCCAATCTTTTGATTC 1016
439714- GGTTGGCGCGGA 438608_67_95_R GATCATACGAGA 438608_17_45_F
2331 ASD_NC006570- TTTTATGCTTAAAGTTG 709 ASD_NC006570-439714-
TCTGCCTGAGATGTCGA 1128 439714- GTTTTATTGGTTGGC 438608_107_134_R
AAAAAACGTTG 438608_9_40_F 2332 GALE_AF513299_171_ TCAGCTAGACCTTTTAG
280 GALE_AF513299_241_271_R TCTCACCTACAGCTTTA 1122 200_F
GTAAAGCTAAGCT AAGCCAGCAAAATG 2333 GALE_AF513299_168_
TTATCAGCTAGACCTTT 658 GALE_AF513299_245_271_R TCTCACCTACAGCTTTA
1121 199_F TAGGTAAAGCTAAGC AAGCCAGCAA 2334 GALE_AF513299_168_
TTATCAGCTAGACCTTT 658 GALE_AF513299_233_264_R TACAGCTTTAAAGCCAG 883
199_F TAGGTAAAGCTAAGC CAAAATGAATTACAG 2335 GALE_AF513299_169_
TCCCAGCTAGACCTTTT 319 GALE_AF513299_252_279_R TTCAACACTCTCACCTA
1374 198_F AGGTAAAGCTAAG CAGCTTTAAAG 2336 PLA_AF053945_7371_
TTGAGAAGACATCCGGC 680 PLA_AF053945_7434_7468_R TACGTATGTAAATTCC 900
7403_F TCACGTTATTATGGTA GCAAAGACTTTGGCAT TAG 2337
PLA_AF053945_7377_ TGACATCCGGCTCACGT 443 PLA_AF053945_7428_7455_R
TCCGCAAAGACTTTGGC 1035 7403_F TATTATGGTA ATTAGGTGTGA 2338
PLA_AF053945_7377_ TGACATCCGGCTCACGT 444 PLA_AF053945_7430_7460_R
TAAATTCCGCAAAGACT 854 7404_F TATTATGGTAC TTGGCATTAGGTGT 2339
CAF_AF053947_ TCCGTTATCGCCATTGC 329 CAF_AF053947_33498_
TAAGAGTGATGCGGGCT 866 33412_33441_F ATTATTTGGAACT 33523_R GGTTCAACA
2340 CAF_AF053947_ TGCATTATTTGGAACTA 499 CAF_AF053947_33483_
TGGTTCAACAAGAGTTG 1308 33426_33458_F TTGCAACTGCTAATGC 33507_R
CCGTTGCA 2341 CAF_AF053947_ TCAGTTCCGTTATCGCC 291
CAF_AF053947_33483_ TTCAACAAGAGTTGCCG 1373 33407_33429_F ATTGCA
33504_R TTGCA 2342 CAF_AF053947_ TCAGTTCCGTTATCGCC 293
CAF_AF053947_33494_ TGATGCGGGCTGGTTCA 1184 33407_33431_F ATTGCATT
33517_R ACAAGAG 2344 GAPA_NC_002505_1_ TCAATGAACGATCAACA 260
GAPA_NC_002505_29_58_R_1 TCCTTTATGCAACTTGG 1060 28_F_1 AGTGATTGATG
TATCAACAGGAAT 2472 OMPA_NC000117_68_ TGCCTGTAGGGAATCCT 507
OMPA_NC000117_145_167_R TCACACCAAGTAGTGCA 967 89_F GCTGA AGGATC
2473 OMPA_NC000117_798_ TGATTACCATGAGTGGC 475
OMPA_NC000117_865_893_R TCAAAACTTGCTCTAGA 947 821_F AAGCAAG
CCATTTAACTCC 2474 OMPA_NC000117_645_ TGCTCAATCTAAACCTA 521
OMPA_NC000117_757_777_R TGTCGCAGCATCTGTTC 1328 671_F AAGTCGAAGA
CTGC 2475 OMPA_NC000117_947_ TAACTGCATGGAACCCT 157
OMPA_NC000117_1011_ TGACAGGACACAATCTG 1153 973_F TCTTTACTAG 1040_R
CATGAAGTCTGAG 2476 OMPA_NC000117_774_ TACTGGAACAAAGTCTG 196
OMPA_NC000117_871_894_R TTCAAAAGTTGCTCGAG 1371 795_F CGACC ACCATTG
2477 OMPA_NC000117_457_ TTCTATCTCGTTGGTTT 676
OMPA_NC000117_511_534_R TAAAGAGACGTTTGGTA 851 483_R ATTCGGAGTT
GTTCATTTGC 2478 OMPA_NC000117_687_ TAGCCCAGCACAATTTG 212
OMPA_NC000117_787_816_R TTGCCATTCATGGTATT 1406 710_F TGATTCA
TAAGTGTAGCAGA 2479 OMPA_NC000117_540_ TGGCGTAGTAGAGCTAT 571
OMPA_NC000117_649_672_R TTCTTGAACGCGAGGTT 1395 566_F TTACAGACAC
TCGATTG 2480 OMPA_NC000117_338_ TGCACGATGCGGAATGG 492
OMPA_NC000117_417_444_R TCCTTTAAAATAACCGC 1058 360_F TTCACA
TAGTAGCTCCT 2481 OMP2_NC000117_18_ TATGACCAAACTCATCA 234
OMP2_NC000117_71_91_R TCCCGCTGGCAAATAAA 1025 40_F GACGAG CTCG 2482
OMP2_NC000117_354_ TGCTACGGTAGGATCTC 516 OMP2_NC000117_445_471_R
TGGATCACTGCTTACGA 1270 382_F CTTATCCTATTG ACTCAGCTTC 2483
OMP2_NC000117_ TGGAAAGGTGTTGCAGC 537 OMP2_NC000117_1396_
TACGTTTGTATCTTCTG 903 1297_1319_F TACTCA 1419_R CAGAACC 2484
OMP2_NC000117_ TCTGGTCCAACAAAAGG 407 OMP2_NC000117_1541_
TCCTTTCAATGTTACAG 1062 1465_1493_F AACGATTACAGG 1569_R AAAACTCTACAG
2485 OMP2_NC000117_44_ TGACGATCTTCGCGGTG 450
OMP2_NC000117_120_148_R TGTCAGCTAAGCTAATA 1323 66_F ACTAGT
ACGTTTGTAGAG 2486 OMP2_NC000117_166_ TGACAGCGAAGAAGGTT 441
OMP2_NC000117_240_261_R TTGACATCGTCCCTCTT 1396 190_F AGACTTGTCC
CACAG 2487 GYRA_NC000117_514_ TCAGGCATTGCGGTTGG 287
GYRA_NC000117_640_660_R TGCTGTAGGGAAATCAG 1251 536_F GATGGC GGCC
2488 GYRA_NC000117_801_ TGTGAATAAATCACGAT 636
GYRA_NC000117_871_893_R TTGTCAGACTCATCGCG 1419 827_F TGATTGAGCA
AACATC 2489 GYRA_NC002952_219_ TGTCATGGGTAAATATC 632
GYRA_NC002952_319_345_R
TCCATCCATAGAACCAA 1010 242_F ACCCTCA AGTTACCTTG 2490
GYRA_NC002952_964_ TACAAGCACTCCCAGCT 176 GYRA_NC002952_1024_
TCGCAGCGTGCGTGGCA 1073 983_F GCA 1041_R C 2491 GYRA_NC002952_
TCGCCCGCGAGGACGT 366 GYRA_NC002952_1546_ TTGGTGCGCTTGGCGTA 1416
1505_1520_F 1562_R 2492 GYRA_NC002952_59_ TCAGCTACATCGACTAT 279
GYRA_NC002952_124_143_R TGGCGATGCACTGGCTT 1279 81_F GCGATG GAG 2493
GYRA_NC002952_216_ TGACGTCATCGGTAAGT 452 GYRA_NC002952_313_333_R
TCCGAAGTTGCCCTGGC 1032 239_F ACCACCC CGTC 2494 GYRA_NC002952_219_
TGTACTCGGTAAGTATC 625 GYRA_NC002952_308_330_R TAAGTTACCTTGCCCGT 873
242_2_F ACCCGCA CAACCA 2495 GYRA_NC002952_115_ TGAGATGGATTTAAACC
453 GYRA_NC002952_220_242_R TGCGGGTGATACTTACC 1236 141_F TGTTCACCGC
GAGTAC 2496 GYRA_NC002952_517_ TCAGGCATTGCGGTTGG 287
GYRA_NC002952_643_663_R TGCTGTAGGGAAATCAG 1251 539_F GATGGC GGCC
2497 GYRA_NC002952_273_ TCGTATGGCTCAATGGT 380
GYRA_NC002952_338_360_R TGCGGCAGCACTATCAC 1234 293_F GGAG CATCCA
2498 GYRA_NC000912_257_ TGAGTAAGTTCCACCCG 462
GYRA_NC000912_346_370_R TCGAGCCGAAGTTACCC 1067 278_F CACGG TGTCCGTC
2504 ARCC_NC003923- TAGTpGATpAGAACpTp 229 ARCC_NC003923-2725050-
TCpTpTpTpCpGTATAA 1116 2725050- GTAGGCpACpAATpCpG
2724595_214_239P_R AAAGGACpCpAATpTpG 2724595_135_161P_F T G 2505
PTA_NC003923- TCTTGTpTpTpATGCpT 417 PTA_NC003923-628885-
TACpACpCpTGGTpTpT 904 628885- pGGTAAAGCAGATGG 629355_314_342P_R
pCpGTpTpTpTpGATGA 629355_237_263P_F TpTpTpGTA 2517 CJMLST_ST1_1852_
TTTGCGGATGAAGTAGG 708 CJMLST_ST1_1945_1977_R TGTTTTATGTGTAGTTG 1355
1883_F TGCCTATCTTTTTGC AGCTTACTACATGAGC 2518 CJMLST_ST1_2963_
TGAAATTGCTACAGGCC 428 CJMLST_ST1_3073_3097_R TCCCCATCTCCGCAAAG 1020
2992_F CTTTAGGACAAGG ACAATAAA 2519 CJMLST_ST1_2350_
TGCTTTTGATGGTGATG 535 CJMLST_ST1_2447_2481_R TCTACAACACTTGATTG 1117
2378_F CAGATCGTTTGG TAATTTGCCTTGTTCTT T 2520 CJMLST_ST1_654_
TATGTCCAAGAAGCATA 240 CJMLST_ST1_725_756_R TCGGAAACAAAGAATTC 1084
684_F GCAAAAAAAGCAAT ATTTTCTGGTCCAAA 2521 CJMLST_ST1_360_
TCCTGTTATTCCTGAAG 347 CJMLST_ST1_454_487_R TGCTATATGCTACAACT 1245
395_F TAGTTAATCAAGTTTGT GGTTCAAAAACATTAAG TA 2522 CJMLST_ST1_1231_
TGGCAGTTTTACAAGGT 564 CJMLST_ST1_1312_1340_R TTTAGCTACTATTCTAG 1427
1258_F GCTGTTTCATC CTGCCATTTCCA 2523 CJMLST_ST1_3543_
TGCTGTAGCTTATCGCG 529 CJMLST_ST1_3656_3685_R TCAAAGAACCAGCACCT 950
3574_F AAATGTCTTTGATTT AATTCATCATTTA 2524 CJMLST_ST1_1_17_F
TAAAACTTTTGCCGTAA 145 CJMLST_ST1_55_84_R TGTTCCAATAGCAGTTC 1348
TGATGGGTGAAGATAT CGCCCAAATTGAT 2525 CJMLST_ST1_1312_
TGGAAATGGCAGCTAGA 538 CJMLST_ST1_1383_1417_R TTTCCCCGATCTAAATT 1432
1342_F ATAGTAGCTAAAAT TGGATAAGCCATAGGAA A 2526 CJMLST_ST1_2254_
TGGGCCTAATGGGCTTA 582 CJMLST_ST1_2352_2379_R TCCAAACGATCTGCATC 996
2286_F ATATCAATGAAAATTG ACCATCAAAAG 2527 CJMLST_ST1_1380_
TGCTTTCCTATGGCTTA 534 CJMLST_ST1_1486_1520_R TGCATGAAGCATAAAAA 1205
1411_F TCCAAATTTAGATCG CTGTATCAAGTGCTTTT A 2528 CJMLST_ST1_3413_
TTGTAAATGCCGGTGCT 692 CJMLST_ST1_3511_3542_R TGCTTGCTCAAATCATC 1257
3437_F TCAGATCC ATAAACAATTAAAGC 2529 CJMLST_ST1_1130_
TACGCGTCTTGAAGCGT 189 CJMLST_ST1_1203_1230_R TAGGATGAGCATTATCA 920
1156_F TTCGTTATGA GGGAAAGAATC 2530 CJMLST_ST1_2840_
TGGGGCTTTGCTTTATA 591 CJMLST_ST1_2940_2973_R TAGCGATTTCTACTCCT 917
2872_F GTTTTTTACATTTAAG AGAGTTGAAATTTCAGG 2531 CJMLST_ST1_2058_
TATTCAAGGTGGTCCTT 241 CJMLST_ST1_2131_2162_R TTGGTTCTTACTTGTTT 1417
2084_F TGATGCATGT TGCATAAACTTTCCA 2532 CJMLST_ST1_553_
TCCTGATGCTCAAAGTG 344 CJMLST_ST1_655_685_R TATTGCTTTTTTTGCTA 942
585_F CTTTTTTAGATCCTTT TGCTTCTTGGACAT 2564 GLTA_NC002163-
TCATGTTGAGCTTAAAC 299 GLTA_NC002163-1604930- TTTTGCTCATGATCTGC 1443
1604930- CTATAGAAGTAAAAGC 1604529_352_380_R ATGAAGCATAAA
1604529_306_338_F 2565 UNCA_NC002163- TCCCCCACGCTTTAATT 322
UNCA_NC002163-112166- TCGACCTGGAGGACGAC 1065 112166-
GTTTATGATGATTTGAG 112647_146_171_R GTAAAATCA 112647_80_113_F 2566
UNCA_NC002163- TAATGATGAATTAGGTG 170 UNCA_NC002163-112166-
TGGGATAACATTGGTTG 1285 112166- CGGGTTCTTT 112647_294_329_R
GAATATAAGCAGAAACA 112647_233_259_F TC 2567 PGM_NC002163-
TCTTGATACTTGTAATG 414 PGM_NC002163-327773- TCCATCGCCAGTTTTTG 1012
327773- TGGGCGATAAATATGT 328270_365_396_R CATAATCGCTAAAAA
328270_273_305_F 2568 TKT_NC002163- TTATGAAGCGTGTTCTT 661
TKT_NC002163-1569415- TCAAAACGCATTTTTAC 946 1569415- TAGCAGGACTTCA
1569873_350_383_R ATCTTCGTTAAAGGCTA 1569873_255_284_F 2570
GLTA_NC002163- TCGTCTTTTTGATTCTT 381 GLTA_NC002163-1604930-
TGTTCATGTTTAAATGA 1347 1604930- TCCCTGATAATGC 1604529_109_142_R
TCAGGATAAAAAGCACT 1604529_39_68_F 2571 TKT_NC002163-
TGATCTTAAAAATTTCC 472 TKT_NC002163-1569415- TGCCATAGCAAAGCCTA 1214
1569415- GCCAACTTCATTC 1569903_139_162_R CAGCATT 1569903_33_62_F
2572 TKT_NC002163- TAAGGTTTATTGTCTTT 164 TKT_NC002163-1569415-
TACATCTCCTTCGATAG 886 1569415- GTGGAGATGGGGATTT 1569903_313_345_R
AAATTTCATTGCTATC 1569903_207_239_F 2573 TKT_NC002163-
TAGCCTTTAACGAAAAT 213 TKT_NC002163-1569415- TAAGACAAGGTTTTGTG 865
1569415- GTAAAAATGCGTTTTGA 1569903_449_481_R GATTTTTTAGCTTGTT
1569903_350_383_F 2574 TKT_NC002163- TTCAAAAACTCCAGGCC 665
TKT_NC002163-1569415- TTGCCATAGCAAAGCCT 1405 1569415-
ATCCTGAAATTTCAAC 1569903_139_163_R ACAGCATT 1569903_60_92_F 2575
GLTA_NC002163- TCGTCTTTTTGATTCTT 382 GLTA_NC002163-1604930-
TGCCATTTCCATGTACT 1216 1604930- TCCCTGATAATGCTC 1604529_139_168_R
CTTCTCTAACATT 1604529_39_70_F 2576 GLYA_NC002163- TCAGCTATTTTTCCAGG
281 GLYA_NC002163-367572- ATTGCTTCTTACTTGCT 756 367572-
TATCCAAGGTGG 368079_476_508_R TAGCATAAATTTTCCA 368079_386_414_F
2577 GLYA_NC002163- TGGTGCGAGTGCTTATG 611 GLYA_NC002163-367572-
TGCTCACCTGCTACAAC 1246 367572- CTCGTATTAT 368079_242_270_R
AAGTCCAGCAAT 368079_148_174_F 2578 GLYA_NC002163- TGTAAGCTCTACAACCC
622 GLYA_NC002163-367572- TTCCACCTTGGATACCT 1381 367572-
ACAAAACCTTACG 368079_384_416_R GGAAAAATAGCTGAAT 368079_298_327_F
2579 GLYA_NC002163- TGGTGGACATTTAACAC 614 GLYA_NC002163-367572-
TCAAGCTCTACACCATA 961 367572- ATGGTGCAAA 368079_52_81_R
AAAAAAGCTCTCA 368079_1_27_F 2580 PGM_NC002163- TGAGCAATGGGGCTTTG
455 PGM_NC002163-327746- TTTGCTCTCCGCCAAAG 1438 327746-
AAAGAATTTTTAAAT 328270_356_379_R TTTCCAC 328270_254_285_F 2581
PGM_NC002163- TGAAAAGGGTGAAGTAG 425 PGM_NC002163-327746-
TGCCCCATTGCTCATGA 1219 327746- CAAATGGAGATAG 328270_241_267_R
TAGTAGCTAC 328270_153_182_F 2582 PGM_NC002163- TGGCCTAATGGGCTTAA
568 PGM_NC002163-327746- TGCACGCAAACGCTTTA 1200 327746-
TATCAATGAAAATTG 328270_79_102_R CTTCAGC 328270_19_50_F 2583
UNCA_NC002163- TAAGCATGCTGTGGCTT 160 UNCA_NC002163-112166-
TGCCCTTTCTAAAAGTC 1220 112166- ATCGTGAAATG 112647_196_225_R
TTGAGTGAAGATA 112647_114_141_F 2584 UNCA_NC002163-
TGCTTCGGATCCAGCAG 532 UNCA_NC002163-112166- TGCATGCTTACTCAAAT 1206
112166- CACTTCAATA 112647_88_123_R CATCATAAACAATTAAA 112647_3_29_F
GC 2585 ASPA_NC002163- TTAATTTGCCAAAAATG 652 ASPA_NC002163-96692-
TGCAAAAGTAACGGTTA 1192 96692- CAACCAGGTAG 97166_403_432_R
CATCTGCTCCAAT 97166_308_335_F 2586 ASPA_NC002163- TCGCGTTGCAACAAAAC
370 ASPA_NC002163-96692- TCATGATAGAACTACCT 991 96692-
TTTCTAAAGTATGT 97166_316_346_R GGTTGCATTTTTGG 97166_228_258_F 2587
GLNA_NC002163- TGGAATGATGATAAAGA 547 GLNA_NC002163-658085-
TGAGTTTGAACCATTTC 1176 658085- TTTCGCAGATAGCTA 657609_340_371_R
AGAGCGAATATCTAC 657609_244_275_F 2588 TKT_NC002163-
TCGCTACAGGCCCTTTA 371 TKT_NC002163-1569415- TCCCCATCTCCGCAAAG 1020
1569415- GGACAAG 1569903_212_236_R ACAATAAA 1569903_107_130_F 2589
TKT_NC002163- TGTTCTTTAGCAGGACT 642 TKT_NC002163-1569415-
TCCTTGTGCTTCAAAAC 1057 1569415- TCACAAACTTGATAA 1569903_361_393_R
GCATTTTTACATTTTC 1569903_265_296_F 2590 GLYA_NC002163-
TGCCTATCTTTTTGCTG 505 GLYA_NC002163-367572- TCCTCTTGGGCCACGCA 1047
367572- ATATAGCACATATTGC 368095_317_340_R AAGTTTT 368095_214_246_F
2591 GLYA_NC002163- TCCTTTGATGCATGTAA 353 GLYA_NC002163-367572-
TCTTGAGCATTGGTTCT 1141 367572- TTGCTGCAAAAGC 368095_485_516_R
TACTTGTTTTGCATA 368095_415_444_F
2592 PGM_NC002163_21_ TCCTAATGGACTTAATA 332 PGM_NC002163_116_142_R
TCAAACGATCCGCATCA 949 54_F TCAATGAAAATTGTGGA CCATCAAAAG 2593
PGM_NC002163_149_ TAGATGAAAAAGGCGAA 207 PGM_NC002163_247_277_R
TCCCCTTTAAAGCACCA 1023 176_F GTGGCTAATGG TTACTCATTATAGT 2594
GLNA_NC002163- TGTCCAAGAAGCATAGC 633 GLNA_NC002163-658085-
TCAAAAACAAAGAATTC 945 658085- AAAAAAAGCAA 657609_148_179_R
ATTTTCTGGTCCAAA 657609_79_106_F 2595 ASPA_NC002163-
TCCTGTTATTCCTGAAG 347 ASPA_NC002163-96685- TCAAGCTATATGCTACA 960
96685- TAGTTAATCAAGTTTGT 97196_467_497_R ACTGGTTCAAAAAC
97196_367_402_F TA 2596 ASPA_NC002163- TGCCGTAATGATAGGTG 502
ASPA_NC002163-96685- TACAACCTTCGGATAAT 880 96685-97196_1_33_F
AAGATATACAAAGAGT 97196_95_127_R CAGGATGAGAATTAAT 2597
ASPA_NC002163- TGGAACAGGAATTAATT 540 ASPA_NC002163-96685-
TAAGCTCCCGTATCTTG 872 96685- CTCATCCTGATTATCC 97196_185_210_R
AGTCGCCTC 97196_85_117_F 2598 PGM_NC002163- TGGCAGCTAGAATAGTA 563
PGM_NC002163-327746- TCACGATCTAAATTTGC 975 327746- GCTAAAATCCCTAC
328270_230_261_R ATAAGCCATAGGAAA 328270_165_195_F 2599
PGM_NC002163- TGGGTCGTGGTTTTACA 593 PGM_NC002163-327746-
TTTTGCTCATGATCTGC 1443 327746- GAAAATTTCTTATATAT 328270_353_381_R
ATGAAGCATAAA 328270_252_286_F G 2600 PGM_NC002163-
TGGGATGAAAAAGCGTT 577 PGM_NC002163-327746- TGATAAAAAGCACTAAG 1178
327746- CTTTTATCCATGA 328270_95_123_R CGATGAAACAGC 328270_1_30_F
2601 PGM_NC002163- TAAACACGGCTTTCCTA 146 PGM_NC002163-327746-
TCAAGTGCTTTTACTTC 963 327746- TGGCTTATCCAAAT 328270_314_345_R
TATAGGTTTAAGCTC 328270_220_250_F 2602 UNCA_NC002163-
TGTAGCTTATCGCGAAA 628 UNCA_NC002163-112166- TGCTTGCTCTTTCAAGC 1258
112166- TGTCTTTGATTTT 112647_199_229_R AGTCTTGAATGAAG
112647_123_152_F 2603 UNCA_NC002163- TCCAGATGGACAAATTT 313
UNCA_NC002163-112166- TCCGAAACTTGTTTTGT 1031 112166-
TCTTAGAAACTGATTT 112647_430_461_R AGCTTTAATTTGAGC 112647_333_365_F
2734 GYRA_AY291534_237_ TCACCCTCATGGTGATT 265
GYRA_AY291534_268_288_R TTGCGCCATACGTACCA 1407 264_F CAGCTGTTTAT
TCGT 2735 GYRA_AY291534_224_ TAATCGGTAAGTATCAC 167
GYRA_AY291534_256_285_R TGCCATACGTACCATCG 1213 252_F CCTCATGGTGAT
TTTCATAAACAGC 2736 GYRA_AY291534_170_ TAGGAATTACGGCTGAT 221
GYRA_AY291534_268_288_R TTGCGCCATACGTACCA 1407 198_F AAAGCGTATAAA
TCGT 2737 GYRA_AY291534_224_ TAATCGGTAAGTATCAC 167
GYRA_AY291534_319_346_R TATCGACAGATCCAAAG 935 252_F CCTCATGGTGAT
TTACCATGCCC 2738 GYRA_NC002953- TAAGGTATGACACCGGA 163
GYRA_NC002953-7005- TCTTGAGCCATACGTAC 1142 7005-9668_166_195_
TAAATCATATAAA 9668_265_287_R CATTGC F 2739 GYRA_NC002953-
TAATGGGTAAATATCAC 171 GYRA_NC002953-7005- TATCCATTGAACCAAAG 933
7005-9668_221_249_ CCTCATGGTGAC 9668_316_343_R TTACCTTGGCC F 2740
GYRA_NC002953- TAATGGGTAAATATCAC 171 GYRA_NC002953-7005-
TAGCCATACGTACCATT 912 7005-9668_221_249_ CCTCATGGTGAC
9668_253_283_R GCTTCATAAATAGA F 2741 GYRA_NC002953-
TCACCCTCATGGTGACT 264 GYRA_NC002953-7005- TCTTGAGCCATACGTAC 1142
7005-9668_234_261_ CATCTATTTAT 9668_265_287_R CATTGC F 2842
CAPC_AF188935- TGGGATTATTGTTATCC 578 CAPC_AF188935-56074-
TGGTAACCCTTGTCTTT 1299 56074- TGTTATGCCATTTGAGA 55628_348_378_R
GAATTGTATTTGCA 55628_271_304_F 2843 CAPC_AF188935-
TGATTATTGTTATCCTG 476 CAPC_AF188935-56074- TGTAACCCTTGTCTTTG 1314
56074- TTATGCpCpATpTpTpG 55628_349_377P_R AATpTpGTATpTpTpGC
55628_273_303P_F AG 2844 CAPC_AF188935- TCCGTTGATTATTGTTA 331
CAPC_AF188935-56074- TGTTAATGGTAACCCTT 1344 56074-
TCCTGTTATGCCATTTG 55628_349_384_R GTCTTTGAATTGTATTT 55628_268_303_F
AG GC 2845 CAPC_AF188935- TCCGTTGATTATTGTTA 331
CAPC_AF188935-56074- TAACCCTTGTCTTTGAA 860 56074- TCCTGTTATGCCATTTG
55628_337_375_R TTGTATTTGCAATTAAT 55628_268_303_F AG CCTGG 2846
PARC_X95819_33_58_ TCCAAAAAAATCAGCGC 302 PARC_X95819_121_153_R
TAAAGGATAGCGGTAAC 852 F GTACAGTGG TAAATGGCTGAGCCAT 2847
PARC_X95819_65_92_ TACTTGGTAAATACCAC 199 PARC_X95819_157_178_R
TACCCCAGTTCCCCTGA 889 F CCACATGGTGA CCTTC 2848 PARC_X95819_69_93_
TGGTAAATACCACCCAC 596 PARC_X95819_97_128_R TGAGCCATGAGTACCAT 1169 F
ATGGTGAC GGCTTCATAACATGC 2849 PARC_NC003997- TTCCGTAAGTCGGCTAA 668
PARC_NC003997-3362578- TCCAAGTTTGACTTAAA 1001 3362578- AACAGTCG
3365001_256_283_R CGTACCATCGC 3365001_181_205_F 2850 PARC_NC003997-
TGTAACTATCACCCGCA 621 PARC_NC003997-3362578- TCGTCAACACTACCATT 1099
3362578- CGGTGAT 3365001_304_335_R ATTACCATGCATCTC
3365001_217_240_F 2851 PARC_NC003997- TGTAACTATCACCCGCA 621
PARC_NC003997-3362578- TGACTTAAACGTACCAT 1162 3362578- CGGTGAT
3365001_244_275_R CGCTTCATATACAGA 3365001_217_240_F 2852
GYRA_AY642140_-1_ TAAATCTGCCCGTGTCG 150 GYRA_AY642140_71_100_R
TGCTAAAGTCTTGAGCC 1242 24_F TTGGTGAC ATACGAACAATGG 2853
GYRA_AY642140_26_ TAATCGGTAAATATCAC 166 GYRA_AY642140_121_146_R
TCGATCGAACCGAAGTT 1069 54_F CCGCATGGTGAC ACCCTGACC 2854
GYRA_AY642140_26_ TAATCGGTAAATATCAC 166 GYRA_AY642140_58_89_R
TGAGCCATACGAACAAT 1168 54_F CCGCATGGTGAC GGTTTCATAAACAGC 2860
CYA_AF065404_1348_ TCCAACGAAGTACAATA 305 CYA_AF065404_1448_1472_R
TCAGCTGTTAACGGCTT 983 1379_F CAAGACAAAAGAAGG CAAGACCC 2861
LEF_BA_AF065404_ TCGAAAGCTTTTGCATA 354 LEF_BA_AF065404_843_
TCTTTAAGTTCTTCCAA 1144 751_781_F TTATATCGAGCCAC 881_R
GGATAGATTTATTTCTT GTTCG 2862 LEF_BA_AF065404_ TGCATATTATATCGAGC 498
LEF_BA_AF065404_843_ TCTTTAAGTTCTTCCAA 1144 762_788_F CACAGCATCG
881_R GGATAGATTTATTTCTT GTTCG 2917 MUTS_AY698802_106_
TCCGCTGAATCTGTCGC 326 MUTS_AY698802_172_193_R TGCGGTCTGGCGCATAT
1237 125_F CGC AGGTA 2918 MUTS_AY698802_172_ TACCTATATGCGCCAGA 187
MUTS_AY698802_228_252_R TCAATCTCGACTTTTTG 965 192_F CCGC TGCCGGTA
2919 MUTS_AY698802_228_ TACCGGCGCAAAAAGTC 186
MUTS_AY698802_314_342_R TCGGTTTCAGTCATCTC 1097 252_F GAGATTGG
CACCATAAAGGT 2920 MUTS_AY698802_315_ TCTTTATGGTGGAGATG 419
MUTS_AY698802_413_433_R TGCCAGCGACAGACCAT 1210 342_F ACTGAAACCGA
CGTA 2921 MUTS_AY698802_394_ TGGGCGTGGAACGTCCA 585
MUTS_AY698802_497_519_R TCCGGTAACTGGGTCAG 1040 411_F C CTCGAA 2922
AB_MLST-11-OIF007_ TGGGcGATGCTGCgAAA 583 AB_MLST-11-OIF007_1110_
TAGTATCACCACGTACA 923 991_1018_F TGGTTAAAAGA 1137_R CCCGGATCAGT
2927 GAPA_NC002505_694_ TCAATGAACGACCAACA 259
GAPA_NC_002505_29_58_R_1 TCCTTTATGCAACTTGG 1060 721_F AGTGATTGATG
TATCAACAGGAAT 2928 GAPA_NC002505_694_ TCGATGAACGACCAACA 361
GAPA_NC002505_769_798_ TCCTTTATGCAACTTGG 1061 721_2_F AGTGATTGATG
2_R TATCAACCGGAAT 2929 GAPA_NC002505_694_ TCGATGAACGACCAACA 361
GAPA_NC002505_769_798_ TCCTTTATGCAACTTAG 1059 721_2_F AGTGATTGATG
3_R TATCAACCGGAAT 2932 INFB_EC_1364_1394_ TTGCTCGTGGTGCACAA 688
INFB_EC_1439_1468_R TTGCTGCTTTCGCATGG 1410 F GTAACGGATATTAC
TTAATCGCTTCAA 2933 INFB_EC_1364_1394_ TTGCTCGTGGTGCAIAA 689
INFB_EC_1439_1468_R TTGCTGCTTTCGCATGG 1410 2_F GTAACGGATATIAC
TTAATCGCTTCAA 2934 INFB_EC_80_110_F TTGCCCGCGGTGCGGAA 685
INFB_EC_1439_1468_R TTGCTGCTTTCGCATGG 1410 GTAACCGATATTAC
TTAATCGCTTCAA 2949 ACS_NC002516- TCGGCGCCTGCCTGATG 376
ACS_NC002516-970624- TGGACCACGCCGAAGAA 1265 970624- A
971013_364_383_R CGG 971013_299_316_F 2950 ARO_NC002516-
TCACCGTGCCGTTCAAG 267 ARO_NC002516-26883- TGTGTTGTCGCCGCGCA 1341
26883-27380_4_26_F GAAGAG 27380_111_128_R G 2951
ARO_NC002516-26883- TTTCGAAGGGCCTTTCG 705 ARO_NC002516-26883-
TCCTTGGCATACATCAT 1056 27380_356_377_F ACCTG 27380_459_484_R
GTCGTAGCA 2952 GUA_NC002516- TGGACTCCTCGGTGGTC 551
GUA_NC002516-4226546- TCGGCGAACATGGCCAT 1091 4226546- GC
4226174_127_146_R CAC 4226174_23_41_F 2953 GUA_NC002516-
TGACCAGGTGATGGCCA 448 GUA_NC002516-4226546- TGCTTCTCTTCCGGGTC 1256
4226546- TGTTCG 4226174_214_233_R GGC 4226174_120_142_F 2954
GUA_NC002516- TTTTGAAGGTGATCCGT 710 GUA_NC002516-4226546-
TGCTTGGTGGCTTCTTC 1259 4226546- GCCAACG 4226174_265_287_R GTCGAA
4226174_155_178_F 2955 GUA_NC002516- TTCCTCGGCCGCCTGGC 670
GUA_NC002516-4226546- TGCGAGGAACTTCACGT 1229 4226546-
4226174_288_309_R CCTGC 4226174_190_206_F 2956 GUA_NC002516-
TCGGCCGCACCTTCATC 374 GUA_NC002516-4226546- TCGTGGGCCTTGCCGGT 1111
4226546- GAAGT 4226174_355_371_R
4226174_242_263_F 2957 MUT_NC002516- TGGAAGTCATCAAGCGC 545
MUT_NC002516-5551158- TCACGGGCCAGCTCGTC 978 5551158- CTGGC
5550717_99_116_R T 5550717_5_26_F 2958 MUT_NC002516-
TCGAGCAGGCGCTGCCG 358 MUT_NC002516-5551158- TCACCATGCGCCCGTTC 971
5551158- 5550717_256_277_R ACATA 5550717_152_168_F 2959
NUO_NC002516- TCAACCTCGGCCCGAAC 249 NUO_NC002516-2984589-
TCGGTGGTGGTAGCCGA 1095 2984589- CA 2984954_97_117_R TCTC
2984954_8_26_F 2960 NUO_NC002516- TACTCTCGGTGGAGAAG 195
NUC_NC002516-2984589- TTCAGGTACAGCAGGTG 1376 2984589- CTCGC
2984954_301_326_R GTTCAGGAT 2984954_218_239_F 2961 PPS_NC002516-
TCCACGGTCATGGAGCG 311 PPS_NC002516-1915014- TCCATTTCCGACACGTC 1014
1915014- CTA 1915383_140_165_R GTTGATCAC 1915383_44_63_F 2962
PPS_NC002516- TCGCCATCGTCACCAAC 365 PPS_NC002516-1915014-
TCCTGGCCATCCTGCAG 1052 1915014- CG 1915383_341_360_R GAT
1915383_240_258_F 2963 TRP_NC002516- TGCTGGTACGGGTCGAG 527
TRP_NC002516-671831- TCGATCTCCTTGGCGTC 1071 671831- GA
672273_131_150_R CGA 672273_24_42_F 2964 TRP_NC002516-
TGCACATCGTGTCCAAC 490 TRP_NC002516-671831- TGATCTCCATGGCGCGG 1182
671831- GTCAC 672273_362_383_R ATCTT 672273_261_282_F 2972
AB_MLST-11- TGGGIGATGCTGCIAAA 592 AB_MLST-11- TAGTATCACCACGTACI 924
OIF007_1007_1034_F TGGTTAAAAGA OIF007_1126_1153_R CCIGGATCAGT 2993
OMPU_NC002505- TTCCCACCGATATCATG 667 OMPU_NC002505_544_567_R
TCGGTCAGCAAAACGGT 1094 674828- GCTTACCACGG AGCTTGC 675880_428_455_F
2994 GAPA_NC002505- TCCTCAATGAACGAICA 335 GAPA_NC002505-506780-
TTTTCCCTTTATGCAAC 1442 506780- ACAAGTGATTGATG 507937_769_802_R
TTAGTATCAACIGGAAT 507937_691_721_F 2995 GAPA_NC002505-
TCCTCIATGAACGAICA 339 GAPA_NC002505-506780- TCCATACCTTTATGCAA 1008
506780- ACAAGTGATTGATG 507937_769_803_R CTTIGTATCAACIGGAA
507937_691_721_2_F T 2996 GAPA_NC002505- TCTCGATGAACGACCAA 396
GAPA_NC002505-506780- TCGGAAATATTCTTTCA 1085 506780- CAAGTGATTGATG
507937_785_817_R ATACCTTTATGCAACT 507937_692_721_F 2997
GAPA_NC002505- TCCTCGATGAACGAICA 337 GAPA_NC002505-506780-
TCGGAAATATTCTTTCA 1085 506780- ACAAGTIATTGATG 507937_785_817_R
ATACCTTTATGCAACT 507937_691_721_3_F 2998 GAPA_NC002505-
TCCTCAATGAATGATCA 336 GAPA_NC002505-506780- TCGGAAATATTCTTTCA 1087
506780- ACAAGTGATTGATG 507937_784_817_R ATICCTTTITGCAACTT
507937_691_721_4_F 2999 GAPA_NC002505- TCCTCIATGAAIGAICA 340
GAPA_NC002505-506780- TCGGAAATATTCTTTCA 1086 506780- ACAAGTIATTGATG
507937_784_817_2_R ATACCTTTATGCAACTT 507937_691_721_5_F 3000
GAPA_NC002505- TCCTCGATGAATGAICA 338 GAPA_NC002505-506780-
TTTCAATACCTTTATGC 1430 506780- ACAAGTIATTGATG 507937_769_805_R
AACTTIGTATCAACIGG 507937_691_721_6_F AAT 3001 CTXB_NC002505-
TCAGCATATGCACATGG 275 CTXB_NC002505-1566967- TCCCGGCTAGAGATTCT 1026
1566967- AACACCTCA 1567341_139_163_R GTATACGA 1567341_46_71_F 3002
CTXB_NC002505- TCAGCATATGCACATGG 274 CTXB_NC002505-1566967-
TCCGGCTAGAGATTCTG 1038 1566967- AACACCTC 1567341_132_162_R
TATACGAAAATATC 1567341_46_70_F 3003 CTXB_NC002505-
TCAGCATATGCACATGG 274 CTXB_NC002505-1566967- TGCCGTATACGAAAATA 1225
1566967- AACACCTC 1567341_118_150_R TCTTATCATTTAGCGT
1567341_46_70_F 3004 TUFB_NC002758- TACAGGCCGTGTTGAAC 180
TUFB_NC002758-615038- TCAGCGTAGTCTAATAA 982 615038- GTGG
616222_778_809_R TTTACGGAACATTTC 616222_684_704_F 3005
TUFB_NC002758- TGCCGTGTTGAACGTGG 503 TUFB_NC002758-615038-
TGCTTCAGCGTAGTCTA 1255 615038- TCAAAT 616222_783_813_R
ATAATTTACGGAAC 616222_688_710_F 3006 TUFB_NC002758-
TGTGGTCAAATCAAAGT 638 TUFB_NC002758-615038- TGCGTAGTCTAATAATT 1238
615038- TGGTGAAGAA 616222_778_807_R TACGGAACATTTC 616222_700_726_F
3007 TUFB_NC002758- TGGTCAAATCAAAGTTG 607 TUFB_NC002758-615038-
TGCGTAGTCTAATAATT 1238 615038- GTGAAGAA 616222_778_807_R
TACGGAACATTTC 616222_702_726_F 3008 TUFB_NC002758-
TGAACGTGGTCAAATCA 431 TUFB_NC002758-615038- TCACCAGCTTCAGCGTA 970
615038- AAGTTGGTGAAGAA 616222_785_818_R GTCTAATAATTTACGGA
616222_696_726_F 3009 TUFB_NC002758- TCGTGTTGAACGTGGTC 386
TUFB_NC002758-615038- TCTTCAGCGTAGTCTAA 1134 615038- AAATCAAAGT
616222_778_812_R TAATTTACGGAACATTT 616222_690_716_F C 3010
MECI-R_NC003923- TCACATATCGTGAGCAA 261 MECI-R_NC003923-41798-
TGTGATATGGAGGTGTA 1332 41798-41609_36_59_ TGAACTG 41609_89_112_R
GAAGGTG F 3011 MECI-R_NC003923- TGGGCGTGAGCAATGAA 584
MECI-R_NC003923-41798- TGGGATGGAGGTGTAGA 1287 41798-41609_40_66_
CTGATTATAC 41609_81_110_R AGGTGTTATCATC F 3012 MECI-R_NC003923-
TGGACACATATCGTGAG 549 MECI-R_NC003923-41798- TGGGATGGAGGTGTAGA 1286
41798- CAATGAACTGA 41609_81_110_R AGGTGTTATCATC 41609_33_60_2_F
3013 MECI-R_NC003923- TGGGTTTACACATATCG 595 MECI-R_NC003923-41798-
TGGGGATATGGAGGTGT 1290 41798-41609_29_60_ TGAGCAATGAACTGA
41609_81_113_R AGAAGGTGTTATCATC F 3014 MUPR_X75439_2490_
TGGGCTCTTTCTCGCTT 587 MUPR_X75439_2548_2570_R TCTGGCTGCGGAAGTGA
1130 2514_F AAACACCT AATCGT 3015 MUPR_X75439_2490_
TGGGCTCTTTCTCGCTT 586 MUPR_X75439_2547_2568_R TGGCTGCGGAAGTGAAA
1281 2513_F AAACACC TCGTA 3016 MUPR_X75439_2482_ TAGATAATTGGGCTCTT
205 MUPR_X75439_2551_2573_R TAATCTGGCTGCGGAAG 876 2510_F
TCTCGCTTAAAC TGAAAT 3017 MUPR_X75439_2490_ TGGGCTCTTTCTCGCTT 587
MUPR_X75439_2549_2573_R TAATCTGGCTGCGGAAG 877 2514_F AAACACCT
TGAAATCG 3018 MUPR_X75439_2482_ TAGATAATTGGGCTCTT 205
MUPR_X75439_2559_2589_R TGGTATATTCGTTAATT 1303 2510_F TCTCGCTTAAAC
AATCTGGCTGCGGA 3019 MUPR_X75439_2490_ TGGGCTCTTTCTCGCTT 587
MUPR_X75439_2554_2581_R TCGTTAATTAATCTGGC 1112 2514_F AAACACCT
TGCGGAAGTGA 3020 AROE_NC003923- TGATGGCAAGTGGATAG 474
AROE_NC003923-1674726- TAAGCAATACCTTTACT 868 1674726- GGTATAATACAG
1674277_309_335_R TGCACCACCT 1674277_204_232_F 3021 AROE_NC003923-
TGGCGAGTGGATAGGGT 570 AROE_NC003923-1674726- TTCATAAGCAATACCTT 1378
1674726- ATAATACAG 1674277_311_339_R TACTTGCACCAC 1674277_207_232_F
3022 AROE_NC003923- TGGCpAAGTpGGATpAG 572 AROE_NC003923-1674726-
TAAGCAATACCpTpTpT 867 1674726- GGTpATpAATpACpAG 1674277_311_335P_R
pACTpTpGCpACpCpAC 1674277_207_232P_F 3023 ARCC_NC003923-
TCTGAAATGAATAGTGA 398 ARCC_NC003923-2725050- TCTTCTTCTTTCGTATA 1137
2725050- TAGAACTGTAGGCAC 2724595_214_245_R AAAAGGACCAATTGG
2724595_124_155_F 3024 ARCC_NC003923- TGAATAGTGATAGAACT 437
ARCC_NC003923-2725050- TCTTCTTTCGTATAAAA 1139 2725050-
GTAGGCACAATCGT 2724595_212_242_R AGGACCAATTGGTT 2724595_131_161_F
3025 ARCC_NC003923- TGAATAGTGATAGAACT 437 ARCC_NC003923-2725050-
TGCGCTAATTCTTCAAC 1232 2725050- GTAGGCACAATCGT 2724595_232_260_R
TTCTTCTTTCGT 2724595_131_161_F 3026 PTA_NC003923- TACAATGCTTGTTTATG
177 PTA_NC003923-628885- TGTTCTTGATACACCTG 1350 628885-
CTGGTAAAGCAG 629355_322_351_R GTTTCGTTTTGAT 629355_231_259_F 3027
PTA_NC003923- TACAATGCTTGTTTATG 177 PTA_NC003923-628885-
TGGTACACCTGGTTTCG 1301 628885- CTGGTAAAGCAG 629355_314_345_R
TTTTGATGATTTGTA 629355_231_259_F 3028 PTA_NC003923-
TCTTGTTTATGCTGGTA 418 PTA_NC003923-628885- TGTTCTTGATACACCTG 1350
628885- AAGCAGATGG 629355_322_351_R GTTTCGTTTTGAT
629355_237_263_F
[0372] Primer pair name codes and reference sequences are shown in
Table 3. The primer name code typically represents the gene to
which the given primer pair is targeted. The primer pair name may
include specific coordinates with respect to a reference sequence
defined by an extraction of a section of sequence or defined by a
GenBank gi number, or the corresponding complementary sequence of
the extraction, or the entire GenBank gi number as indicated by the
label "no extraction." Where "no extraction" is indicated for a
reference sequence, the coordinates of a primer pair named to the
reference sequence are with respect to the GenBank gi listing. Gene
abbreviations are shown in bold type in the "Gene Name" column.
[0373] To determine the exact primer hybridization coordinates of a
given pair of primers on a given bioagent nucleic acid sequence and
to determine the sequences, molecular masses and base compositions
of an amplification product to be obtained upon amplification of
nucleic acid of a known bioagent with known sequence information in
the region of interest with a given pair of primers, one with
ordinary skill in bioinformatics is capable of obtaining alignments
of the primers of the present invention with the GenBank gi number
of the relevant nucleic acid sequence of the known bioagent. For
example, the reference sequence GenBank gi numbers (Table 3)
provide the identities of the sequences which can be obtained from
GenBank. Alignments can be done using a bioinformatics tool such as
BLASTn provided to the public by NCBI (Bethesda, Md.).
Alternatively, a relevant GenBank sequence may be downloaded and
imported into custom programmed or commercially available
bioinformatics programs wherein the alignment can be carried out to
determine the primer hybridization coordinates and the sequences,
molecular masses and base compositions of the amplification
product. For example, to obtain the hybridization coordinates of
primer pair number 2095 (SEQ ID NOs: 456:1261), First the forward
primer (SEQ ID NO: 456) is subjected to a BLASTn search on the
publicly available NCBI BLAST website. "RefSeq_Genomic" is chosen
as the BLAST database since the gi numbers refer to genomic
sequences. The BLAST query is then performed. Among the top results
returned is a match to GenBank gi number 21281729 (Accession Number
NC.sub.--003923). The result shown below, indicates that the
forward primer hybridizes to positions 1530282 . . . 1530307 of the
genomic sequence of Staphylococcus aureus subsp. aureus MW2
(represented by gi number 21281729).
Staphylococcus aureus subsp. aureus MW2, complete genome
Length=2820462
Features in this part of subject sequence:
[0374] Panton-Valentine leukocidin chain F precursor
Score=52.0 bits (26), Expect=2e-05
Identities=26/26 (100%), Gaps=0/26 (0%)
[0375] Strand=Plus/Plus TABLE-US-00003 Query 1
TGAGCTGCATCAACTGTATTGGATAG 26 |||||||||||||||||||||||||| Sbjct
1530282 TGAGCTGCATCAACTGTATTGGATAG 1530307
[0376] The hybridization coordinates of the reverse primer (SEQ ID
NO: 1261) can be determined in a similar manner and thus, the
bioagent identifying amplicon can be defined in terms of genomic
coordinates. The query/subject arrangement of the result would be
presented in Strand=Plus/Minus format because the reverse strand
hybridizes to the reverse complement of the genomic sequence. The
preceding sequence analyses are well known to one with ordinary
skill in bioinformatics and thus, Table 3 contains sufficient
information to determine the primer hybridization coordinates of
any of the primers of Table 2 to the applicable reference sequences
described therein. TABLE-US-00004 TABLE 3 Primer Name Codes and
Reference Sequence Reference GenBank gi Primer name code Gene Name
Organism number 16S_EC 16S rRNA (16S ribosomal RNA gene)
Escherichia coli 16127994 23S_EC 23S rRNA (23S ribosomal RNA gene)
Escherichia coli 16127994 CAPC_BA capC (capsule biosynthesis gene)
Bacillus anthracis 6470151 CYA_BA cya (cyclic AMP gene) Bacillus
anthracis 4894216 DNAK_EC dnaK (chaperone dnaK gene) Escherichia
coli 16127994 GROL_EC groL (chaperonin groL) Escherichia coli
16127994 HFLB_EC hflb (cell division protein peptidase Escherichia
coli 16127994 ftsH) INFB_EC infB (protein chain initiation factor
Escherichia coli 16127994 infB gene) LEF_BA lef (lethal factor)
Bacillus anthracis 21392688 PAG_BA pag (protective antigen)
Bacillus anthracis 21392688 RPLB_EC rplB (50S ribosomal protein L2)
Escherichia coli 16127994 RPOB_EC rpoB (DNA-directed RNA polymerase
beta Escherichia coli 6127994 chain) RPOC_EC rpoC (DNA-directed RNA
polymerase Escherichia coli 16127994 beta' chain) SP101ET_SPET_11
Artificial Sequence Concatenation Artificial 15674250 comprising:
Sequence* - gki (glucose kinase) partial gene gtr (glutamine
transporter protein) sequences of murI (glutamate racemase)
Streptococcus mutS (DNA mismatch repair protein) pyogenes xpt
(xanthine phosphoribosyl transferase) yqiL (acetyl-CoA-acetyl
transferase) tkt (transketolase) SSPE_BA sspE (small acid-soluble
spore Bacillus anthracis 30253828 protein) TUFB_EC tufB (Elongation
factor Tu) Escherichia coli 16127994 VALS_EC valS (Valyl-tRNA
synthetase) Escherichia coli 16127994 ASPS_EC aspS (Aspartyl-tRNA
synthetase) Escherichia coli 16127994 CAF1_AF053947 caf1 (capsular
protein caf1) Yersinia pestis 2996286 INV_U22457 inv (invasin)
Yersinia pestis 1256565 LL_NC003143 Y. pestis specific chromosomal
genes - Yersinia pestis 16120353 difference region BONTA_X52066
BoNT/A (neurotoxin type A) Clostridium 40381 botulinum MECA_Y14051
mecA methicillin resistance gene Staphylococcus 2791983 aureus
TRPE_AY094355 trpE (anthranilate synthase (large Acinetobacter
20853695 component)) baumanii RECA_AF251469 recA (recombinase A)
Acinetobacter 9965210 baumanii GYRA_AF100557 gyrA (DNA gyrase
subunit A) Acinetobacter 4240540 baumanii GYRB_AB008700 gyrB (DNA
gyrase subunit B) Acinetobacter 4514436 baumanii WAAA_Z96925 waaA
(3-deoxy-D-manno-octulosonic-acid Acinetobacter 2765828
transferase) baumanii CJST_CJ Artificial Sequence Concatenation
Artificial 15791399 comprising: Sequence* - tkt (transketolase)
partial gene glyA (serine hydroxymethyltransferase) sequences of
gltA (citrate synthase) Campylobacter aspA (aspartate ammonia
lyase) jejuni glnA (glutamine synthase) pgm (phosphoglycerate
mutase) uncA (ATP synthetase alpha chain) RNASEP_BDP RNase P
(ribonuclease P) Bordetella 33591275 pertussis RNASEP_BKM RNase P
(ribonuclease P) Burkholderia 53723370 mallei RNASEP_BS RNase P
(ribonuclease P) Bacillus subtilis 16077068 RNASEP_CLB RNase P
(ribonuclease P) Clostridium 18308982 perfringens RNASEP_EC RNase P
(ribonuclease P) Escherichia coli 16127994 RNASEP_RKP RNase P
(ribonuclease P) Rickettsia 15603881 prowazekii RNASEP_SA RNase P
(ribonuclease P) Staphylococcus 15922990 aureus RNASEP_VBC RNase P
(ribonuclease P) Vibrio cholerae 15640032 ICD_CXB icd (isocitrate
dehydrogenase) Coxiella burnetii 29732244 IS1111A multi-locus
IS1111A insertion element Acinetobacter 29732244 baumannii
OMPA_AY485227 ompA (outer membrane protein A) Rickettsia 40287451
prowazekii OMPB_RKP ompB (outer membrane protein B) Rickettsia
15603881 prowazekii GLTA_RKP gltA (citrate synthase) Vibrio
cholerae 15603881 TOXR_VBC toxR (transcription regulator toxR)
Francisella 15640032 tularensis ASD_FRT asd (Aspartate semialdehyde
Francisella 56707187 dehydrogenase) tularensis GALE_FRT galE
(UDP-glucose 4-epimerase) Shigella flexneri 56707187 IPAH_SGF ipaH
(invasion plasmid antigen) Campylobacter 30061571 jejuni HUPB_CJ
hupB (DNA-binding protein Hu-beta) Coxiella burnetii 15791399
AB_MLST Artificial Sequence Concatenation Artificial Sequenced
comprising: Sequence* - in-house trpE (anthranilate synthase
component partial gene (SEQ ID I)) sequences of NO: 1444) adk
(adenylate kinase) Acinetobacter mutY (adenine glycosylase)
baumannii fumC (fumarate hydratase) efp (elongation factor p) ppa
(pyrophosphate phospho- hydratase MUPR_X75439 mupR (mupriocin
resistance gene) Staphylococcus 438226 aureus PARC_X95819 parC
(topoisomerase IV) Acinetobacter 1212748 baumannii SED_M28521 sed
(enterotoxin D) Staphylococcus 1492109 aureus PLA_AF053945 pla
(plasminogen activator) Yersinia pestis 2996216 SEJ_AF053140 sej
(enterotoxin J) Staphylococcus 3372540 aureus GYRA_NC000912 gyrA
(DNA gyrase subunit A) Mycoplasma 13507739 pneumoniae ACS_NC002516
acsA (Acetyl CoA Synthase) Pseudomonas 15595198 aeruginosa
ARO_NC002516 aroE (shikimate 5-dehydrogenase Pseudomonas 15595198
aeruginosa GUA_NC002516 guaA (GMP synthase) Pseudomonas 15595198
aeruginosa MUT_NC002516 mutL (DNA mismatch repair protein)
Pseudomonas 15595198 aeruginosa NUO_NC002516 nuoD (NADH
dehydrogenase I chain C, D) Pseudomonas 15595198 aeruginosa
PPS_NC002516 ppsA (Phosphoenolpyruvate synthase) Pseudomonas
15595198 aeruginosa TRP_NC002516 trpE (Anthranilate synthetase
Pseudomonas 15595198 component I) aeruginosa OMP2_NC000117 ompB
(outer membrane protein B) Chlamydia 15604717 trachomatis
OMPA_NC000117 ompA (outer membrane protein B) Chlamydia 15604717
trachomatis GYRA_NC000117 gyrA (DNA gyrase subunit A) Chlamydia
15604717 trachomatis CTXA_NC002505 ctxA (Cholera toxin A subunit)
Vibrio cholerae 15640032 CTXB_NC002505 ctxB (Cholera toxin B
subunit) Vibrio cholerae 15640032 FUR_NC002505 fur (ferric uptake
regulator protein) Vibrio cholerae 15640032 GAPA_NC_002505 gapA
(glyceraldehyde-3-phosphate Vibrio cholerae 15640032 dehydrogenase)
GYRB_NC002505 gyrB (DNA gyrase subunit B) Vibrio cholerae 15640032
OMPU_NC002505 ompU (outer membrane protein) Vibrio cholerae
15640032 TCPA_NC002505 tcpA (toxin-coregulated pilus) Vibrio
cholerae 15640032 ASPA_NC002163 aspA (aspartate ammonia lyase)
Campylobacter 15791399 jejuni GLNA_NC002163 glnA (glutamine
synthetase) Campylobacter 15791399 jejuni GLTA_NC002163 gltA
(glutamate synthase) Campylobacter 15791399 jejuni GLYA_NC002163
glyA (serine hydroxymethyltransferase) Campylobacter 15791399
jejuni PGM_NC002163 pgm (phosphoglyceromutase) Campylobacter
15791399 jejuni TKT_NC002163 tkt (transketolase) Campylobacter
15791399 jejuni UNCA_NC002163 uncA (ATP synthetase alpha chain)
Campylobacter 15791399 jejuni AGR-III_NC003923 agr-III (accessory
gene regulator-III) Staphylococcus 21281729 aureus ARCC_NC003923
arcC (carbamate kinase) Staphylococcus 21281729 aureus
AROE_NC003923 aroE (shikimate 5-dehydrogenase Staphylococcus
21281729 aureus BSA-A_NC003923 bsa-a (glutathione peroxidase)
Staphylococcus 21281729 aureus BSA-B_NC003923 bsa-b (epidermin
biosynthesis protein Staphylococcus 21281729 EpiB) aureus
GLPF_NC003923 glpF (glycerol transporter) Staphylococcus 21281729
aureus GMK_NC003923 gmk (guanylate kinase) Staphylococcus 21281729
aureus MECI-R_NC003923 mecR1 (truncated methicillin Staphylococcus
21281729 resistance protein) aureus PTA_NC003923 pta (phosphate
acetyltransferase) Staphylococcus 21281729 aureus PVLUK_NC003923
pvluk (Panton-Valentine leukocidin Staphylococcus 21281729 chain F
precursor) aureus SA442_NC003923 sa442 gene Staphylococcus 21281729
aureus SEA_NC003923 sea (staphylococcal enterotoxin A
Staphylococcus 21281729 precursor) aureus SEC_NC003923 sec4
(enterotoxin type C precursor) Staphylococcus 21281729 aureus
TPI_NC003923 tpi (triosephosphate isomerase) Staphylococcus
21281729 aureus YQI_NC003923 yqi (acetyl-CoA C-acetyltransferase
Staphylococcus 21281729 homologue) aureus GALE_AF513299 galE
(galactose epimerase) Francisella 23506418 tularensis VVHA_NC004460
vVhA (cytotoxin, cytolysin precursor) Vibrio vulnificus 27366463
TDH_NC004605 tdh (thermostable direct hemolysin A) Vibrio 28899855
parahaemolyticus AGR-II_NC002745 agr-II (accessory gene
regulator-II) Staphylococcus 29165615 aureus PARC_NC003997 parC
(topoisomerase IV) Bacillus anthracis 30260195 GYRA_AY291534 gyrA
(DNA gyrase subunit A) Bacillus anthracis 31323274 AGR-I_AJ617706
agr-I (accessory gene regulator-I) Staphylococcus 46019543 aureus
AGR-IV_AJ617711 agr-IV (accessory gene regulator-III)
Staphylococcus 46019563 aureus BLAZ_NC002952 blaZ (beta lactamase
III) Staphylococcus 49482253 aureus ERMA_NC002952 ermA (rRNA
methyltransferase A) Staphylococcus 49482253 aureus ERMB_Y13600
ermB (rRNA methyltransferase B) Staphylococcus 49482253 aureus
SEA-SEE_NC002952 sea (staphylococcal enterotoxin A Staphylococcus
49482253 precursor) aureus SEA-SEE_NC002952 sea (staphylococcal
enterotoxin A Staphylococcus 49482253 precursor) aureus
SEE_NC002952 sea (staphylococcal enterotoxin A Staphylococcus
49482253 precursor) aureus SEH_NC002953 seh (staphylococcal
enterotoxin H) Staphylococcus 49484912 aureus ERMC_NC005908 ermC
(rRNA methyltransferase C) Staphylococcus 49489772 aureus
MUTS_AY698802 mutS (DNA mismatch repair protein) Shigella boydii
52698233 NUC_NC002758 nuc (staphylococcal nuclease) Staphylococcus
57634611 aureus SEB_NC002758 seb (enterotoxin type B precursor)
Staphylococcus 57634611 aureus SEG_NC002758 seg (staphylococcal
enterotoxin G) Staphylococcus 57634611 aureus SEI_NC002758 sei
(staphylococcal enterotoxin I) Staphylococcus 57634611 aureus
TSST_NC002758 tsst (toxic shock syndrome toxin-1) Staphylococcus
57634611 aureus TUFB_NC002758 tufB (Elongation factor Tu)
Staphylococcus 57634611 aureus
Note: artificial reference sequences represent concatenations of
partial gene extractions from the indicated reference gi number.
Partial sequences were used to create the concatenated sequence
because complete gene sequences were not necessary for primer
design.
Example 2
Sample Preparation and PCR
[0377] Genomic DNA was prepared from samples using the DNeasy
Tissue Kit (Qiagen, Valencia, Calif.) according to the
manufacturer's protocols.
[0378] All PCR reactions were assembled in 50 .mu.L reaction
volumes in a 96-well microtiter plate format using a Packard MPII
liquid handling robotic platform and M. J. Dyad thermocyclers (MJ
research, Waltham, Mass.) or Eppendorf Mastercycler thermocyclers
(Eppendorf, Westbury, N.Y.). The PCR reaction mixture consisted of
4 units of Amplitaq Gold, 1.times. buffer II (Applied Biosystems,
Foster City, Calif.), 1.5 mM MgCl.sub.2, 0.4 M betaine, 800 .mu.M
dNTP mixture and 250 nM of each primer. The following typical PCR
conditions were used: 95.degree. C. for 10 min followed by 8 cycles
of 95.degree. C. for 30 seconds, 48.degree. C. for 30 seconds, and
72.degree. C. 30 seconds with the 48.degree. C. annealing
temperature increasing 0.9.degree. C. with each of the eight
cycles. The PCR was then continued for 37 additional cycles of
95.degree. C. for 15 seconds, 56.degree. C. for 20 seconds, and
72.degree. C. 20 seconds.
Example 3
Purification of PCR Products for Mass Spectrometry with Ion
Exchange Resin-Magnetic Beads
[0379] For solution capture of nucleic acids with ion exchange
resin linked to magnetic beads, 25 .mu.l of a 2.5 mg/mL suspension
of BioClone amine terminated superparamagnetic beads were added to
25 to 50 .mu.l of a PCR (or RT-PCR) reaction containing
approximately 10 .mu.M of a typical PCR amplification product. The
above suspension was mixed for approximately 5 minutes by vortexing
or pipetting, after which the liquid was removed after using a
magnetic separator. The beads containing bound PCR amplification
product were then washed three times with 50 mM ammonium
bicarbonate/50% MeOH or 100 mM ammonium bicarbonate/50% MeOH,
followed by three more washes with 50% MeOH. The bound PCR amplicon
was eluted with a solution of 25 mM piperidine, 25 mM imidazole,
35% MeOH which included peptide calibration standards.
Example 4
Mass Spectrometry and Base Composition Analysis
[0380] The ESI-FTICR mass spectrometer is based on a Bruker
Daltonics (Billerica, Mass.) Apex II 70e electrospray ionization
Fourier transform ion cyclotron resonance mass spectrometer that
employs an actively shielded 7 Tesla superconducting magnet. The
active shielding constrains the majority of the fringing magnetic
field from the superconducting magnet to a relatively small volume.
Thus, components that might be adversely affected by stray magnetic
fields, such as CRT monitors, robotic components, and other
electronics, can operate in close proximity to the FTICR
spectrometer. All aspects of pulse sequence control and data
acquisition were performed on a 600 MHz Pentium II data station
running Bruker's Xmass software under Windows NT 4.0 operating
system. Sample aliquots, typically 15 .mu.l, were extracted
directly from 96-well microtiter plates using a CTC HTS PAL
autosampler (LEAP Technologies, Carrboro, N.C.) triggered by the
FTICR data station. Samples were injected directly into a 10 .mu.l
sample loop integrated with a fluidics handling system that
supplies the 100 .mu.l/hr flow rate to the ESI source. Ions were
formed via electrospray ionization in a modified Analytica
(Branford, Conn.) source employing an off axis, grounded
electrospray probe positioned approximately 1.5 cm from the
metalized terminus of a glass desolvation capillary. The
atmospheric pressure end of the glass capillary was biased at 6000
V relative to the ESI needle during data acquisition. A
counter-current flow of dry N.sub.2 was employed to assist in the
desolvation process. Ions were accumulated in an external ion
reservoir comprised of an rf-only hexapole, a skimmer cone, and an
auxiliary gate electrode, prior to injection into the trapped ion
cell where they were mass analyzed. Ionization duty cycles greater
than 99% were achieved by simultaneously accumulating ions in the
external ion reservoir during ion detection. Each detection event
consisted of 1M data points digitized over 2.3 s. To improve the
signal-to-noise ratio (S/N), 32 scans were co-added for a total
data acquisition time of 74 s.
[0381] The ESI-TOF mass spectrometer is based on a Bruker Daltonics
MicroTOF.TM.. Ions from the ESI source undergo orthogonal ion
extraction and are focused in a reflectron prior to detection. The
TOF and FTICR are equipped with the same automated sample handling
and fluidics described above. Ions are formed in the standard
MicroTOF.TM. ESI source that is equipped with the same off-axis
sprayer and glass capillary as the FTICR ESI source. Consequently,
source conditions were the same as those described above. External
ion accumulation was also employed to improve ionization duty cycle
during data acquisition. Each detection event on the TOF was
comprised of 75,000 data points digitized over 75 .mu.s.
[0382] The sample delivery scheme allows sample aliquots to be
rapidly injected into the electrospray source at high flow rate and
subsequently be electrosprayed at a much lower flow rate for
improved ESI sensitivity. Prior to injecting a sample, a bolus of
buffer was injected at a high flow rate to rinse the transfer line
and spray needle to avoid sample contamination/carryover. Following
the rinse step, the autosampler injected the next sample and the
flow rate was switched to low flow. Following a brief equilibration
delay, data acquisition commenced. As spectra were co-added, the
autosampler continued rinsing the syringe and picking up buffer to
rinse the injector and sample transfer line. In general, two
syringe rinses and one injector rinse were required to minimize
sample carryover. During a routine screening protocol a new sample
mixture was injected every 106 seconds. More recently a fast wash
station for the syringe needle has been implemented which, when
combined with shorter acquisition times, facilitates the
acquisition of mass spectra at a rate of just under one
spectrum/minute.
[0383] Raw mass spectra were post-calibrated with an internal mass
standard and deconvoluted to monoisotopic molecular masses.
Unambiguous base compositions were derived from the exact mass
measurements of the complementary single-stranded oligonucleotides.
Quantitative results are obtained by comparing the peak heights
with an internal PCR calibration standard present in every PCR well
at 500 molecules per well. Calibration methods are commonly owned
and disclosed in U.S. Provisional Patent Application Ser. No.
60/545,425 which is incorporated herein by reference in
entirety.
Example 5
De Novo Determination of Base Composition of Amplification Products
Using Molecular Mass Modified Deoxynucleotide Triphosphates
[0384] Because the molecular masses of the four natural nucleobases
have a relatively narrow molecular mass range (A=313.058,
G=329.052, C=289.046, T=304.046--See Table 4), a persistent source
of ambiguity in assignment of base composition can occur as
follows: two nucleic acid strands having different base composition
may have a difference of about 1 Da when the base composition
difference between the two strands is GA (-15.994) combined with CT
(+15.000). For example, one 99-mer nucleic acid strand having a
base composition of A.sub.27G.sub.30C.sub.21T.sub.2, has a
theoretical molecular mass of 30779.058 while another 99-mer
nucleic acid strand having a base composition of
A.sub.26G.sub.31C.sub.22T.sub.20 has a theoretical molecular mass
of 30780.052. A 1 Da difference in molecular mass may be within the
experimental error of a molecular mass measurement and thus, the
relatively narrow molecular mass range of the four natural
nucleobases imposes an uncertainty factor.
[0385] The present invention provides for a means for removing this
theoretical 1 Da uncertainty factor through amplification of a
nucleic acid with one mass-tagged nucleobase and three natural
nucleobases. The term "nucleobase" as used herein is synonymous
with other terms in use in the art including "nucleotide,"
"deoxynucleotide," "nucleotide residue," "deoxynucleotide residue,"
"nucleotide triphosphate (NTP)," or deoxynucleotide triphosphate
(dNTP).
[0386] Addition of significant mass to one of the 4 nucleobases
(dNTPs) in an amplification reaction, or in the primers themselves,
will result in a significant difference in mass of the resulting
amplification product (significantly greater than 1 Da) arising
from ambiguities arising from the G A combined with CT event (Table
4). Thus, the same the G A (-15.994) event combined with 5-Iodo-CT
(-110.900) event would result in a molecular mass difference of
126.894. If the molecular mass of the base composition
A.sub.27G.sub.30 5-Iodo-C.sub.21T.sub.21 (33422.958) is compared
with A.sub.26G.sub.315-Iodo-C.sub.22T.sub.20, (33549.852) the
theoretical molecular mass difference is +126.894. The experimental
error of a molecular mass measurement is not significant with
regard to this molecular mass difference. Furthermore, the only
base composition consistent with a measured molecular mass of the
99-mer nucleic acid is A.sub.27G.sub.305-Iodo-C.sub.21T.sub.21. In
contrast, the analogous amplification without the mass tag has 18
possible base compositions. TABLE-US-00005 TABLE 4 Molecular Masses
of Natural Nucleobases and the Mass-Modified Nucleobase 5-Iodo-C
and Mass Differences Resulting from Transitions Nucleobase
Molecular Mass Transition Molecular Mass A 313.058 A-->T -9.012
A 313.058 A-->C -24.012 A 313.058 A-->5-Iodo-C 101.888 A
313.058 A-->G 15.994 T 304.046 T-->A 9.012 T 304.046 T-->C
-15.000 T 304.046 T-->5-Iodo-C 110.900 T 304.046 T-->G 25.006
C 289.046 C-->A 24.012 C 289.046 C-->T 15.000 C 289.046
C-->G 40.006 5-Iodo-C 414.946 5-Iodo-C-->A -101.888 5-Iodo-C
414.946 5-Iodo-C-->T -110.900 5-Iodo-C 414.946 5-Iodo-C-->G
-85.894 G 329.052 G-->A -15.994 G 329.052 G-->T -25.006 G
329.052 G-->C -40.006 G 329.052 G-->5-Iodo-C 85.894
[0387] Mass spectra of bioagent-identifying amplicons were analyzed
independently using a maximum-likelihood processor, such as is
widely used in radar signal processing. This processor, referred to
as GenX, first makes maximum likelihood estimates of the input to
the mass spectrometer for each primer by running matched filters
for each base composition aggregate on the input data. This
includes the GenX response to a calibrant for each primer.
[0388] The algorithm emphasizes performance predictions culminating
in probability-of-detection versus probability-of-false-alarm plots
for conditions involving complex backgrounds of naturally occurring
organisms and environmental contaminants. Matched filters consist
of a priori expectations of signal values given the set of primers
used for each of the bioagents. A genomic sequence database is used
to define the mass base count matched filters. The database
contains the sequences of known bacterial bioagents and includes
threat organisms as well as benign background organisms. The latter
is used to estimate and subtract the spectral signature produced by
the background organisms. A maximum likelihood detection of known
background organisms is implemented using matched filters and a
running-sum estimate of the noise covariance. Background signal
strengths are estimated and used along with the matched filters to
form signatures which are then subtracted. The maximum likelihood
process is applied to this "cleaned up" data in a similar manner
employing matched filters for the organisms and a running-sum
estimate of the noise-covariance for the cleaned up data.
[0389] The amplitudes of all base compositions of
bioagent-identifying amplicons for each primer are calibrated and a
final maximum likelihood amplitude estimate per organism is made
based upon the multiple single primer estimates. Models of all
system noise are factored into this two-stage maximum likelihood
calculation. The processor reports the number of molecules of each
base composition contained in the spectra. The quantity of
amplification product corresponding to the appropriate primer set
is reported as well as the quantities of primers remaining upon
completion of the amplification reaction.
[0390] Base count blurring can be carried out as follows.
"Electronic PCR" can be conducted on nucleotide sequences of the
desired bioagents to obtain the different expected base counts that
could be obtained for each primer pair. See for example,
ncbi.nlm.nih.gov/sutils/e-pcr/; Schuler, Genome Res. 7:541-50,
1997. In one illustrative embodiment, one or more spreadsheets,
such as Microsoft Excel workbooks contain a plurality of
worksheets. First in this example, there is a worksheet with a name
similar to the workbook name; this worksheet contains the raw
electronic PCR data. Second, there is a worksheet named "filtered
bioagents base count" that contains bioagent name and base count;
there is a separate record for each strain after removing sequences
that are not identified with a genus and species and removing all
sequences for bioagents with less than 10 strains. Third, there is
a worksheet, "Sheet1" that contains the frequency of substitutions,
insertions, or deletions for this primer pair. This data is
generated by first creating a pivot table from the data in the
"filtered bioagents base count" worksheet and then executing an
Excel VBA macro. The macro creates a table of differences in base
counts for bioagents of the same species, but different strains.
One of ordinary skill in the art may understand additional pathways
for obtaining similar table differences without undo
experimentation.
[0391] Application of an exemplary script, involves the user
defining a threshold that specifies the fraction of the strains
that are represented by the reference set of base counts for each
bioagent. The reference set of base counts for each bioagent may
contain as many different base counts as are needed to meet or
exceed the threshold. The set of reference base counts is defined
by taking the most abundant strain's base type composition and
adding it to the reference set and then the next most abundant
strain's base type composition is added until the threshold is met
or exceeded. The current set of data was obtained using a threshold
of 55%, which was obtained empirically.
[0392] For each base count not included in the reference base count
set for that bioagent, the script then proceeds to determine the
manner in which the current base count differs from each of the
base counts in the reference set. This difference may be
represented as a combination of substitutions, Si=Xi, and
insertions, Ii=Yi, or deletions, Di=Zi. If there is more than one
reference base count, then the reported difference is chosen using
rules that aim to minimize the number of changes and, in instances
with the same number of changes, minimize the number of insertions
or deletions. Therefore, the primary rule is to identify the
difference with the minimum sum (Xi+Yi) or (Xi+Zi), e.g., one
insertion rather than two substitutions. If there are two or more
differences with the minimum sum, then the one that will be
reported is the one that contains the most substitutions.
[0393] Differences between a base count and a reference composition
are categorized as one, two, or more substitutions, one, two, or
more insertions, one, two, or more deletions, and combinations of
substitutions and insertions or deletions. The different classes of
nucleobase changes and their probabilities of occurrence have been
delineated in U.S. Patent Application Publication No. 2004209260
(U.S. application Ser. No. 10/418,514) which is incorporated herein
by reference in entirety.
Example 6
Use of Broad Range Survey and Division Wide Primer Pairs for
Identification of Bacteria in an Epidemic Surveillance
Investigation
[0394] This investigation employed a set of 16 primer pairs which
is herein designated the "surveillance primer set" and comprises
broad range survey primer pairs, division wide primer pairs and a
single Bacillus clade primer pair. The surveillance primer set is
shown in Table 5 and consists of primer pairs originally listed in
Table 2. This surveillance set comprises primers with T
modifications (note TMOD designation in primer names) which
constitutes a functional improvement with regard to prevention of
non-templated adenylation (vide supra) relative to originally
selected primers which are displayed below in the same row. Primer
pair 449 (non-T modified) has been modified twice. Its predecessors
are primer pairs 70 and 357, displayed below in the same row.
Primer pair 360 has also been modified twice and its predecessors
are primer pairs 17 and 118. TABLE-US-00006 TABLE 5 Bacterial
Primer Pairs of the Surveillance Primer Set Forward Reverse Primer
Primer Primer Pair (SEQ ID (SEQ ID No. Forward Primer Name NO:)
Reverse Primer Name NO:) Target Gene 346 16S_EC_713_732_TMOD_F 202
16S_EC_789_809_TMOD_R 1110 16S rRNA 10 16S_EC_713_732_F 21
16S_EC_789_809 798 16S rRNA 347 16S_EC_785_806_TMOD_F 560
16S_EC_880_897_TMOD_R 1278 16S rRNA 11 16S_EC_785_806_F 118
16S_EC_880_897_R 830 16S rRNA 348 16S_EC_960_981_TMOD_F 706
16S_EC_1054_1073_TMOD_R 895 16S rRNA 14 16S_EC_960_981_F 672
16S_EC_1054_1073_R 735 16S rRNA 349 23S_EC_1826_1843_TMOD_F 401
23S_EC_1906_1924_TMOD_R 1156 23S rRNA 16 23S_EC_1826_1843_F 80
23S_EC_1906_1924_R 805 23S rRNA 352 INFB_EC_1365_1393_TMOD_F 687
INFB_EC_1439_1467_TMOD_R 1411 infB 34 INFB_EC_1365_1393_F 524
INFB_EC_1439_1467_R 1248 infB 354 RPOC_EC_2218_2241_TMOD_F 405
RPOC_EC_2313_2337_TMOD_R 1072 rpoC 52 RPOC_EC_2218_2241_F 81
RPOC_EC_2313_2337_R 790 rpoC 355 SSPE_BA_115_137_TMOD_F 255
SSPE_BA_197_222_TMOD_R 1402 sspE 58 SSPE_BA_115_137_F 45
SSPE_BA_197_222_R 1201 sspE 356 RPLB_EC_650_679_TMOD_F 232
RPLB_EC_739_762_TMOD_R 592 rplB 66 RPLB_EC_650_679_F 98
RPLB_EC_739_762_R 999 rplB 358 VALS_EC_1105_1124_TMOD_F 385
VALS_EC_1195_1218_TMOD_R 1093 valS 71 VALS_EC_1105_1124_F 77
VALS_EC_1195_1218_R 795 valS 359 RPOB_EC_1845_1866_TMOD_F 659
RPOB_EC_1909_1929_TMOD_R 1250 rpoB 72 RPOB_EC_1845_1866_F 233
RPOB_EC_1909_1929_R 825 rpoB 360 23S_EC_2646_2667_TMOD_F 409
23S_EC_2745_2765_TMOD_R 1434 23S rRNA 118 23S_EC_2646_2667_F 84
23S_EC_2745_2765_R 1389 23S rRNA 17 23S_EC_2645_2669_F 408
23S_EC_2744_2761_R 1252 23S rRNA 361 16S_EC_1090_1111_2_TMOD_F 697
16S_EC_1175_1196_TMOD_R 1398 16S rRNA 3 16S_EC_1090_1111_2_F 651
16S_EC_1175_1196_R 1159 16S rRNA 362 RPOB_EC_3799_3821_TMOD_F 581
RPOB_EC_3862_3888_TMOD_R 1325 rpoB 289 RPOB_EC_3799_3821_F 124
RPOB_EC_3862_3888_R 840 rpoB 363 RPOC_EC_2146_2174_TMOD_F 284
RPOC_EC_2227_2245_TMOD_R 898 rpoC 290 RPOC_EC_2146_2174_F 52
RPOC_EC_2227_2245_R 736 rpoC 367 TUFB_EC_957_979_TMOD_F 308
TUFB_EC_1034_1058_TMOD_R 1276 tufB 293 TUFB_EC_957_979_F 55
TUFB_EC_1034_1058_R 829 tufB 449 RPLB_EC_690_710_F 309
RPLB_EC_737_758_R 1336 rplB 357 RPLB_EC_688_710_TMOD_F 296
RPLB_EC_736_757_TMOD_R 1337 rplB 67 RPLB_EC_688_710_F 54
RPLB_EC_736_757_R 842 rplB
[0395] The 16 primer pairs of the surveillance set are used to
produce bioagent identifying amplicons whose base compositions are
sufficiently different amongst all known bacteria at the species
level to identify, at a reasonable confidence level, any given
bacterium at the species level. As shown in Tables 6A-E, common
respiratory bacterial pathogens can be distinguished by the base
compositions of bioagent identifying amplicons obtained using the
16 primer pairs of the surveillance set. In some cases,
triangulation identification improves the confidence level for
species assignment. For example, nucleic acid from Streptococcus
pyogenes can be amplified by nine of the sixteen surveillance
primer pairs and Streptococcus pneumoniae can be amplified by ten
of the sixteen surveillance primer pairs. The base compositions of
the biogent identifying amplicons are identical for only one of the
analogous bioagent identifying amplicons and differ in all of the
remaining analogous bioagent identifying amplicons by up to four
bases per bioagent identifying amplicon. The resolving power of the
surveillance set was confirmed by determination of base
compositions for 120 isolates of respiratory pathogens representing
70 different bacterial species and the results indicated that
natural variations (usually only one or two base substitutions per
bioagent identifying amplicon) amongst multiple isolates of the
same species did not prevent correct identification of major
pathogenic organisms at the species level.
[0396] Bacillus anthracis is a well known biological warfare agent
which has emerged in domestic terrorism in recent years. Since it
was envisioned to produce bioagent identifying amplicons for
identification of Bacillus anthracis, additional drill-down
analysis primers were designed to target genes present on virulence
plasmids of Bacillus anthracis so that additional confidence could
be reached in positive identification of this pathogenic organism.
Three drill-down analysis primers were designed and are listed in
Tables 2 and 6. In Table 6, the drill-down set comprises primers
with T modifications (note TMOD designation in primer names) which
constitutes a functional improvement with regard to prevention of
non-templated adenylation (vide supra) relative to originally
selected primers which are displayed below in the same row.
TABLE-US-00007 TABLE 6 Drill-Down Primer Pairs for Confirmation of
Identification of Bacillus anthracis Forward Reverse Primer Primer
Primer Pair (SEQ ID (SEQ ID No. Forward Primer Name NO:) Reverse
Primer Name NO:) Target Gene 350 CAPC_BA_274_303_TMOD_F 476
CAPC_BA_349_376_TMOD_R 1314 capC 24 CAPC_BA_274_303_F 109
CAPC_BA_349_376_R 837 capC 351 CYA_BA_1353_1379_TMOD_F 355
CYA_BA_1448_1467_TMOD_R 1423 cyA 30 CYA_BA_1353_1379_F 64
CYA_BA_1448_1467_R 1342 cyA 353 LEF_BA_756_781_TMOD_F 220
LEF_BA_843_872_TMOD_R 1394 lef 37 LEF_BA_756_781_F 26
LEF_BA_843_872_R 1135 lef
[0397] Phylogenetic coverage of bacterial space of the sixteen
surveillance primers of Table 5 and the three Bacillus anthracis
drill-down primers of Table 6 is shown in FIG. 3 which lists common
pathogenic bacteria. FIG. 3 is not meant to be comprehensive in
illustrating all species identified by the primers. Only pathogenic
bacteria are listed as representative examples of the bacterial
species that can be identified by the primers and methods of the
present invention. Nucleic acid of groups of bacteria enclosed
within the polygons of FIG. 3 can be amplified to obtain bioagent
identifying amplicons using the primer pair numbers listed in the
upper right hand corner of each polygon. Primer coverage for
polygons within polygons is additive. As an illustrative example,
bioagent identifying amplicons can be obtained for Chlamydia
trachomatis by amplification with, for example, primer pairs
346-349, 360 and 361, but not with any of the remaining primers of
the surveillance primer set. On the other hand, bioagent
identifying amplicons can be obtained from nucleic acid originating
from Bacillus anthracis (located within 5 successive polygons)
using, for example, any of the following primer pairs: 346-349,
360, 361 (base polygon), 356, 449 (second polygon), 352 (third
polygon), 355 (fourth polygon), 350, 351 and 353 (fifth polygon).
Multiple coverage of a given organism with multiple primers
provides for increased confidence level in identification of the
organism as a result of enabling broad triangulation
identification.
[0398] In Tables 7A-E, base compositions of respiratory pathogens
for primer target regions are shown. Two entries in a cell,
represent variation in ribosomal DNA operons. The most predominant
base composition is shown first and the minor (frequently a single
operon) is indicated by an asterisk (*). Entries with NO DATA mean
that the primer would not be expected to prime this species due to
mismatches between the primer and target region, as determined by
theoretical PCR. TABLE-US-00008 TABLE 7A Base Compositions of
Common Respiratory Pathogens for Bioagent Identifying Amplicons
Corresponding to Primer Pair Nos: 346, 347 and 348 Primer 346
Primer 347 Primer 348 Organism Strain [A G C T] [A G C T] [A G C T]
Klebsiella MGH78578 [29 32 25 13] [23 38 28 26] [26 32 28 30]
pneumoniae [29 31 25 13]* [23 37 28 26]* [26 31 28 30]* Yersinia
pestis CO-92 Biovar [29 32 25 13] [22 39 28 26] [29 30 28 29]
Orientalis [30 30 27 29]* Yersinia pestis KIM5 P12 (Biovar [29 32
25 13] [22 39 28 26] [29 30 28 29] Mediaevalis) Yersinia pestis
91001 [29 32 25 13] [22 39 28 26] [29 30 28 29] [30 30 27 29]*
Haemophilus KW20 [28 31 23 17] [24 37 25 27] [29 30 28 29]
influenzae Pseudomonas PAO1 [30 31 23 15] [26 36 29 24] [26 32 29
29] aeruginosa [27 36 29 23]* Pseudomonas Pf0-1 [30 31 23 15] [26
35 29 25] [28 31 28 29] fluorescens Pseudomonas KT2440 [30 31 23
15] [28 33 27 27] [27 32 29 28] putida Legionella Philadelphia-1
[30 30 24 15] [33 33 23 27] [29 28 28 31] pneumophila Francisella
schu 4 [32 29 22 16] [28 38 26 26] [25 32 28 31] tularensis
Bordetella Tohama I [30 29 24 16] [23 37 30 24] [30 32 30 26]
pertussis Burkholderia J2315 [29 29 27 14] [27 32 26 29] [27 36 31
24] cepacia [20 42 35 19]* Burkholderia K96243 [29 29 27 14] [27 32
26 29] [27 36 31 24] pseudomallei Neisseria FA 1090, ATCC [29 28 24
18] [27 34 26 28] [24 36 29 27] gonorrhoeae 700825 Neisseria MC58
(serogroup B) [29 28 26 16] [27 34 27 27] [25 35 30 26]
meningitidis Neisseria serogroup C, FAM18 [29 28 26 16] [27 34 27
27] [25 35 30 26] meningitidis Neisseria Z2491 (serogroup A) [29 28
26 16] [27 34 27 27] [25 35 30 26] meningitidis Chlamydophila
TW-183 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila
AR39 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila
CWL029 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila
J138 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Corynebacterium
NCTC13129 [29 34 21 15] [22 38 31 25] [22 33 25 34] diphtheriae
Mycobacterium k10 [27 36 21 15] [22 37 30 28] [21 36 27 30] avium
Mycobacterium 104 [27 36 21 15] [22 37 30 28] [21 36 27 30] avium
Mycobacterium CSU#93 [27 36 21 15] [22 37 30 28] [21 36 27 30]
tuberculosis Mycobacterium CDC 1551 [27 36 21 15] [22 37 30 28] [21
36 27 30] tuberculosis Mycobacterium H37Rv (lab strain) [27 36 21
15] [22 37 30 28] [21 36 27 30] tuberculosis Mycoplasma M129 [31 29
19 20] NO DATA NO DATA pneumoniae Staphylococcus MRSA252 [27 30 21
21] [25 35 30 26] [30 29 30 29] aureus [29 31 30 29]*
Staphylococcus MSSA476 [27 30 21 21] [25 35 30 26] [30 29 30 29]
aureus [30 29 29 30]* Staphylococcus COL [27 30 21 21] [25 35 30
26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus Mu50 [27 30
21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]*
Staphylococcus MW2 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus
[30 29 29 30]* Staphylococcus N315 [27 30 21 21] [25 35 30 26] [30
29 30 29] aureus [30 29 29 30]* Staphylococcus NCTC 8325 [27 30 21
21] [25 35 30 26] [30 29 30 29] aureus [25 35 31 26]* [30 29 29 30]
Streptococcus NEM316 [26 32 23 18] [24 36 31 25] [25 32 29 30]
agalactiae [24 36 30 26]* Streptococcus NC_002955 [26 32 23 18] [23
37 31 25] [29 30 25 32] equi Streptococcus MGAS8232 [26 32 23 18]
[24 37 30 25] [25 31 29 31] pyogenes Streptococcus MGAS315 [26 32
23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus SSI-1 [26
32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus
MGAS10394 [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes
Streptococcus Manfredo (M5) [26 32 23 18] [24 37 30 25] [25 31 29
31] pyogenes Streptococcus SF370 (M1) [26 32 23 18] [24 37 30 25]
[25 31 29 31] pyogenes Streptococcus 670 [26 32 23 18] [25 35 28
28] [25 32 29 30] pneumoniae Streptococcus R6 [26 32 23 18] [25 35
28 28] [25 32 29 30] pneumoniae Streptococcus TIGR4 [26 32 23 18]
[25 35 28 28] [25 32 30 29] pneumoniae Streptococcus NCTC7868 [25
33 23 18] [24 36 31 25] [25 31 29 31] gordonii Streptococcus NCTC
12261 [26 32 23 18] [25 35 30 26] [25 32 29 30] mitis [24 31 35
29]* Streptococcus UA159 [24 32 24 19] [25 37 30 24] [28 31 26 31]
mutans
[0399] TABLE-US-00009 TABLE 7B Base Compositions of Common
Respiratory Pathogens for Bioagent Identifying Amplicons
Corresponding to Primer Pair Nos: 349, 360, and 356 Primer 349
Primer 360 Primer 356 Organism Strain [A G C T] [A G C T] [A G C T]
Klebsiella MGH78578 [25 31 25 22] [33 37 25 27] NO DATA pneumoniae
Yersinia pestis CO-92 Biovar [25 31 27 20] [34 35 25 28] NO DATA
Orientalis [25 32 26 20]* Yersinia pestis KIM5 P12 (Biovar [25 31
27 20] [34 35 25 28] NO DATA Mediaevalis) [25 32 26 20]* Yersinia
pestis 91001 [25 31 27 20] [34 35 25 28] NO DATA Haemophilus KW20
[28 28 25 20] [32 38 25 27] NO DATA influenzae Pseudomonas PAO1 [24
31 26 20] [31 36 27 27] NO DATA aeruginosa [31 36 27 28]*
Pseudomonas Pf0-1 NO DATA [30 37 27 28] NO DATA fluorescens [30 37
27 28] Pseudomonas KT2440 [24 31 26 20] [30 37 27 28] NO DATA
putida Legionella Philadelphia-1 [23 30 25 23] [30 39 29 24] NO
DATA pneumophila Francisella schu 4 [26 31 25 19] [32 36 27 27] NO
DATA tularensis Bordetella Tohama I [21 29 24 18] [33 36 26 27] NO
DATA pertussis Burkholderia J2315 [23 27 22 20] [31 37 28 26] NO
DATA cepacia Burkholderia K96243 [23 27 22 20] [31 37 28 26] NO
DATA pseudomallei Neisseria FA 1090, ATCC 700825 [24 27 24 17] [34
37 25 26] NO DATA gonorrhoeae Neisseria MC58 (serogroup B) [25 27
22 18] [34 37 25 26] NO DATA meningitidis Neisseria serogroup C,
FAM18 [25 26 23 18] [34 37 25 26] NO DATA meningitidis Neisseria
Z2491 (serogroup A) [25 26 23 18] [34 37 25 26] NO DATA
meningitidis Chlamydophila TW-183 [30 28 27 18] NO DATA NO DATA
pneumoniae Chlamydophila AR39 [30 28 27 18] NO DATA NO DATA
pneumoniae Chlamydophila CWL029 [30 28 27 18] NO DATA NO DATA
pneumoniae Chlamydophila J138 [30 28 27 18] NO DATA NO DATA
pneumoniae Corynebacterium NCTC13129 NO DATA [29 40 28 25] NO DATA
diphtheriae Mycobacterium k10 NO DATA [33 35 32 22] NO DATA avium
Mycobacterium 104 NO DATA [33 35 32 22] NO DATA avium Mycobacterium
CSU#93 NO DATA [30 36 34 22] NO DATA tuberculosis Mycobacterium CDC
1551 NO DATA [30 36 34 22] NO DATA tuberculosis Mycobacterium H37Rv
(lab strain) NO DATA [30 36 34 22] NO DATA tuberculosis Mycoplasma
M129 [28 30 24 19] [34 31 29 28] NO DATA pneumoniae Staphylococcus
MRSA252 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus
Staphylococcus MSSA476 [26 30 25 20] [31 38 24 29] [33 30 31 27]
aureus Staphylococcus COL [26 30 25 20] [31 38 24 29] [33 30 31 27]
aureus Staphylococcus Mu50 [26 30 25 20] [31 38 24 29] [33 30 31
27] aureus Staphylococcus MW2 [26 30 25 20] [31 38 24 29] [33 30 31
27] aureus Staphylococcus N315 [26 30 25 20] [31 38 24 29] [33 30
31 27] aureus Staphylococcus NCTC 8325 [26 30 25 20] [31 38 24 29]
[33 30 31 27] aureus Streptococcus NEM316 [28 31 22 20] [33 37 24
28] [37 30 28 26] agalactiae Streptococcus NC_002955 [28 31 23 19]
[33 38 24 27] [37 31 28 25] equi Streptococcus MGAS8232 [28 31 23
19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus MGAS315 [28
31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus SSI-1
[28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus
MGAS10394 [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes
Streptococcus Manfredo (M5) [28 31 23 19] [33 37 24 28] [38 31 29
23] pyogenes Streptococcus SF370 (M1) [28 31 23 19] [33 37 24 28]
[38 31 29 23] pyogenes [28 31 22 20]* Streptococcus 670 [28 31 22
20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus R6 [28 31
22 20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus TIGR4
[28 31 22 20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus
NCTC7868 [28 32 23 20] [34 36 24 28] [36 31 29 25] gordonii
Streptococcus NCTC 12261 [28 31 22 20] [34 36 24 28] [37 30 29 25]
mitis [29 30 22 20]* Streptococcus UA159 [26 32 23 22] [34 37 24
27] NO DATA mutans
[0400] TABLE-US-00010 TABLE 7C Base Compositions of Common
Respiratory Pathogens for Bioagent Identifying Amplicons
Corresponding to Primer Pair Nos: 449, 354, and 352 Primer 449
Primer 354 Primer 352 Organism Strain [A G C T] [A G C T] [A G C T]
Klebsiella MGH78578 NO DATA [27 33 36 26] NO DATA pneumoniae
Yersinia pestis CO-92 Biovar NO DATA [29 31 33 29] [32 28 20 25]
Orientalis Yersinia pestis KIM5 P12 (Biovar NO DATA [29 31 33 29]
[32 28 20 25] Mediaevalis) Yersinia pestis 91001 NO DATA [29 31 33
29] NO DATA Haemophilus KW20 NO DATA [30 29 31 32] NO DATA
influenzae Pseudomonas PAO1 NO DATA [26 33 39 24] NO DATA
aeruginosa Pseudomonas Pf0-1 NO DATA [26 33 34 29] NO DATA
fluorescens Pseudomonas KT2440 NO DATA [25 34 36 27] NO DATA putida
Legionella Philadelphia-1 NO DATA NO DATA NO DATA pneumophila
Francisella schu 4 NO DATA [33 32 25 32] NO DATA tularensis
Bordetella Tohama I NO DATA [26 33 39 24] NO DATA pertussis
Burkholderia J2315 NO DATA [25 37 33 27] NO DATA cepacia
Burkholderia K96243 NO DATA [25 37 34 26] NO DATA pseudomallei
Neisseria FA 1090, ATCC 700825 [17 23 22 10] [29 31 32 30] NO DATA
gonorrhoeae Neisseria MC58 (serogroup B) NO DATA [29 30 32 31] NO
DATA meningitidis Neisseria serogroup C, FAM18 NO DATA [29 30 32
31] NO DATA meningitidis Neisseria Z2491 (serogroup A) NO DATA [29
30 32 31] NO DATA meningitidis Chlamydophila TW-183 NO DATA NO DATA
NO DATA pneumoniae Chlamydophila AR39 NO DATA NO DATA NO DATA
pneumoniae Chlamydophila CWL029 NO DATA NO DATA NO DATA pneumoniae
Chlamydophila J138 NO DATA NO DATA NO DATA pneumoniae
Corynebacterium NCTC13129 NO DATA NO DATA NO DATA diphtheriae
Mycobacterium k10 NO DATA NO DATA NO DATA avium Mycobacterium 104
NO DATA NO DATA NO DATA avium Mycobacterium CSU#93 NO DATA NO DATA
NO DATA tuberculosis Mycobacterium CDC 1551 NO DATA NO DATA NO DATA
tuberculosis Mycobacterium H37Rv (lab strain) NO DATA NO DATA NO
DATA tuberculosis Mycoplasma M129 NO DATA NO DATA NO DATA
pneumoniae Staphylococcus MRSA252 [17 20 21 17] [30 27 30 35] [36
24 19 26] aureus Staphylococcus MSSA476 [17 20 21 17] [30 27 30 35]
[36 24 19 26] aureus Staphylococcus COL [17 20 21 17] [30 27 30 35]
[35 24 19 27] aureus Staphylococcus Mu50 [17 20 21 17] [30 27 30
35] [36 24 19 26] aureus Staphylococcus MW2 [17 20 21 17] [30 27 30
35] [36 24 19 26] aureus Staphylococcus N315 [17 20 21 17] [30 27
30 35] [36 24 19 26] aureus Staphylococcus NCTC 8325 [17 20 21 17]
[30 27 30 35] [35 24 19 27] aureus Streptococcus NEM316 [22 20 19
14] [26 31 27 38] [29 26 22 28] agalactiae Streptococcus NC_002955
[22 21 19 13] NO DATA NO DATA equi Streptococcus MGAS8232 [23 21 19
12] [24 32 30 36] NO DATA pyogenes Streptococcus MGAS315 [23 21 19
12] [24 32 30 36] NO DATA pyogenes Streptococcus SSI-1 [23 21 19
12] [24 32 30 36] NO DATA pyogenes Streptococcus MGAS10394 [23 21
19 12] [24 32 30 36] NO DATA pyogenes Streptococcus Manfredo (M5)
[23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus SF370
(M1) [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus 670
[22 20 19 14] [25 33 29 35] [30 29 21 25] pneumoniae Streptococcus
R6 [22 20 19 14] [25 33 29 35] [30 29 21 25] pneumoniae
Streptococcus TIGR4 [22 20 19 14] [25 33 29 35] [30 29 21 25]
pneumoniae Streptococcus NCTC7868 [21 21 19 14] NO DATA [29 26 22
28] gordonii Streptococcus NCTC 12261 [22 20 19 14] [26 30 32 34]
NO DATA mitis Streptococcus UA159 NO DATA NO DATA NO DATA
mutans
[0401] TABLE-US-00011 TABLE 7D Base Compositions of Common
Respiratory Pathogens for Bioagent Identifying Amplicons
Corresponding to Primer Pair Nos: 355, 358, and 359 Primer 355
Primer 358 Primer 359 Organism Strain [A G C T] [A G C T] [A G C T]
Klebsiella MGH78578 NO DATA [24 39 33 20] [25 21 24 17] pneumoniae
Yersinia pestis CO-92 Biovar NO DATA [26 34 35 21] [23 23 19 22]
Orientalis Yersinia pestis KIM5 P12 (Biovar NO DATA [26 34 35 21]
[23 23 19 22] Mediaevalis) Yersinia pestis 91001 NO DATA [26 34 35
21] [23 23 19 22] Haemophilus KW20 NO DATA NO DATA NO DATA
influenzae Pseudomonas PAO1 NO DATA NO DATA NO DATA aeruginosa
Pseudomonas Pf0-1 NO DATA NO DATA NO DATA fluorescens Pseudomonas
KT2440 NO DATA [21 37 37 21] NO DATA putida Legionella
Philadelphia-1 NO DATA NO DATA NO DATA pneumophila Francisella schu
4 NO DATA NO DATA NO DATA tularensis Bordetella Tohama I NO DATA NO
DATA NO DATA pertussis Burkholderia J2315 NO DATA NO DATA NO DATA
cepacia Burkholderia K96243 NO DATA NO DATA NO DATA pseudomallei
Neisseria FA 1090, ATCC 700825 NO DATA NO DATA NO DATA gonorrhoeae
Neisseria MC58 (serogroup B) NO DATA NO DATA NO DATA meningitidis
Neisseria serogroup C, FAM18 NO DATA NO DATA NO DATA meningitidis
Neisseria Z2491 (serogroup A) NO DATA NO DATA NO DATA meningitidis
Chlamydophila TW-183 NO DATA NO DATA NO DATA pneumoniae
Chlamydophila AR39 NO DATA NO DATA NO DATA pneumoniae Chlamydophila
CWL029 NO DATA NO DATA NO DATA pneumoniae Chlamydophila J138 NO
DATA NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA
NO DATA NO DATA diphtheriae Mycobacterium k10 NO DATA NO DATA NO
DATA avium Mycobacterium 104 NO DATA NO DATA NO DATA avium
Mycobacterium CSU#93 NO DATA NO DATA NO DATA tuberculosis
Mycobacterium CDC 1551 NO DATA NO DATA NO DATA tuberculosis
Mycobacterium H37Rv (lab strain) NO DATA NO DATA NO DATA
tuberculosis Mycoplasma M129 NO DATA NO DATA NO DATA pneumoniae
Staphylococcus MRSA252 NO DATA NO DATA NO DATA aureus
Staphylococcus MSSA476 NO DATA NO DATA NO DATA aureus
Staphylococcus COL NO DATA NO DATA NO DATA aureus Staphylococcus
Mu50 NO DATA NO DATA NO DATA aureus Staphylococcus MW2 NO DATA NO
DATA NO DATA aureus Staphylococcus N315 NO DATA NO DATA NO DATA
aureus Staphylococcus NCTC 8325 NO DATA NO DATA NO DATA aureus
Streptococcus NEM316 NO DATA NO DATA NO DATA agalactiae
Streptococcus NC_002955 NO DATA NO DATA NO DATA equi Streptococcus
MGAS8232 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS315 NO
DATA NO DATA NO DATA pyogenes Streptococcus SSI-1 NO DATA NO DATA
NO DATA pyogenes Streptococcus MGAS10394 NO DATA NO DATA NO DATA
pyogenes Streptococcus Manfredo (M5) NO DATA NO DATA NO DATA
pyogenes Streptococcus SF370 (M1) NO DATA NO DATA NO DATA pyogenes
Streptococcus 670 NO DATA NO DATA NO DATA pneumoniae Streptococcus
R6 NO DATA NO DATA NO DATA pneumoniae Streptococcus TIGR4 NO DATA
NO DATA NO DATA pneumoniae Streptococcus NCTC7868 NO DATA NO DATA
NO DATA gordonii Streptococcus NCTC 12261 NO DATA NO DATA NO DATA
mitis Streptococcus UA159 NO DATA NO DATA NO DATA mutans
[0402] TABLE-US-00012 TABLE 7E Base Compositions of Common
Respiratory Pathogens for Bioagent Identifying Amplicons
Corresponding to Primer Pair Nos: 362, 363, and 367 Primer 362
Primer 363 Primer 367 Organism Strain [A G C T] [A G C T] [A G C T]
Klebsiella MGH78578 [21 33 22 16] [16 34 26 26] NO DATA pneumoniae
Yersinia pestis CO-92 Biovar [20 34 18 20] NO DATA NO DATA
Orientalis Yersinia pestis KIM5 P12 (Biovar [20 34 18 20] NO DATA
NO DATA Mediaevalis) Yersinia pestis 91001 [20 34 18 20] NO DATA NO
DATA Haemophilus KW20 NO DATA NO DATA NO DATA influenzae
Pseudomonas PAO1 [19 35 21 17] [16 36 28 22] NO DATA aeruginosa
Pseudomonas Pf0-1 NO DATA [18 35 26 23] NO DATA fluorescens
Pseudomonas KT2440 NO DATA [16 35 28 23] NO DATA putida Legionella
Philadelphia-1 NO DATA NO DATA NO DATA pneumophila Francisella schu
4 NO DATA NO DATA NO DATA tularensis Bordetella Tohama I [20 31 24
17] [15 34 32 21] [26 25 34 19] pertussis Burkholderia J2315 [20 33
21 18] [15 36 26 25] [25 27 32 20] cepacia Burkholderia K96243 [19
34 19 20] [15 37 28 22] [25 27 32 20] pseudomallei Neisseria FA
1090, ATCC 700825 NO DATA NO DATA NO DATA gonorrhoeae Neisseria
MC58 (serogroup B) NO DATA NO DATA NO DATA meningitidis Neisseria
serogroup C, FAM18 NO DATA NO DATA NO DATA meningitidis Neisseria
Z2491 (serogroup A) NO DATA NO DATA NO DATA meningitidis
Chlamydophila TW-183 NO DATA NO DATA NO DATA pneumoniae
Chlamydophila AR39 NO DATA NO DATA NO DATA pneumoniae Chlamydophila
CWL029 NO DATA NO DATA NO DATA pneumoniae Chlamydophila J138 NO
DATA NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA
NO DATA NO DATA diphtheriae Mycobacterium k10 [19 34 23 16] NO DATA
[24 26 35 19] avium Mycobacterium 104 [19 34 23 16] NO DATA [24 26
35 19] avium Mycobacterium CSU#93 [19 31 25 17] NO DATA [25 25 34
20] tuberculosis Mycobacterium CDC 1551 [19 31 24 18] NO DATA [25
25 34 20] tuberculosis Mycobacterium H37Rv (lab strain) [19 31 24
18] NO DATA [25 25 34 20] tuberculosis Mycoplasma M129 NO DATA NO
DATA NO DATA pneumoniae Staphylococcus MRSA252 NO DATA NO DATA NO
DATA aureus Staphylococcus MSSA476 NO DATA NO DATA NO DATA aureus
Staphylococcus COL NO DATA NO DATA NO DATA aureus Staphylococcus
Mu50 NO DATA NO DATA NO DATA aureus Staphylococcus MW2 NO DATA NO
DATA NO DATA aureus Staphylococcus N315 NO DATA NO DATA NO DATA
aureus Staphylococcus NCTC 8325 NO DATA NO DATA NO DATA aureus
Streptococcus NEM316 NO DATA NO DATA NO DATA agalactiae
Streptococcus NC_002955 NO DATA NO DATA NO DATA equi Streptococcus
MGAS8232 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS315 NO
DATA NO DATA NO DATA pyogenes Streptococcus SSI-1 NO DATA NO DATA
NO DATA pyogenes Streptococcus MGAS10394 NO DATA NO DATA NO DATA
pyogenes Streptococcus Manfredo (M5) NO DATA NO DATA NO DATA
pyogenes Streptococcus SF370 (M1) NO DATA NO DATA NO DATA pyogenes
Streptococcus 670 NO DATA NO DATA NO DATA pneumoniae Streptococcus
R6 [20 30 19 23] NO DATA NO DATA pneumoniae Streptococcus TIGR4 [20
30 19 23] NO DATA NO DATA pneumoniae Streptococcus NCTC7868 NO DATA
NO DATA NO DATA gordonii Streptococcus NCTC 12261 NO DATA NO DATA
NO DATA mitis Streptococcus UA159 NO DATA NO DATA NO DATA
mutans
[0403] Four sets of throat samples from military recruits at
different military facilities taken at different time points were
analyzed using the primers of the present invention. The first set
was collected at a military training center from Nov. 1 to Dec. 20,
2002 during one of the most severe outbreaks of pneumonia
associated with group A Streptococcus in the United States since
1968. During this outbreak, fifty-one throat swabs were taken from
both healthy and hospitalized recruits and plated on blood agar for
selection of putative group A Streptococcus colonies. A second set
of 15 original patient specimens was taken during the height of
this group A Streptococcus-associated respiratory disease outbreak.
The third set were historical samples, including twenty-seven
isolates of group A Streptococcus, from disease outbreaks at this
and other military training facilities during previous years. The
fourth set of samples was collected from five geographically
separated military facilities in the continental U.S. in the winter
immediately following the severe November/December 2002
outbreak.
[0404] Pure colonies isolated from group A Streptococcus-selective
media from all four collection periods were analyzed with the
surveillance primer set. All samples showed base compositions that
precisely matched the four completely sequenced strains of
Streptococcus pyogenes. Shown in FIG. 4 is a 3D diagram of base
composition (axes A, G and C) of bioagent identifying amplicons
obtained with primer pair number 14 (a precursor of primer pair
number 348 which targets 16S rRNA). The diagram indicates that the
experimentally determined base compositions of the clinical samples
closely match the base compositions expected for Streptococcus
pyogenes and are distinct from the expected base compositions of
other organisms.
[0405] In addition to the identification of Streptococcus pyogenes,
other potentially pathogenic organisms were identified
concurrently. Mass spectral analysis of a sample whose nucleic acid
was amplified by primer pair number 349 (SEQ ID NOs: 401:1156)
exhibited signals of bioagent identifying amplicons with molecular
masses that were found to correspond to analogous base compositions
of bioagent identifying amplicons of Streptococcus pyogenes (A27
G32 C24 T18), Neisseria meningitidis (A25 G27 C22 T18), and
Haemophilus influenzae (A28 G28 C25 T20) (see FIG. 5 and Table 7B).
These organisms were present in a ratio of 4:5:20 as determined by
comparison of peak heights with peak height of an internal PCR
calibration standard as described in commonly owned U.S. Patent
Application Ser. No. 60/545,425 which is incorporated herein by
reference in its entirety.
[0406] Since certain division-wide primers that target housekeeping
genes are designed to provide coverage of specific divisions of
bacteria to increase the confidence level for identification of
bacterial species, they are not expected to yield bioagent
identifying amplicons for organisms outside of the specific
divisions. For example, primer pair number 356 (SEQ ID NOs:
449:1380) primarily amplifies the nucleic acid of members of the
classes Bacilli and Clostridia and is not expected to amplify
proteobacteria such as Neisseria meningitidis and Haemophilus
influenzae. As expected, analysis of the mass spectrum of
amplification products obtained with primer pair number 356 does
not indicate the presence of Neisseria meningitidis and Haemophilus
influenzae but does indicate the presence of Streptococcus pyogenes
(FIGS. 3 and 6, Table 7B). Thus, these primers or types of primers
can confirm the absence of particular bioagents from a sample.
[0407] The 15 throat swabs from military recruits were found to
contain a relatively small set of microbes in high abundance. The
most common were Haemophilus influenza, Neisseria meningitides, and
Streptococcus pyogenes. Staphylococcus epidermidis, Moraxella
cattarhalis, Corynebacterium pseudodiphtheriticum, and
Staphylococcus aureus were present in fewer samples. An equal
number of samples from healthy volunteers from three different
geographic locations, were identically analyzed. Results indicated
that the healthy volunteers have bacterial flora dominated by
multiple, commensal non-beta-hemolytic Streptococcal species,
including the viridans group streptococci (S. parasangunis, S.
vestibularis, S. mitis, S. oralis and S. pneumoniae; data not
shown), and none of the organisms found in the military recruits
were found in the healthy controls at concentrations detectable by
mass spectrometry. Thus, the military recruits in the midst of a
respiratory disease outbreak had a dramatically different microbial
population than that experienced by the general population in the
absence of epidemic disease.
Example 7
Triangulation Genotyping Analysis for Determination of emm-Type of
Streptococcus pyogenes in Epidemic Surveillance
[0408] As a continuation of the epidemic surveillance investigation
of Example 6, determination of sub-species characteristics
(genotyping) of Streptococcus pyogenes, was carried out based on a
strategy that generates strain-specific signatures according to the
rationale of Multi-Locus Sequence Typing (MLST). In classic MLST
analysis, internal fragments of several housekeeping genes are
amplified and sequenced (Enright et al. Infection and Immunity,
2001, 69, 2416-2427). In classic MLST analysis, internal fragments
of several housekeeping genes are amplified and sequenced. In the
present investigation, bioagent identifying amplicons from
housekeeping genes were produced using drill-down primers and
analyzed by mass spectrometry. Since mass spectral analysis results
in molecular mass, from which base composition can be determined,
the challenge was to determine whether resolution of emm
classification of strains of Streptococcus pyogenes could be
determined.
[0409] For the purpose of development of a triangulation genotyping
assay, an alignment was constructed of concatenated alleles of
seven MLST housekeeping genes (glucose kinase (gki), glutamine
transporter protein (gtr), glutamate racemase (murI), DNA mismatch
repair protein (mutS), xanthine phosphoribosyl transferase (xpt),
and acetyl-CoA acetyl transferase (yqiL)) from each of the 212
previously emm-typed strains of Streptococcus pyogenes. From this
alignment, the number and location of primer pairs that would
maximize strain identification via base composition was determined.
As a result, 6 primer pairs were chosen as standard drill-down
primers for determination of emm-type of Streptococcus pyogenes.
These six primer pairs are displayed in Table 8. This drill-down
set comprises primers with T modifications (note TMOD designation
in primer names) which constitutes a functional improvement with
regard to prevention of non-templated adenylation (vide supra)
relative to originally selected primers which are displayed below
in the same row. TABLE-US-00013 TABLE 8 Triangulation Genotyping
Analysis Primer Pairs for Group A Streptococcus Drill-Down Forward
Primer Primer (SEQ ID Reverse Primer Target Pair No. Forward Primer
Name NO:) Reverse Primer Name (SEQ ID NO:) Gene 442
SP101_SPET11_358_387_TMOD_F 588 SP101_SPET11_448_473_TMOD_R 998 gki
80 SP101_SPET11_358_387_F 126 SP101_SPET11_448_473_TMOD_R 766 gki
443 SP101_SPET11_600_629_TMOD_F 348 SP101_SPET11_686_714_TMOD_R
1018 gtr 81 SP101_SPET11_600_629_F 62 SP101_SPET11_686_714_R 772
gtr 426 SP101_SPET11_1314_1336_TMOD_F 363
SP101_SPET11_1403_1431_TMOD_R 849 murI 86 SP101_SPET11_1314_1336_F
68 SP101_SPET11_1403_1431_R 711 murI 430
SP101_SPET11_1807_1835_TMOD_F 235 SP101_SPET11_1901_1927_TMOD_R
1439 mutS 90 SP101_SPET11_1807_1835_F 33 SP101_SPET11_1901_1927_R
1412 mutS 438 SP101_SPET11_3075_3103_TMOD_F 473
SP101_SPET11_3168_3196_TMOD_R 875 xpt 96 SP101_SPET11_3075_3103_F
108 SP101_SPET11_3168_3196_R 715 xpt 441
SP101_SPET11_3511_3535_TMOD_F 531 SP101_SPET11_3605_3629_TMOD_R
1294 yqiL 98 SP101_SPET11_3511_3535_F 116 SP101_SPET11_3605_3629_R
832 yqiL
[0410] The primers of Table 8 were used to produce bioagent
identifying amplicons from nucleic acid present in the clinical
samples. The bioagent identifying amplicons which were subsequently
analyzed by mass spectrometry and base compositions corresponding
to the molecular masses were calculated.
[0411] Of the 51 samples taken during the peak of the
November/December 2002 epidemic (Table 9A-C rows 1-3), all except
three samples were found to represent emm3, a Group A Streptococcus
genotype previously associated with high respiratory virulence. The
three outliers were from samples obtained from healthy individuals
and probably represent non-epidemic strains. Archived samples
(Tables 9A-C rows 5-13) from historical collections showed a
greater heterogeneity of base compositions and emm types as would
be expected from different epidemics occurring at different places
and dates. The results of the mass spectrometry analysis and emm
gene sequencing were found to be concordant for the epidemic and
historical samples. TABLE-US-00014 TABLE 9A Base Composition
Analysis of Bioagent Identifying Amplicons of Group A Streptococcus
samples from Six Military Installations Obtained with Primer Pair
Nos. 426 and 430 emm-type by murI mutS # of Mass emm-Gene Location
(Primer Pair (Primer Pair Instances Spectrometry Sequencing
(sample) Year No. 426) No. 430) 48 3 3 MCRD San 2002 A39 G25 C20
T34 A38 G27 C23 T33 2 6 6 Diego A40 G24 C20 T34 A38 G27 C23 T33 1
28 28 (Cultured) A39 G25 C20 T34 A38 G27 C23 T33 15 3 ND A39 G25
C20 T34 A38 G27 C23 T33 6 3 3 NHRC San 2003 A39 G25 C20 T34 A38 G27
C23 T33 3 5, 58 5 Diego- A40 G24 C20 T34 A38 G27 C23 T33 6 6 6
Archive A40 G24 C20 T34 A38 G27 C23 T33 1 11 11 (Cultured) A39 G25
C20 T34 A38 G27 C23 T33 3 12 12 A40 G24 C20 T34 A38 G26 C24 T33 1
22 22 A39 G25 C20 T34 A38 G27 C23 T33 3 25, 75 75 A39 G25 C20 T34
A38 G27 C23 T33 4 44/61, 82, 9 44/61 A40 G24 C20 T34 A38 G26 C24
T33 2 53, 91 91 A39 G25 C20 T34 A38 G27 C23 T33 1 2 2 Ft. 2003 A39
G25 C20 T34 A38 G27 C24 T32 2 3 3 Leonard A39 G25 C20 T34 A38 G27
C23 T33 1 4 4 Wood A39 G25 C20 T34 A38 G27 C23 T33 1 6 6 (Cultured)
A40 G24 C20 T34 A38 G27 C23 T33 11 25 or 75 75 A39 G25 C20 T34 A38
G27 C23 T33 1 25, 75, 33, 75 A39 G25 C20 T34 A38 G27 C23 T33 34, 4,
52, 84 1 44/61 or 82 44/61 A40 G24 C20 T34 A38 G26 C24 T33 or 9 2 5
or 58 5 A40 G24 C20 T34 A38 G27 C23 T33 3 1 1 Ft. Sill 2003 A40 G24
C20 T34 A38 G27 C23 T33 2 3 3 (Cultured) A39 G25 C20 T34 A38 G27
C23 T33 1 4 4 A39 G25 C20 T34 A38 G27 C23 T33 1 28 28 A39 G25 C20
T34 A38 G27 C23 T33 1 3 3 Ft. 2003 A39 G25 C20 T34 A38 G27 C23 T33
1 4 4 Benning A39 G25 C20 T34 A38 G27 C23 T33 3 6 6 (Cultured) A40
G24 C20 T34 A38 G27 C23 T33 1 11 11 A39 G25 C20 T34 A38 G27 C23 T33
1 13 94** A40 G24 C20 T34 A38 G27 C23 T33 1 44/61 or 82 82 A40 G24
C20 T34 A38 G26 C24 T33 or 9 1 5 or 58 58 A40 G24 C20 T34 A38 G27
C23 T33 1 78 or 89 89 A39 G25 C20 T34 A38 G27 C23 T33 2 5 or 58 ND
Lackland 2003 A40 G24 C20 T34 A38 G27 C23 T33 1 2 AFB A39 G25 C20
T34 A38 G27 C24 T32 1 81 or 90 (Throat A40 G24 C20 T34 A38 G27 C23
T33 1 78 Swabs) A38 G26 C20 T34 A38 G27 C23 T33 3*** No detection
No detection No detection 7 3 ND MCRD San 2002 A39 G25 C20 T34 A38
G27 C23 T33 1 3 ND Diego No detection A38 G27 C23 T33 1 3 ND
(Throat No detection No detection 1 3 ND Swabs) No detection No
detection 2 3 ND No detection A38 G27 C23 T33 3 No detection ND No
detection No detection
[0412] TABLE-US-00015 TABLE 9B Base Composition Analysis of
Bioagent Identifying Amplicons of Group A Streptococcus samples
from Six Military Installations Obtained with Primer Pair Nos. 438
and 441 emm-type by xpt yqiL # of Mass emm-Gene Location (Primer
Pair (Primer Pair Instances Spectrometry Sequencing (sample) Year
No. 438) No. 441) 48 3 3 MCRD San 2002 A30 G36 C20 T36 A40 G29 C19
T31 2 6 6 Diego A30 G36 C20 T36 A40 G29 C19 T31 1 28 28 (Cultured)
A30 G36 C20 T36 A41 G28 C18 T32 15 3 ND A30 G36 C20 T36 A40 G29 C19
T31 6 3 3 NHRC San 2003 A30 G36 C20 T36 A40 G29 C19 T31 3 5, 58 5
Diego- A30 G36 C20 T36 A40 G29 C19 T31 6 6 6 Archive A30 G36 C20
T36 A40 G29 C19 T31 1 11 11 (Cultured) A30 G36 C20 T36 A40 G29 C19
T31 3 12 12 A30 G36 C19 T37 A40 G29 C19 T31 1 22 22 A30 G36 C20 T36
A40 G29 C19 T31 3 25, 75 75 A30 G36 C20 T36 A40 G29 C19 T31 4
44/61, 82, 9 44/61 A30 G36 C20 T36 A41 G28 C19 T31 2 53, 91 91 A30
G36 C19 T37 A40 G29 C19 T31 1 2 2 Ft. 2003 A30 G36 C20 T36 A40 G29
C19 T31 2 3 3 Leonard A30 G36 C20 T36 A40 G29 C19 T31 1 4 4 Wood
A30 G36 C19 T37 A41 G28 C19 T31 1 6 6 (Cultured) A30 G36 C20 T36
A40 G29 C19 T31 11 25 or 75 75 A30 G36 C20 T36 A40 G29 C19 T31 1
25, 75, 33, 75 A30 G36 C19 T37 A40 G29 C19 T31 34, 4, 52, 84 1
44/61 or 82 44/61 A30 G36 C20 T36 A41 G28 C19 T31 or 9 2 5 or 58 5
A30 G36 C20 T36 A40 G29 C19 T31 3 1 1 Ft. Sill 2003 A30 G36 C19 T37
A40 G29 C19 T31 2 3 3 (Cultured) A30 G36 C20 T36 A40 G29 C19 T31 1
4 4 A30 G36 C19 T37 A41 G28 C19 T31 1 28 28 A30 G36 C20 T36 A41 G28
C18 T32 1 3 3 Ft. 2003 A30 G36 C20 T36 A40 G29 C19 T31 1 4 4
Benning A30 G36 C19 T37 A41 G28 C19 T31 3 6 6 (Cultured) A30 G36
C20 T36 A40 G29 C19 T31 1 11 11 A30 G36 C20 T36 A40 G29 C19 T31 1
13 94** A30 G36 C20 T36 A41 G28 C19 T31 1 44/61 or 82 82 A30 G36
C20 T36 A41 G28 C19 T31 or 9 1 5 or 58 58 A30 G36 C20 T36 A40 G29
C19 T31 1 78 or 89 89 A30 G36 C20 T36 A41 G28 C19 T31 2 5 or 58 ND
Lackland 2003 A30 G36 C20 T36 A40 G29 C19 T31 1 2 AFB A30 G36 C20
T36 A40 G29 C19 T31 1 81 or 90 (Throat A30 G36 C20 T36 A40 G29 C19
T31 1 78 Swabs) A30 G36 C20 T36 A41 G28 C19 T31 3*** No detection
No detection No detection 7 3 ND MCRD San 2002 A30 G36 C20 T36 A40
G29 C19 T31 1 3 ND Diego A30 G36 C20 T36 A40 G29 C19 T31 1 3 ND
(Throat A30 G36 C20 T36 No detection 1 3 ND Swabs) No detection A40
G29 C19 T31 2 3 ND A30 G36 C20 T36 A40 G29 C19 T31 3 No detection
ND No detection No detection
[0413] TABLE-US-00016 TABLE 9C Base Composition Analysis of
Bioagent Identifying Amplicons of Group A Streptococcus samples
from Six Military Installations Obtained with Primer Pair Nos. 438
and 441 emm-type by gki gtr # of Mass emm-Gene Location (Primer
Pair ((Primer Pair Instances Spectrometry Sequencing (sample) Year
No. 442) No. 443) 48 3 3 MCRD San 2002 A32 G35 C17 T32 A39 G28 C16
T32 2 6 6 Diego A31 G35 C17 T33 A39 G28 C15 T33 1 28 28 (Cultured)
A30 G36 C17 T33 A39 G28 C16 T32 15 3 ND A32 G35 C17 T32 A39 G28 C16
T32 6 3 3 NHRC San 2003 A32 G35 C17 T32 A39 G28 C16 T32 3 5, 58 5
Diego- A30 G36 C20 T30 A39 G28 C15 T33 6 6 6 Archive A31 G35 C17
T33 A39 G28 C15 T33 1 11 11 (Cultured) A30 G36 C20 T30 A39 G28 C16
T32 3 12 12 A31 G35 C17 T33 A39 G28 C15 T33 1 22 22 A31 G35 C17 T33
A38 G29 C15 T33 3 25, 75 75 A30 G36 C17 T33 A39 G28 C15 T33 4
44/61, 82, 9 44/61 A30 G36 C18 T32 A39 G28 C15 T33 2 53, 91 91 A32
G35 C17 T32 A39 G28 C16 T32 1 2 2 Ft. 2003 A30 G36 C17 T33 A39 G28
C15 T33 2 3 3 Leonard A32 G35 C17 T32 A39 G28 C16 T32 1 4 4 Wood
A31 G35 C17 T33 A39 G28 C15 T33 1 6 6 (Cultured) A31 G35 C17 T33
A39 G28 C15 T33 11 25 or 75 75 A30 G36 C17 T33 A39 G28 C15 T33 1
25, 75, 33, 75 A30 G36 C17 T33 A39 G28 C15 T33 34, 4, 52, 84 1
44/61 or 82 44/61 A30 G36 C18 T32 A39 G28 C15 T33 or 9 2 5 or 58 5
A30 G36 C20 T30 A39 G28 C15 T33 3 1 1 Ft. Sill 2003 A30 G36 C18 T32
A39 G28 C15 T33 2 3 3 (Cultured) A32 G35 C17 T32 A39 G28 C16 T32 1
4 4 A31 G35 C17 T33 A39 G28 C15 T33 1 28 28 A30 G36 C17 T33 A39 G28
C16 T32 1 3 3 Ft. 2003 A32 G35 C17 T32 A39 G28 C16 T32 1 4 4
Benning A31 G35 C17 T33 A39 G28 C15 T33 3 6 6 (Cultured) A31 G35
C17 T33 A39 G28 C15 T33 1 11 11 A30 G36 C20 T30 A39 G28 C16 T32 1
13 94** A30 G36 C19 T31 A39 G28 C15 T33 1 44/61 or 82 82 A30 G36
C18 T32 A39 G28 C15 T33 or 9 1 5 or 58 58 A30 G36 C20 T30 A39 G28
C15 T33 1 78 or 89 89 A30 G36 C18 T32 A39 G28 C15 T33 2 5 or 58 ND
Lackland 2003 A30 G36 C20 T30 A39 G28 C15 T33 1 2 AFB A30 G36 C17
T33 A39 G28 C15 T33 1 81 or 90 (Throat A30 G36 C17 T33 A39 G28 C15
T33 1 78 Swabs) A30 G36 C18 T32 A39 G28 C15 T33 3*** No detection
No detection No detection 7 3 ND MCRD San 2002 A32 G35 C17 T32 A39
G28 C16 T32 1 3 ND Diego No detection No detection 1 3 ND (Throat
A32 G35 C17 T32 A39 G28 C16 T32 1 3 ND Swabs) A32 G35 C17 T32 No
detection 2 3 ND A32 G35 C17 T32 No detection 3 No detection ND No
detection No detection
Example 8
Design of Calibrant Polynucleotides Based on Bioagent Identifying
Amplicons for Identification of Species of Bacteria (Bacterial
Bioagent Identifying Amplicons)
[0414] This example describes the design of 19 calibrant
polynucleotides based on bacterial bioagent identifying amplicons
corresponding to the primers of the broad surveillance set (Table
5) and the Bacillus anthracis drill-down set (Table 6).
[0415] Calibration sequences were designed to simulate bacterial
bioagent identifying amplicons produced by the T modified primer
pairs shown in Tables 5 and 6 (primer names have the designation
"TMOD"). The calibration sequences were chosen as a representative
member of the section of bacterial genome from specific bacterial
species which would be amplified by a given primer pair. The model
bacterial species upon which the calibration sequences are based
are also shown in Table 10. For example, the calibration sequence
chosen to correspond to an amplicon produced by primer pair no. 361
is SEQ ID NO: 1445. In Table 10, the forward (_F) or reverse (_R)
primer name indicates the coordinates of an extraction representing
a gene of a standard reference bacterial genome to which the primer
hybridizes e.g.: the forward primer name
16S_EC.sub.--713.sub.--732_TMOD_F indicates that the forward primer
hybridizes to residues 713-732 of the gene encoding 16S ribosomal
RNA in an E. coli reference sequence (in this case, the reference
sequence is an extraction consisting of residues 4033120-4034661 of
the genomic sequence of E. coli K12 (GenBank gi number 16127994).
Additional gene coordinate reference information is shown in Table
11. The designation "TMOD" in the primer names indicates that the
5' end of the primer has been modified with a non-matched template
T residue which prevents the PCR polymerase from adding
non-templated adenosine residues to the 5' end of the amplification
product, an occurrence which may result in miscalculation of base
composition from molecular mass data (vide supra).
[0416] The 19 calibration sequences described in Tables 10 and 11
were combined into a single calibration polynucleotide sequence
(SEQ ID NO: 1464--which is herein designated a "combination
calibration polynucleotide") which was then cloned into a
pCR.RTM.-Blunt vector (Invitrogen, Carlsbad, Calif.). This
combination calibration polynucleotide can be used in conjunction
with the primers of Tables 5 or 6 as an internal standard to
produce calibration amplicons for use in determination of the
quantity of any bacterial bioagent. Thus, for example, when the
combination calibration polynucleotide vector is present in an
amplification reaction mixture, a calibration amplicon based on
primer pair 346 (16S rRNA) will be produced in an amplification
reaction with primer pair 346 and a calibration amplicon based on
primer pair 363 (rpoC) will be produced with primer pair 363.
Coordinates of each of the 19 calibration sequences within the
calibration polynucleotide (SEQ ID NO: 1464) are indicated in Table
11. TABLE-US-00017 TABLE 10 Bacterial Primer Pairs for Production
of Bacterial Bioagent Identifying Amplicons and Corresponding
Representative Calibration Sequences Calibra- Forward Reverse
Calibration tion Primer Primer Sequence Sequence Primer (SEQ ID
(SEQ ID Model (SEQ ID Pair No. Forward Primer Name NO:) Reverse
Primer Name NO:) Species NO:) 361 16S_EC_1090_1111_2_TMOD_F 697
16S_EC_1175_1196_TMOD_R 1398 Bacillus 1445 anthracis 346
16S_EC_713_732_TMOD_F 202 16S_EC_789_809_TMOD_R 1110 Bacillus 1446
anthracis 347 16S_EC_785_806_TMOD_F 560 16S_EC_880_897_TMOD_R 1278
Bacillus 1447 anthracis 348 16S_EC_960_981_TMOD_F 706
16S_EC_1054_1073_TMOD_R 895 Bacillus 1448 anthracis 349
23S_EC_1826_1843_TMOD_F 401 23S_EC_1906_1924_TMOD_R 1156 Bacillus
1449 anthracis 360 23S_EC_2646_2667_TMOD_F 409
23S_EC_2745_2765_TMOD_R 1434 Bacillus 1450 anthracis 350
CAPC_BA_274_303_TMOD_F 476 CAPC_BA_349_376_TMOD_R 1314 Bacillus
1451 anthracis 351 CYA_BA_1353_1379_TMOD_F 355
CYA_BA_1448_1467_TMOD_R 1423 Bacillus 1452 anthracis 352
INFB_EC_1365_1393_TMOD_F 687 INFB_EC_1439_1467_TMOD_R 1411 Bacillus
1453 anthracis 353 LEF_BA_756_781_TMOD_F 220 LEF_BA_843_872_TMOD_R
1394 Bacillus 1454 anthracis 356 RPLB_EC_650_679_TMOD_F 449
RPLB_EC_739_762_TMOD_R 1380 Clostridium 1455 botulinum 449
RPLB_EC_690_710_F 309 RPLB_EC_737_758_R 1336 Clostridium 1456
botulinum 359 RPOB_EC_1845_1866_TMOD_F 659 RPOB_EC_1909_1929_TMOD_R
1250 Yersinia 1457 Pestis 362 RPOB_EC_3799_3821_TMOD_F 581
RPOB_EC_3862_3888_TMOD_R 1325 Burkholderia 1458 mallei 363
RPOC_EC_2146_2174_TMOD_F 284 RPOC_EC_2227_2245_TMOD_R 898
Burkholderia 1459 mallei 354 RPOC_EC_2218_2241_TMOD_F 405
RPOC_EC_2313_2337_TMOD_R 1072 Bacillus 1460 anthracis 355
SSPE_BA_115_137_TMOD_F 255 SSPE_BA_197_222_TMOD_R 1402 Bacillus
1461 anthracis 367 TUFB_EC_957_979_TMOD_F 308
TUFB_EC_1034_1058_TMOD_R 1276 Burkholderia 1462 mallei 358
VALS_EC_1105_1124_TMOD_F 385 VALS_EC_1195_1218_TMOD_R 1093 Yersinia
1463 Pestis
[0417] TABLE-US-00018 TABLE 11 Primer Pair Gene Coordinate
References and Calibration Polynucleotide Sequence Coordinates
within the Combination Calibration Polynucleotide Coordinates of
Gene Extraction Calibration Sequence in Bacterial Coordinates
Reference GenBank GI Combination Calibration Gene and of Genomic or
Plasmid No. of Genomic (G) or Primer Polynucleotide (SEQ ID Species
Sequence Plasmid (P) Sequence Pair No. NO: 1464) 16S E. coli
4033120 . . . 4034661 16127994 (G) 346 16 . . . 109 16S E. coli
4033120 . . . 4034661 16127994 (G) 347 83 . . . 190 16S E. coli
4033120 . . . 4034661 16127994 (G) 348 246 . . . 353 16S E. coli
4033120 . . . 4034661 16127994 (G) 361 368 . . . 469 23S E. coli
4166220 . . . 4169123 16127994 (G) 349 743 . . . 837 23S E. coli
4166220 . . . 4169123 16127994 (G) 360 865 . . . 981 rpoB E. coli.
4178823 . . . 4182851 16127994 (G) 359 1591 . . . 1672 (complement
strand) rpoB E. coli 4178823 . . . 4182851 16127994 (G) 362 2081 .
. . 2167 (complement strand) rpoC E. coli 4182928 . . . 4187151
16127994 (G) 354 1810 . . . 1926 rpoC E. coli 4182928 . . . 4187151
16127994 (G) 363 2183 . . . 2279 infB E. coli 3313655 . . . 3310983
16127994 (G) 352 1692 . . . 1791 (complement strand) tufB E. coli
4173523 . . . 4174707 16127994 (G) 367 2400 . . . 2498 rplB E. coli
3449001 . . . 3448180 16127994 (G) 356 1945 . . . 2060 rplB E. coli
3449001 . . . 3448180 16127994 (G) 449 1986 . . . 2055 valS E. coli
4481405 . . . 4478550 16127994 (G) 358 1462 . . . 1572 (complement
strand) capC 56074 . . . 55628 (complement 6470151 (P) 350 2517 . .
. 2616 B. anthracis strand) cya 156626 . . . 154288 4894216 (P) 351
1338 . . . 1449 B. anthracis (complement strand) lef 127442 . . .
129921 4894216 (P) 353 1121 . . . 1234 B. anthracis sspE 226496 . .
. 226783 30253828 (G) 355 1007-1104 B. anthracis
Example 9
Use of a Calibration Polynucleotide for Determining the Quantity of
Bacillus Anthracis in a Sample Containing a Mixture of Microbes
[0418] The process described in this example is shown in FIG. 2.
The capC gene is a gene involved in capsule synthesis which resides
on the pX02 plasmid of Bacillus anthracis. Primer pair number 350
(see Tables 10 and 11) was designed to identify Bacillus anthracis
via production of a bacterial bioagent identifying amplicon. Known
quantities of the combination calibration polynucleotide vector
described in Example 8 were added to amplification mixtures
containing bacterial bioagent nucleic acid from a mixture of
microbes which included the Ames strain of Bacillus anthracis. Upon
amplification of the bacterial bioagent nucleic acid and the
combination calibration polynucleotide vector with primer pair no.
350, bacterial bioagent identifying amplicons and calibration
amplicons were obtained and characterized by mass spectrometry. A
mass spectrum measured for the amplification reaction is shown in
FIG. 7. The molecular masses of the bioagent identifying amplicons
provided the means for identification of the bioagent from which
they were obtained (Ames strain of Bacillus anthracis) and the
molecular masses of the calibration amplicons provided the means
for their identification as well. The relationship between the
abundance (peak height) of the calibration amplicon signals and the
bacterial bioagent identifying amplicon signals provides the means
of calculation of the copies of the pX02 plasmid of the Ames strain
of Bacillus anthracis. Methods of calculating quantities of
molecules based on internal calibration procedures are well known
to those of ordinary skill in the art.
[0419] Averaging the results of 10 repetitions of the experiment
described above, enabled a calculation that indicated that the
quantity of Ames strain of Bacillus anthracis present in the sample
corresponds to approximately 10 copies of pX02 plasmid.
Example 10
Triangulation Genotyping Analysis of Campylobacter Species
[0420] A series of triangulation genotyping analysis primers were
designed as described in Example 1 with the objective of
identification of different strains of Campylobacter jejuni. The
primers are listed in Table 12 with the designation "CJST_CJ."
Housekeeping genes to which the primers hybridize and produce
bioagent identifying amplicons include: tkt (transketolase), glyA
(serine hydroxymethyltransferase), gltA (citrate synthase), aspA
(aspartate ammonia lyase), glnA (glutamine synthase), pgm
(phosphoglycerate mutase), and uncA (ATP synthetase alpha chain).
TABLE-US-00019 TABLE 12 Campylobacter Genotyping Primer Pairs
Primer Pair Forward Primer Reverse Primer No. Forward Primer Name
(SEQ ID NO:) Reverse Primer Name (SEQ ID NO:) Target Gene 1053
CJST_CJ_1080_1110_F 681 CJST_CJ_1166_1198_R 1022 gltA 1047
CJST_CJ_584_616_F 315 CJST_CJ_663_692_R 1379 glnA 1048
CJST_CJ_360_394_F 346 CJST_CJ_442_476_R 955 aspA 1049
CJST_CJ_2636_2668_F 504 CJST_CJ_2753_2777_R 1409 tkt 1054
CJST_CJ_2060_2090_F 323 CJST_CJ_2148_2174_R 1068 pgm 1064
CJST_CJ_1680_1713_F 479 CJST_CJ_1795_1822_R 938 glyA
[0421] The primers were used to amplify nucleic acid from 50 food
product samples provided by the USDA, 25 of which contained
Campylobacter jejuni and 25 of which contained Campylobacter coli.
Primers used in this study were developed primarily for the
discrimination of Campylobacter jejuni clonal complexes and for
distinguishing Campylobacter jejuni from Campylobacter coli. Finer
discrimination between Campylobacter coli types is also possible by
using specific primers targeted to loci where closely-related
Campylobacter coli isolates demonstrate polymorphisms between
strains. The conclusions of the comparison of base composition
analysis with sequence analysis are shown in Tables 13A-C.
TABLE-US-00020 TABLE 13A Results of Base Composition Analysis of 50
Campylobacter Samples with Drill-down MLST Primer Pair Nos: 1048
and 1047 Base Base Composition of Composition of MLST type or
Bioagent Bioagent Clonal MLST Type Identifying Identifying Complex
by or Clonal Amplicon Amplicon Base Complex by Obtained with
Obtained with Isolate Composition Sequence Primer Pair No: Primer
Pair Group Species origin analysis analysis Strain 1048 (aspA) No:
1047 (glnA) J-1 C. jejuni Goose ST 690/ ST 991 RM3673 A30 G25 C16
T46 A47 G21 C16 T25 692/707/991 J-2 C. jejuni Human Complex ST 356,
RM4192 A30 G25 C16 T46 A48 G21 C17 T23 206/48/353 complex 353 J-3
C. jejuni Human Complex ST 436 RM4194 A30 G25 C15 T47 A48 G21 C18
T22 354/179 J-4 C. jejuni Human Complex 257 ST 257, RM4197 A30 G25
C16 T46 A48 G21 C18 T22 complex 257 J-5 C. jejuni Human Complex 52
ST 52, RM4277 A30 G25 C16 T46 A48 G21 C17 T23 complex 52 J-6 C.
jejuni Human Complex 443 ST 51, RM4275 A30 G25 C15 T47 A48 G21 C17
T23 complex RM4279 A30 G25 C15 T47 A48 G21 C17 T23 443 J-7 C.
jejuni Human Complex 42 ST 604, RM1864 A30 G25 C15 T47 A48 G21 C18
T22 complex 42 J-8 C. jejuni Human Complex ST 362, RM3193 A30 G25
C15 T47 A48 G21 C18 T22 42/49/362 complex 362 J-9 C. jejuni Human
Complex ST 147, RM3203 A30 G25 C15 T47 A47 G21 C18 T23 45/283
Complex 45 C. jejuni Human Consistent ST 828 RM4183 A31 G27 C20 T39
A48 G21 C16 T24 C-1 C. coli with 74 ST 832 RM1169 A31 G27 C20 T39
A48 G21 C16 T24 closely ST 1056 RM1857 A31 G27 C20 T39 A48 G21 C16
T24 Poultry related ST 889 RM1166 A31 G27 C20 T39 A48 G21 C16 T24
sequence ST 829 RM1182 A31 G27 C20 T39 A48 G21 C16 T24 types (none
ST 1050 RM1518 A31 G27 C20 T39 A48 G21 C16 T24 belong to a ST 1051
RM1521 A31 G27 C20 T39 A48 G21 C16 T24 clonal ST 1053 RM1523 A31
G27 C20 T39 A48 G21 C16 T24 complex) ST 1055 RM1527 A31 G27 C20 T39
A48 G21 C16 T24 ST 1017 RM1529 A31 G27 C20 T39 A48 G21 C16 T24 ST
860 RM1840 A31 G27 C20 T39 A48 G21 C16 T24 ST 1063 RM2219 A31 G27
C20 T39 A48 G21 C16 T24 ST 1066 RM2241 A31 G27 C20 T39 A48 G21 C16
T24 ST 1067 RM2243 A31 G27 C20 T39 A48 G21 C16 T24 ST 1068 RM2439
A31 G27 C20 T39 A48 G21 C16 T24 Swine ST 1016 RM3230 A31 G27 C20
T39 A48 G21 C16 T24 ST 1069 RM3231 A31 G27 C20 T39 A48 G21 C16 T24
ST 1061 RM1904 A31 G27 C20 T39 A48 G21 C16 T24 Unknown ST 825
RM1534 A31 G27 C20 T39 A48 G21 C16 T24 ST 901 RM1505 A31 G27 C20
T39 A48 G21 C16 T24 C-2 C. coli Human ST 895 ST 895 RM1532 A31 G27
C19 T40 A48 G21 C16 T24 C-3 C. coli Poultry Consistent ST 1064
RM2223 A31 G27 C20 T39 A48 G21 C16 T24 with 63 ST 1082 RM1178 A31
G27 C20 T39 A48 G21 C16 T24 closely ST 1054 RM1525 A31 G27 C20 T39
A48 G21 C16 T24 related ST 1049 RM1517 A31 G27 C20 T39 A48 G21 C16
T24 Marmoset sequence ST 891 RM1531 A31 G27 C20 T39 A48 G21 C16 T24
types (none belong to a clonal complex)
[0422] TABLE-US-00021 TABLE 13B Results of Base Composition
Analysis of 50 Campylobacter Samples with Drill- down MLST Primer
Pair Nos: 1053 and 1064 Base Base Composition of Composition of
MLST type or Bioagent Bioagent Clonal MLST Type Identifying
Identifying Complex by or Clonal Amplicon Amplicon Base Complex by
Obtained with Obtained with Isolate Composition Sequence Primer
Pair Primer Pair Group Species origin analysis analysis Strain No:
1053 (gltA) No: 1064 (glyA) J-1 C. jejuni Goose ST 690/ ST 991
RM3673 A24 G25 C23 T47 A40 G29 C29 T45 692/707/991 J-2 C. jejuni
Human Complex ST 356, RM4192 A24 G25 C23 T47 A40 G29 C29 T45
206/48/353 complex 353 J-3 C. jejuni Human Complex ST 436 RM4194
A24 G25 C23 T47 A40 G29 C29 T45 354/179 J-4 C. jejuni Human Complex
257 ST 257, RM4197 A24 G25 C23 T47 A40 G29 C29 T45 complex 257 J-5
C. jejuni Human Complex 52 ST 52, RM4277 A24 G25 C23 T47 A39 G30
C26 T48 complex 52 J-6 C. jejuni Human Complex 443 ST 51, RM4275
A24 G25 C23 T47 A39 G30 C28 T46 complex RM4279 A24 G25 C23 T47 A39
G30 C28 T46 443 J-7 C. jejuni Human Complex 42 ST 604, RM1864 A24
G25 C23 T47 A39 G30 C26 T48 complex 42 J-8 C. jejuni Human Complex
ST 362, RM3193 A24 G25 C23 T47 A38 G31 C28 T46 42/49/362 complex
362 J-9 C. jejuni Human Complex ST 147, RM3203 A24 G25 C23 T47 A38
G31 C28 T46 45/283 Complex 45 C. jejuni Human Consistent ST 828
RM4183 A23 G24 C26 T46 A39 G30 C27 T47 C-1 C. coli with 74 ST 832
RM1169 A23 G24 C26 T46 A39 G30 C27 T47 closely ST 1056 RM1857 A23
G24 C26 T46 A39 G30 C27 T47 Poultry related ST 889 RM1166 A23 G24
C26 T46 A39 G30 C27 T47 sequence ST 829 RM1182 A23 G24 C26 T46 A39
G30 C27 T47 types (none ST 1050 RM1518 A23 G24 C26 T46 A39 G30 C27
T47 belong to a ST 1051 RM1521 A23 G24 C26 T46 A39 G30 C27 T47
clonal ST 1053 RM1523 A23 G24 C26 T46 A39 G30 C27 T47 complex) ST
1055 RM1527 A23 G24 C26 T46 A39 G30 C27 T47 ST 1017 RM1529 A23 G24
C26 T46 A39 G30 C27 T47 ST 860 RM1840 A23 G24 C26 T46 A39 G30 C27
T47 ST 1063 RM2219 A23 G24 C26 T46 A39 G30 C27 T47 ST 1066 RM2241
A23 G24 C26 T46 A39 G30 C27 T47 ST 1067 RM2243 A23 G24 C26 T46 A39
G30 C27 T47 ST 1068 RM2439 A23 G24 C26 T46 A39 G30 C27 T47 Swine ST
1016 RM3230 A23 G24 C26 T46 A39 G30 C27 T47 ST 1069 RM3231 A23 G24
C26 T46 NO DATA ST 1061 RM1904 A23 G24 C26 T46 A39 G30 C27 T47
Unknown ST 825 RM1534 A23 G24 C26 T46 A39 G30 C27 T47 ST 901 RM1505
A23 G24 C26 T46 A39 G30 C27 T47 C-2 C. coli Human ST 895 ST 895
RM1532 A23 G24 C26 T46 A39 G30 C27 T47 C-3 C. coli Poultry
Consistent ST 1064 RM2223 A23 G24 C26 T46 A39 G30 C27 T47 with 63
ST 1082 RM1178 A23 G24 C26 T46 A39 G30 C27 T47 closely ST 1054
RM1525 A23 G24 C25 T47 A39 G30 C27 T47 related ST 1049 RM1517 A23
G24 C26 T46 A39 G30 C27 T47 Marmoset sequence ST 891 RM1531 A23 G24
C26 T46 A39 G30 C27 T47 types (none belong to a clonal complex)
[0423] TABLE-US-00022 TABLE 13C Results of Base Composition
Analysis of 50 Campylobacter Samples with Drill- down MLST Primer
Pair Nos: 1054 and 1049 Base Base Composition of Composition of
MLST type or Bioagent Bioagent Clonal MLST Type Identifying
Identifying Complex by or Clonal Amplicon Amplicon Base Complex by
Obtained with Obtained with Isolate Composition Sequence Primer
Pair No: Primer Pair Group Species origin analysis analysis Strain
1054 (pgm) No: 1049 (tkt) J-1 C. jejuni Goose ST 690/ ST 991 RM3673
A26 G33 C18 T38 A41 G28 C35 T38 692/707/991 J-2 C. jejuni Human
Complex ST 356, RM4192 A26 G33 C19 T37 A41 G28 C36 T37 206/48/353
complex 353 J-3 C. jejuni Human Complex ST 436 RM4194 A27 G32 C19
T37 A42 G28 C36 T36 354/179 J-4 C. jejuni Human Complex 257 ST 257,
RM4197 A27 G32 C19 T37 A41 G29 C35 T37 complex 257 J-5 C. jejuni
Human complex 52 ST 52, RM4277 A26 G33 C18 T38 A41 G28 C36 T37
complex 52 J-6 C. jejuni Human Complex 443 ST 51, RM4275 A27 G31
C19 T38 A41 G28 C36 T37 complex RM4279 A27 G31 C19 T38 A41 G28 C36
T37 443 J-7 C. jejuni Human Complex 42 ST 604, RM1864 A27 G32 C19
T37 A42 G28 C35 T37 complex 42 J-8 C. jejuni Human Complex ST 362,
RM3193 A26 G33 C19 T37 A42 G28 C35 T37 42/49/362 complex 362 J-9 C.
jejuni Human Complex ST 147, RM3203 A28 G31 C19 T37 A43 G28 C36 T35
45/283 Complex 45 C. jejuni Human Consistent ST 828 RM4183 A27 G30
C19 T39 A46 G28 C32 T36 C-1 C. coli with 74 ST 832 RM1169 A27 G30
C19 T39 A46 G28 C32 T36 closely ST 1056 RM1857 A27 G30 C19 T39 A46
G28 C32 T36 Poultry related ST 889 RM1166 A27 G30 C19 T39 A46 G28
C32 T36 sequence ST 829 RM1182 A27 G30 C19 T39 A46 G28 C32 T36
types (none ST 1050 RM1518 A27 G30 C19 T39 A46 G28 C32 T36 belong
to a ST 1051 RM1521 A27 G30 C19 T39 A46 G28 C32 T36 clonal ST 1053
RM1523 A27 G30 C19 T39 A46 G28 C32 T36 complex) ST 1055 RM1527 A27
G30 C19 T39 A46 G28 C32 T36 ST 1017 RM1529 A27 G30 C19 T39 A46 G28
C32 T36 ST 860 RM1840 A27 G30 C19 T39 A46 G28 C32 T36 ST 1063
RM2219 A27 G30 C19 T39 A46 G28 C32 T36 ST 1066 RM2241 A27 G30 C19
T39 A46 G28 C32 T36 ST 1067 RM2243 A27 G30 C19 T39 A46 G28 C32 T36
ST 1068 RM2439 A27 G30 C19 T39 A46 G28 C32 T36 Swine ST 1016 RM3230
A27 G30 C19 T39 A39 G30 C27 T47 ST 1069 RM3231 A27 G30 C19 T39 A46
G28 C32 T36 ST 1061 RM1904 A27 G30 C19 T39 A46 G28 C32 T36 Unknown
ST 825 RM1534 A27 G30 C19 T39 A46 G28 C32 T36 ST 901 RM1505 A27 G30
C19 T39 A46 G28 C32 T36 C-2 C. coli Human ST 895 ST 895 RM1532 A27
G30 C19 T39 A46 G28 C32 T36 C-3 C. coli Poultry Consistent ST 1064
RM2223 A27 G30 C19 T39 A46 G28 C32 T36 with 63 ST 1082 RM1178 A27
G30 C19 T39 A46 G28 C32 T36 closely ST 1054 RM1525 A27 G30 C19 T39
A46 G28 C32 T36 related ST 1049 RM1517 A27 G30 C19 T39 A46 G28 C32
T36 Marmoset sequence ST 891 RM1531 A27 G30 C19 T39 A46 G28 C32 T36
types (none belong to a clonal complex)
[0424] The base composition analysis method was successful in
identification of 12 different strain groups. Campylobacter jejuni
and Campylobacter coli are generally differentiated by all loci.
Ten clearly differentiated Campylobacter jejuni isolates and 2
major Campylobacter coli groups were identified even though the
primers were designed for strain typing of Campylobacter jejuni.
One isolate (RM4183) which was designated as Campylobacter jejuni
was found to group with Campylobacter coli and also appears to
actually be Campylobacter coli by full MLST sequencing.
Example 11
Identification of Acinetobacter baumannii Using Broad Range Survey
and Division-Wide Primers in Epidemiological Surveillance
[0425] To test the capability of the broad range survey and
division-wide primer sets of Table 5 in identification of
Acinetobacter species, 183 clinical samples were obtained from
individuals participating in, or in contact with individuals
participating in Operation Iraqi Freedom (including US service
personnel, US civilian patients at the Walter Reed Army Institute
of Research (WRAIR), medical staff, Iraqi civilians and enemy
prisoners. In addition, 34 environmental samples were obtained from
hospitals in Iraq, Kuwait, Germany, the United States and the USNS
Comfort, a hospital ship.
[0426] Upon amplification of nucleic acid obtained from the
clinical samples, primer pairs 346-349, 360, 361, 354, 362 and 363
(Table 5) all produced bacterial bioagent amplicons which
identified Acinetobacter baumannii in 215 of 217 samples. The
organism Klebsiella pneumoniae was identified in the remaining two
samples. In addition, 14 different strain types (containing single
nucleotide polymorphisms relative to a reference strain of
Acinetobacter baumannii) were identified and assigned arbitrary
numbers from 1 to 14. Strain type 1 was found in 134 of the sample
isolates and strains 3 and 7 were found in 46 and 9 of the isolates
respectively.
[0427] The epidemiology of strain type 7 of Acinetobacter baumannii
was investigated. Strain 7 was found in 4 patients and 5
environmental samples (from field hospitals in Iraq and Kuwait).
The index patient infected with strain 7 was a pre-war patient who
had a traumatic amputation in March of 2003 and was treated at a
Kuwaiti hospital. The patient was subsequently transferred to a
hospital in Germany and then to WRAIR. Two other patients from
Kuwait infected with strain 7 were found to be non-infectious and
were not further monitored. The fourth patient was diagnosed with a
strain 7 infection in September of 2003 at WRAIR. Since the fourth
patient was not related involved in Operation Iraqi Freedom, it was
inferred that the fourth patient was the subject of a nosocomial
infection acquired at WRAIR as a result of the spread of strain 7
from the index patient.
[0428] The epidemiology of strain type 3 of Acinetobacter baumannii
was also investigated. Strain type 3 was found in 46 samples, all
of which were from patients (US service members, Iraqi civilians
and enemy prisoners) who were treated on the USNS Comfort hospital
ship and subsequently returned to Iraq or Kuwait. The occurrence of
strain type 3 in a single locale may provide evidence that at least
some of the infections at that locale were a result of nosocomial
infections.
[0429] This example thus illustrates an embodiment of the present
invention wherein the methods of analysis of bacterial bioagent
identifying amplicons provide the means for epidemiological
surveillance.
Example 12
Selection and Use of Triangulation Genotyping Analysis Primer Pairs
for Acinetobacter baumanii
[0430] To combine the power of high-throughput mass spectrometric
analysis of bioagent identifying amplicons with the sub-species
characteristic resolving power provided by triangulation genotyping
analysis, an additional 21 primer pairs were selected based on
analysis of housekeeping genes of the genus Acinetobacter. Genes to
which the drill-down triangulation genotyping analysis primers
hybridize for production of bacterial bioagent identifying
amplicons include anthranilate synthase component I (trpE),
adenylate kinase (adk), adenine glycosylase (mutY), fulmarate
hydratase (fumC), and pyrophosphate phospho-hydratase (ppa). These
21 primer pairs are indicated with reference to sequence listings
in Table 14. Primer pair numbers 1151-1154 hybridize to and amplify
segments of trpE. Primer pair numbers 1155-1157 hybridize to and
amplify segments of adk. Primer pair numbers 1158-1164 hybridize to
and amplify segments of mutY. Primer pair numbers 1165-1170
hybridize to and amplify segments of fumC. Primer pair number 1171
hybridizes to and amplifies a segment of ppa. Primer pair numbers:
2846-2848 hybridize to and amplify segments of the parC gene of DNA
topoisomerase which include a codon known to confer quinolone drug
resistance upon sub-types of Acinetobacter baumannii. Primer pair
numbers 2852-2854 hybridize to and amplify segments of the gyrA
gene of DNA gyrase which include a codon known to confer quinolone
drug resistance upon sub-types of Acinetobacter baumannii. Primer
pair numbers 2922 and 2972 are speciating primers which are useful
for identifying different species members of the genus
Acinetobacter. The primer names given in Table 14A (with the
exception of primer pair numbers 2846-2848, 2852-2854) indicate the
coordinates to which the primers hybridize to a reference sequence
which comprises a concatenation of the genes TrpE, efp (elongation
factor p), adk, mutT, fumC, and ppa. For example, the forward
primer of primer pair 1151 is named
AB_MLST-11-OIF007.sub.--62.sub.--91_F because it hybridizes to the
Acinetobacter primer reference sequence of strain type 11 in sample
007 of Operation Iraqi Freedom (OIF) at positions 62 to 91. DNA was
sequenced from strain type 11 and from this sequence data and an
artificial concatenated sequence of partial gene extractions was
assembled for use in design of the triangulation genotyping
analysis primers. The stretches of arbitrary residues "N"s in the
concatenated sequence were added for the convenience of separation
of the partial gene extractions (40N for AB_MLST (SEQ ID NO:
1444)).
[0431] The hybridization coordinates of primer pair numbers
2846-2848 are with respect to GenBank Accession number X95819. The
hybridization coordinates of primer pair numbers 2852-2854 are with
respect to GenBank Accession number AY642140. Sequence residue "I"
appearing in the forward and reverse primers of primer pair number
2972 represents inosine. TABLE-US-00023 TABLE 14A Triangulation
Genotyping Analysis Primer Pairs for Identification of Sub-species
characteristics (Strain Type) of Members of the Bacterial Genus
Acinetobacter Primer Forward Primer Reverse Primer Pair No. Forward
Primer Name (SEQ ID NO:) Reverse Primer Name (SEQ ID NO:) 1151
AB_MLST-11-OIF007_62_91_F 454 AB_MLST-11-OIF007_169_203_R 1418 1152
AB_MLST-11-OIF007_185_214_F 243 AB_MLST-11-OIF007_291_324_R 969
1153 AB_MLST-11-OIF007_260_289_F 541 AB_MLST-11-OIF007_364_393_R
1400 1154 AB_MLST-11-OIF007_206_239_F 436
AB_MLST-11-OIF007_318_344_R 1036 1155 AB_MLST-11-OIF007_522_552_F
378 AB_MLST-11-OIF007_587_610_R 1392 1156
AB_MLST-11-OIF007_547_571_F 250 AB_MLST-11-OIF007_656_686_R 902
1157 AB_MLST-11-OIF007_601_627_F 256 AB_MLST-11-OIF007_710_736_R
881 1158 AB_MLST-11-OIF007_1202_1225_F 384
AB_MLST-11-OIF007_1266_1296_R 878 1159
AB_MLST-11-OIF007_1202_1225_F 384 AB_MLST-11-OIF007_1299_1316_R
1199 1160 AB_MLST-11-OIF007_1234_1264_F 694
AB_MLST-11-OIF007_1335_1362_R 1215 1161
AB_MLST-11-OIF007_1327_1356_F 225 AB_MLST-11-OIF007_1422_1448_R
1212 1162 AB_MLST-11-OIF007_1345_1369_F 383
AB_MLST-11-OIF007_1470_1494_R 1083 1163
AB_MLST-11-OIF007_1351_1375_F 662 AB_MLST-11-OIF007_1470_1494_R
1083 1164 AB_MLST-11-OIF007_1387_1412_F 422
AB_MLST-11-OIF007_1470_1494_R 1083 1165
AB_MLST-11-OIF007_1542_1569_F 194 AB_MLST-11-OIF007_1656_1680_R
1173 1166 AB_MLST-11-OIF007_1566_1593_F 684
AB_MLST-11-OIF007_1656_1680_R 1173 1167
AB_MLST-11-OIF007_1611_1638_F 375 AB_MLST-11-OIF007_1731_1757_R 890
1168 AB_MLST-11-OIF007_1726_1752_F 182
AB_MLST-11-OIF007_1790_1821_R 1195 1169
AB_MLST-11-OIF007_1792_1826_F 656 AB_MLST-11-OIF007_1876_1909_R
1151 1170 AB_MLST-11-OIF007_1792_1826_F 656
AB_MLST-11-OIF007_1895_1927_R 1224 1171
AB_MLST-11-OIF007_1970_2002_F 618 AB_MLST-11-OIF007_2097_2118_R
1157 2846 PARC_X95819_33_58_F 302 PARC_X95819_121_153_R 852 2847
PARC_X95819_33_58_F 199 PARC_X95819_157_178_R 889 2848
PARC_X95819_33_58_F 596 PARC_X95819_97_128_R 1169 2852
GYRA_AY642140_-1_24_F 150 GYRA_AY642140_71_100_R 1242 2853
GYRA_AY642140_26_54_F 166 GYRA_AY642140_121_146_R 1069 2854
GYRA_AY642140_26_54_F 166 GYRA_AY642140_58_89_R 1168 2922
AB_MLST-11-OIF007_991_1018_F 583 AB_MLST-11-OIF007_1110_1137_R 923
2972 AB_MLST-11-OIF007_1007_1034_F 592
AB_MLST-11-OIF007_1126_1153_R 924
[0432] TABLE-US-00024 TABLE 14B Triangulation Genotyping Analysis
Primer Pairs for Identification of Sub-species characteristics
(Strain Type) of Members of the Bacterial Genus Acinetobacter
Forward Primer Primer Reverse Pair (SEQ ID Primer No. NO:) SEQUENCE
(SEQ ID NO:) SEQUENCE 1151 454 TGAGATTGCTGAACATTTAATGCTGATTGA 1418
TTGTACATTTGAAACAATATGCATGACATGTGAAT 1152 243
TATTGTTTCAAATGTACAAGGTGAAGTGCG 969
TCACAGGTTCTACTTCATCAATAATTTCCATTGC 1153 541
TGGAACGTTATCAGGTGCCCCAAAAATTCG 1400 TTGCAATCGACATATCCATTTCACCATGCC
1154 436 TGAAGTGCGTGATGATATCGATGCACTTGATGTA 1036
TCCGCCAAAAACTCCCCTTTTCACAGG 1155 378
TCGGTTTAGTAAAAGAACGTATTGCTCAACC 1392 TTCTGCTTGAGGAATAGTGCGTGG 1156
250 TCAACCTGACTGCGTGAATGGTTGT 902 TACGTTCTACGATTTCTTCATCAGGTACATC
1157 256 TCAAGCAGAAGCTTTGGAAGAAGAAGG 881
TACAACGTGATAAACACGACCAGAAGC 1158 384 TCGTGCCCGCAATTTGCATAAAGC 878
TAATGCCGGGTAGTGCAATCCATTCTTCTAG 1159 384 TCGTGCCCGCAATTTGCATAAAGC
1199 TGCACCTGCGGTCGAGCG 1160 694 TTGTAGCACAGCAAGGCAAATTTCCTGAAAC
1215 TGCCATCCATAATCACGCCATACTGACG 1181 225
TAGGTTTACGTCAGTATGGCGTGATTATGG 1212 TGCCAGTTTCCACATTTCACGTTCGTG
1162 383 TCGTGATTATGGATGGCAACGTGAA 1083 TCGCTTGAGTGTAGTCATGATTGCG
1163 662 TTATGGATGGCAACGTGAAACGCGT 1083 TCGCTTGAGTGTAGTCATGATTGCG
1164 422 TCTTTGCCATTGAAGATGACTTAAGC 1083 TCGCTTGAGTGTAGTCATGATTGCG
1165 194 TACTAGCGGTAAGCTTAAACAAGATTGC 1173
TGAGTCGGGTTCACTTTACCTGGCA 1166 684 TTGCCAATGATATTCGTTGGTTAGCAAG
1173 TGAGTCGGGTTCACTTTACCTGGCA 1167 375
TCGGCGAAATCCGTATTCCTGAAAATGA 890 TACCGGAAGCACCAGCGACATTAATAG 1168
182 TACCACTATTAATGTCGCTGGTGCTTC 1195
TGCAACTGAATAGATTGCAGTAAGTTATAAGC 1169 656
TTATAACTTACTGCAATCTATTCAGTTGCTTGGTG 1151
TGAATTATGCAAGAAGTGATCAATTTTCTCACGA 1170 656
TTATAACTTACTGCAATCTATTCAGTTGCTTGGTG 1224
TGCCGTAACTAACATAAGAGAATTATGCAAGAA 1171 618
TGGTTATGTACCAAATACTTTGTCTGAAGATGG 1157 TGACGGCATCGATACCACCGTC 2846
302 TCCAAAAAAATCAGCGCGTACAGTGG 852
TAAAGGATAGCGGTAACTAAATGGCTGAGCCAT 2847 199
TACTTGGTAAATACCACCCACATGGTGA 889 TACCCCAGTTCCCCTGACCTTC 2848 596
TGGTAAATACCACCCACATGGTGAC 1169 TGAGCCATGAGTACCATGGCTTCATAACATGC
2852 150 TAAATGTGCCCGTGTCGTTGGTGAC 1242
TGCTAAAGTCTTGAGCCATACGAACAATGG 2853 166
TAATCGGTAAATATCACCCGCATGGTGAC 1069 TCGATCGAACCGAAGTTACCCTGACC 2854
166 TAATCGGTAAATATCACCCGCATGGTGAC 1168
TGAGCCATACGAACAATGGTTTCATAAACAGC 2922 583
TGGGCGATGCTGCGAAATGGTTAAAAGA 923 TAGTATCACCACGTACACCCGGATCAGT 2972
592 TGGGIGATGCTGCIAAATGGTTAAAAGA 924
TAGTATCACCACGTACICCIGGATCAGT
[0433] Analysis of bioagent identifying amplicons obtained using
the primers of Table 14B for over 200 samples from Operation Iraqi
Freedom resulted in the identification of 50 distinct strain type
clusters. The largest cluster, designated strain type 11 (ST11)
includes 42 sample isolates, all of which were obtained from US
service personnel and Iraqi civilians treated at the 28.sup.th
Combat Support Hospital in Baghdad. Several of these individuals
were also treated on the hospital ship USNS Comfort. These
observations are indicative of significant epidemiological
correlation/linkage.
[0434] All of the sample isolates were tested against a broad panel
of antibiotics to characterize their antibiotic resistance
profiles. As an example of a representative result from antibiotic
susceptibility testing, ST11 was found to consist of four different
clusters of isolates, each with a varying degree of
sensitivity/resistance to the various antibiotics tested which
included penicillins, extended spectrum penicillins,
cephalosporins, carbepenem, protein synthesis inhibitors, nucleic
acid synthesis inhibitors, anti-metabolites, and anti-cell membrane
antibiotics. Thus, the genotyping power of bacterial bioagent
identifying amplicons, particularly drill-down bacterial bioagent
identifying amplicons, has the potential to increase the
understanding of the transmission of infections in combat
casualties, to identify the source of infection in the environment,
to track hospital transmission of nosocomial infections, and to
rapidly characterize drug-resistance profiles which enable
development of effective infection control measures on a time-scale
previously not achievable.
Example 13
Triangulation Genotyping Analysis and Codon Analysis of
Acinetobacter baumannii Samples from Two Health Care Facilities
[0435] In this investigation, 88 clinical samples were obtained
from Walter Reed Hospital and 95 clinical samples were obtained
from Northwestern Medical Center. All samples from both healthcare
facilities were suspected of containing sub-types of Acinetobacter
baumannii, at least some of which were expected to be resistant to
quinolone drugs. Each of the 183 samples was analyzed by the method
of the present invention. DNA was extracted from each of the
samples and amplified with eight triangulation genotyping analysis
primer pairs represented by primer pair numbers: 1151, 1156, 1158,
1160, 1165, 1167, 1170, and 1171. The DNA was also amplified with
speciating primer pair number 2922 and codon analysis primer pair
numbers 2846-2848 which interrogate a codon present in the parc
gene, and primer pair numbers 2852-2854 which bracket a codon
present in the gyrA gene. The parc and gyrA codon mutations are
both responsible for causing drug resistance in Acinetobacter
baumannii. During evolution of drug resistant strains, the gyrA
mutation usually occurs before the parC mutation. Amplification
products were measured by ESI-TOF mass spectrometry as indicated in
Example 4. The base compositions of the amplification products were
calculated from the average molecular masses of the amplification
products and are shown in Tables 15-18. The entries in each of the
tables are grouped according to strain type number, which is an
arbitrary number assigned to Acinetobacter baumannii strains in the
order of observance beginning from the triangulation genotyping
analysis OIF genotyping study described in Example 12. For example,
strain type 11 which appears in samples from the Walter Reed
Hospital is the same strain as the strain type 11 mentioned in
Example 12. Ibis# refers to the order in which each sample was
analyzed. Isolate refers to the original sample isolate numbering
system used at the location from which the samples were obtained
(either Walter Reed Hospital or Northwestern Medical Center).
ST=strain type. ND=not detected. Base compositions highlighted with
bold type indicate that the base composition is a unique base
composition for the amplification product obtained with the pair of
primers indicated. TABLE-US-00025 TABLE 15A Base Compositions of
Amplification Products of 88 A. baumannii Samples Obtained from
Walter Reed Hospital and Amplified with Codon Analysis Primer Pairs
Targeting the gyrA Gene PP No: 2852 PP No: 2853 PP No: 2854 Species
Ibis# Isolate ST gyrA gyrA gyrA A. baumannii 20 1082 1 A25G23C22T31
A29G28C22T42 A17G13C14T20 A. baumannii 13 854 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 22 1162 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 27 1230 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 31 1367 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 37 1459 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 55 1700 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 64 1777 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 73 1861 10 A25G23C21T32
A29G28C21T43 A17G13C13T21 A. baumannii 74 1877 10 ND A29G28C21T43
A17G13C13T21 A. baumannii 86 1972 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 3 684 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 6 720 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 7 726 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 19 1079 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 21 1123 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 23 1188 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 33 1417 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 34 1431 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 38 1496 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 40 1523 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 42 1640 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 50 1666 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 51 1668 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 52 1695 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 65 1781 11 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 44 1649 12 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 49A 1658.1 12 A25G23C22T31 A29G28C21T43
A17G13C13T21 A. baumannii 49B 1658.2 12 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 56 1707 12 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 80 1893 12 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 5 693 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 8 749 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 10 839 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 14 865 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 16 888 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 29 1326 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 35 1440 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 41 1524 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 46 1652 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 47 1653 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 48 1657 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 57 1709 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 61 1727 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 63 1762 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 67 1806 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 75 1881 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 77 1886 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 1 649 46 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 2 653 46 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 39 1497 16 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 24 1198 15 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 28 1243 15 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 43 1648 15 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 62 1746 15 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 4 689 15 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 68 1822 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 69 1823A 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 70 1823B 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 71 1826 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 72 1860 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 81 1924 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 82 1929 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 85 1966 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 11 841 3 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 32 1415 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 45 1651 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 54 1697 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 58 1712 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 60 1725 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 66 1802 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 76 1883 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 78 1891 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 79 1892 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 83 1947 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 84 1964 24 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 53 1696 24 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 36 1458 49 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 59 1716 9 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 9 805 30 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 18 967 39 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 30 1322 48 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. baumannii 26 1218 50 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. sp. 13TU 15 875 A1 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. sp. 13TU 17 895 A1 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. sp. 3 12 853 B7 A25G22C22T32 A30G29C22T40
A17G13C14T20 A. johnsonii 25 1202 NEW1 A25G22C22T32 A30G29C22T40
A17G13C14T20 A. sp. 2082 87 2082 NEW2 A25G22C22T32 A31G28C22T40
A17G13C14T20
[0436] TABLE-US-00026 TABLE 15B Base Compositions Determined from
A. baumannii DNA Samples Obtained from Walter Reed Hospital and
Amplified with Codon Analysis Primer Pairs Targeting the parC Gene
PP No: 2846 PP No: 2847 PP No: 2848 Species Ibis# Isolate ST parC
parC parC A. baumannii 20 1082 1 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 13 854 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 22 1162 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 27 1230 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 31 1367 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 37 1459 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 55 1700 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 64 1777 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 73 1861 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 74 1877 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 86 1972 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 3 684 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 6 720 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 7 726 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 19 1079 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 21 1123 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 23 1188 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 33 1417 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 34 1431 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 38 1496 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 40 1523 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 42 1640 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 50 1666 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 51 1668 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 52 1695 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 65 1781 11 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 44 1649 12 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 49A 1658.1 12 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 49B 1658.2 12 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 56 1707 12 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 80 1893 12 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 5 693 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 8 749 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 10 839 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 14 865 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 16 888 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 29 1326 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 35 1440 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 41 1524 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 46 1652 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 47 1653 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 48 1657 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 57 1709 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 61 1727 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 63 1762 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 67 1806 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 75 1881 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 77 1886 14 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 1 649 46 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 2 653 46 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 39 1497 16 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 24 1198 15 A33G26C28T34 A29G29C23T33
A16G14C14T16 A. baumannii 28 1243 15 A33G26C28T34 A29G29C23T33
A16G14C14T16 A. baumannii 43 1648 15 A33G26C28T34 A29G29C23T33
A16G14C14T16 A. baumannii 62 1746 15 A33G26C28T34 A29G29C23T33
A16G14C14T16 A. baumannii 4 689 15 A34G25C29T33 A30G27C26T31
A16G14C15T15 A. baumannii 68 1822 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 69 1823A 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 70 1823B 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 71 1826 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 72 1860 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 81 1924 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 82 1929 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 85 1966 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 11 841 3 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 32 1415 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 45 1651 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 54 1697 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 58 1712 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 60 1725 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 66 1802 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 76 1883 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 78 1891 24 A34G25C29T33 A30G27C26T31
A16G14C15T15 A. baumannii 79 1892 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 83 1947 24 A34G25C29T33 A30G27C26T31
A16G14C15T15 A. baumannii 84 1964 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 53 1696 24 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 36 1458 49 A34G26C29T32 A30G28C24T32
A16G14C15T15 A. baumannii 59 1716 9 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 9 805 30 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 18 967 39 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 30 1322 48 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. baumannii 26 1218 50 A33G26C29T33 A29G28C26T31
A16G14C15T15 A. sp. 13TU 15 875 A1 A32G26C28T35 A28G28C24T34
A16G14C15T15 A. sp. 13TU 17 895 A1 A32G26C28T35 A28G28C24T34
A16G14C15T15 A. sp. 3 12 853 B7 A29G26C27T39 A26G32C21T35
A16G14C15T15 A. johnsonii 25 1202 NEW1 A32G28C26T35 A29G29C22T34
A16G14C15T15 A. sp. 2082 87 2082 NEW2 A33G27C26T35 A31G28C20T35
A16G14C15T15
[0437] TABLE-US-00027 TABLE 16A Base Compositions Determined from
A. baumannii DNA Samples Obtained from Northwestern Medical Center
and Amplified with Codon Analysis Primer Pairs Targeting the gyrA
Gene PP No: 2852 PP No: 2853 PP No: 2854 Species Ibis# Isolate ST
gyrA gyrA gyrA A. baumannii 54 536 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 87 665 3 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 8 80 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 9 91 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 10 92 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 11 131 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 12 137 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 21 218 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 26 242 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 94 678 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 1 9 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 2 13 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 3 19 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 4 24 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 5 36 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 6 39 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 13 139 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 15 165 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 16 170 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 17 186 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 20 202 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 22 221 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 24 234 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 25 239 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 33 370 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 34 389 10 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 19 201 14 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 27 257 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 29 301 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 31 354 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 36 422 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 37 424 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 38 434 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 39 473 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 40 482 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 44 512 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 45 516 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 47 522 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 48 526 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 50 528 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 52 531 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 53 533 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 56 542 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 59 550 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 62 556 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 64 557 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 70 588 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 73 603 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 74 605 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 75 606 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 77 611 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 79 622 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 83 643 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 85 653 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 89 669 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 93 674 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 23 228 51 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 32 369 52 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 35 393 52 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 30 339 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 41 485 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 42 493 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 43 502 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 46 520 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 49 527 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 51 529 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 65 562 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 68 579 53 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 57 546 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 58 548 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 60 552 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 61 555 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 63 557 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 66 570 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 67 578 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 69 584 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 71 593 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 72 602 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 76 609 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 78 621 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 80 625 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 81 628 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 82 632 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 84 649 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 86 655 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 88 668 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 90 671 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 91 672 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 92 673 54 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 18 196 55 A25G23C22T31 A29G28C21T43
A17G13C13T21 A. baumannii 55 537 27 A25G23C21T32 A29G28C21T43
A17G13C13T21 A. baumannii 28 263 27 A25G23C22T31 A29G28C22T42
A17G13C14T20 A. sp. 3 14 164 B7 A25G22C22T32 A30G29C22T40
A17G13C14T20 mixture 7 71 -- ND ND A17G13C15T19
[0438] TABLE-US-00028 TABLE 16B Base Compositions Determined from
A. baumannii DNA Samples Obtained from Northwestern Medical Center
and Amplified with Codon Analysis Primer Pairs Targeting the parC
Gene PP No: 2846 PP No: 2847 PP No: 2848 Species Ibis# Isolate ST
parC parC parC A. baumannii 54 536 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 87 665 3 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 8 80 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 9 91 10 A33G26C28T34 A29G28C25T32
A16G14C14T16 A. baumannii 10 92 10 A33G26C28T34 A29G28C25T32 ND A.
baumannii 11 131 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 12 137 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 21 218 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 26 242 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 94 678 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 1 9 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 2 13 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 3 19 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 4 24 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 5 36 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 6 39 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 13 139 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 15 165 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 16 170 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 17 186 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 20 202 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 22 221 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 24 234 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 25 239 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 33 370 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 34 389 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 19 201 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 27 257 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 29 301 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 31 354 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 36 422 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 37 424 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 38 434 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 39 473 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 40 482 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 44 512 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 45 516 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 47 522 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 48 526 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 50 528 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 52 531 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 53 533 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 56 542 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 59 550 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 62 556 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 64 557 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 70 588 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 73 603 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 74 605 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 75 606 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 77 611 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 79 622 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 83 643 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 85 653 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 89 669 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 93 674 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 23 228 51 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 32 369 52 A34G25C28T34 A30G27C25T32 A16G14C14T16 A.
baumannii 35 393 52 A34G25C28T34 A30G27C25T32 A16G14C14T16 A.
baumannii 30 339 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 41 485 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 42 493 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 43 502 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 46 520 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 49 527 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 51 529 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 65 562 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 68 579 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A.
baumannii 57 546 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 58 548 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 60 552 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 61 555 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 63 557 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 66 570 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 67 578 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 69 584 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 71 593 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 72 602 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 76 609 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 78 621 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 80 625 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 81 628 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 82 632 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 84 649 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 86 655 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 88 668 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 90 671 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 91 672 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 92 673 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A.
baumannii 18 196 55 A33G27C28T33 A29G28C25T31 A15G14C15T16 A.
baumannii 55 537 27 A33G26C29T33 A29G28C26T31 A16G14C15T15 A.
baumannii 28 263 27 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. sp. 3
14 164 B7 A35G25C29T32 A30G28C17T39 A16G14C15T15 mixture 7 71 -- ND
ND A17G14C15T14
[0439] TABLE-US-00029 TABLE 17A Base Compositions Determined from
A. baumannii DNA Samples Obtained from Walter Reed Hospital and
Amplified with Speciating Primer Pair No. 2922 and Triangulation
Genotyping Analysis Primer Pair Nos. 1151 and 1156 PP No: 2922 PP
No: 1151 PP No: 1156 Species Ibis# Isolate ST efp trpE Adk A.
baumannii 20 1082 1 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 13 854 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 22 1162 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 27 1230 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 31 1367 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 37 1459 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 55 1700 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 64 1777 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 73 1861 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 74 1877 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 86 1972 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 3 684 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 6 720 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 7 726 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 19 1079 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 21 1123 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 23 1188 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 33 1417 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 34 1431 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 38 1496 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 40 1523 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 42 1640 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 50 1666 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 51 1668 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 52 1695 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 65 1781 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 44 1649 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 49A 1658.1 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 49B 1658.2 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 56 1707 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 80 1893 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 5 693 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 8 749 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 10 839 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 14 865 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 16 888 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 29 1326 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 35 1440 14 A44G35C25T43 ND A44G32C27T37 A. baumannii 41
1524 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 46 1652
14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 47 1653 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 48 1657 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 57 1709 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 61 1727 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 63 1762 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 67 1806 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 75 1881 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 77 1886 14
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 1 649 46
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 2 653 46
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 39 1497 16
A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 24 1198 15
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 28 1243 15
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 43 1648 15
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 62 1746 15
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 4 689 15
A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 68 1822 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 69 1823A 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 70 1823B 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 71 1826 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 72 1860 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 81 1924 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 82 1929 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 85 1966 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 11 841 3
A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 32 1415 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 45 1651 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 54 1697 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 58 1712 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 60 1725 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 66 1802 24
A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 76 1883 24 ND
A43G36C20T43 A44G32C27T37 A. baumannii 78 1891 24 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 79 1892 24 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 83 1947 24 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 84 1964 24 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 53 1696 24 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 36 1458 49 A44G35C25T43
A44G35C22T41 A44G32C27T37 A. baumannii 59 1716 9 A44G35C25T43
A44G35C21T42 A44G32C26T38 A. baumannii 9 805 30 A44G35C25T43
A44G35C19T44 A44G32C27T37 A. baumannii 18 967 39 A45G34C25T43
A44G35C22T41 A44G32C26T38 A. baumannii 30 1322 48 A44G35C25T43
A43G36C20T43 A44G32C27T37 A. baumannii 26 1218 50 A44G35C25T43
A44G35C21T42 A44G32C26T38 A. sp. 13TU 15 875 A1 A47G33C24T43
A46G32C20T44 A44G33C27T36 A. sp. 13TU 17 895 A1 A47G33C24T43
A46G32C20T44 A44G33C27T36 A. sp. 3 12 853 B7 A46G35C24T42
A42G34C20T46 A43G33C24T40 A. johnsonii 25 1202 NEW1 A46G35C23T43
A42G35C21T44 A43G33C23T41 A. sp. 2082 87 2082 NEW2 A46G36C22T43
A42G32C20T48 A42G34C23T41
[0440] TABLE-US-00030 TABLE 17B Base Compositions Determined from
A. baumannii DNA Samples Obtained from Walter Reed Hospital and
Amplified with Triangulation Genotyping Analysis Primer Pair Nos.
1158 and 1160 and 1165 PP No: 1158 PP No: 1160 PP No: 1165 Species
Ibis# Isolate ST mutY mutY fumC A. baumannii 20 1082 1 A27G21C25T22
A32G35C29T33 A40G33C30T36 A. baumannii 13 854 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 22 1162 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 27 1230 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 31 1367 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 37 1459 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 55 1700 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 64 1777 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 73 1861 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 74 1877 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 86 1972 10 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 3 684 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 6 720 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 7 726 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 19 1079 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 21 1123 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 23 1188 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 33 1417 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 34 1431 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 38 1496 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 40 1523 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 42 1640 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 50 1666 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 51 1668 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 52 1695 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 65 1781 11 A27G21C25T22
A32G34C28T35 A40G33C30T36 A. baumannii 44 1649 12 A27G21C26T21
A32G34C29T34 A40G33C30T36 A. baumannii 49A 1658.1 12 A27G21C26T21
A32G34C29T34 A40G33C30T36 A. baumannii 49B 1658.2 12 A27G21C26T21
A32G34C29T34 A40G33C30T36 A. baumannii 56 1707 12 A27G21C26T21
A32G34C29T34 A40G33C30T36 A. baumannii 80 1893 12 A27G21C26T21
A32G34C29T34 A40G33C30T36 A. baumannii 5 693 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 8 749 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 10 839 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 14 865 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 16 888 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 29 1326 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 35 1440 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 41 1524 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 46 1652 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 47 1653 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 48 1657 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 57 1709 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 61 1727 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 63 1762 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 67 1806 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 75 1881 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 77 1886 14 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. baumannii 1 649 46 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 2 653 46 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 39 1497 16 A29G19C26T21
A31G35C29T34 A40G34C29T36 A. baumannii 24 1198 15 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 28 1243 15 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 43 1648 15 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 62 1746 15 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 4 689 15 A29G19C26T21
A31G35C29T34 A40G33C29T37 A. baumannii 68 1822 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 69 1823A 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 70 1823B 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 71 1826 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 72 1860 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 81 1924 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 82 1929 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 85 1966 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 11 841 3 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 32 1415 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 45 1651 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 54 1697 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 58 1712 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 60 1725 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 66 1802 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 76 1883 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 78 1891 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 79 1892 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 83 1947 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 84 1964 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 53 1696 24 A27G21C26T21
A32G35C28T34 A40G33C30T36 A. baumannii 36 1458 49 A27G20C27T21
A32G35C28T34 A40G33C30T36 A. baumannii 59 1716 9 A27G21C25T22
A32G35C28T34 A39G33C30T37 A. baumannii 9 805 30 A27G21C25T22
A32G35C28T34 A39G33C30T37 A. baumannii 18 967 39 A27G21C26T21
A32G35C28T34 A39G33C30T37 A. baumannii 30 1322 48 A28G21C24T22
A32G35C29T33 A40G33C30T36 A. baumannii 26 1218 50 A27G21C25T22
A31G36C28T34 A40G33C29T37 A. sp. 13TU 15 875 A1 A27G21C25T22
A30G36C26T37 A41G34C28T36 A. sp. 13TU 17 895 A1 A27G21C25T22
A30G36C26T37 A41G34C28T36 A. sp. 3 12 853 B7 A26G23C23T23
A30G36C27T36 A39G37C26T37 A. johnsonii 25 1202 NEW1 A25G23C24T23
A30G35C30T34 A38G37C26T38 A. sp. 2082 87 2082 NEW2 A26G22C24T23
A31G35C28T35 A42G34C27T36
[0441] TABLE-US-00031 TABLE 17C Base Compositions Determined from
A. baumannii DNA Samples Obtained from Walter Reed Hospital and
Amplified with Triangulation Genotyping Analysis Primer Pair Nos.
1167 and 1170 and 1171 PP No: 1167 PP No: 1170 PP No: 1171 Species
Ibis# Isolate ST fumC fumC ppa A. baumannii 20 1082 1 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 13 854 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 22 1162 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 27 1230 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 31 1367 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 37 1459 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 55 1700 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 64 1777 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 73 1861 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 74 1877 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 86 1972 10 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 3 684 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 6 720 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 7 726 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 19 1079 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 21 1123 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 23 1188 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 33 1417 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 34 1431 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 38 1496 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 40 1523 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 42 1640 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 50 1666 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 51 1668 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 52 1695 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 65 1781 11 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 44 1649 12 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 49A 1658.1 12 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 49B 1658.2 12 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 56 1707 12 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 80 1893 12 A41G34C34T38
A38G27C21T50 A35G37C33T44 A. baumannii 5 693 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 8 749 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 10 839 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 14 865 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 16 888 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 29 1326 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 35 1440 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 41 1524 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 46 1652 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 47 1653 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 48 1657 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 57 1709 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 61 1727 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 63 1762 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 67 1806 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 75 1881 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 77 1886 14 A40G35C34T38
A38G27C21T50 A35G37C30T47 A. baumannii 1 649 46 A41G35C32T39
A37G28C20T51 A35G37C32T45 A. baumannii 2 653 46 A41G35C32T39
A37G28C20T51 A35G37C32T45 A. baumannii 39 1497 16 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 24 1198 15 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 28 1243 15 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 43 1648 15 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 62 1746 15 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 4 689 15 A41G35C32T39
A37G28C20T51 A35G37C30T47 A. baumannii 68 1822 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 69 1823A 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 70 1823B 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 71 1826 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 72 1860 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 81 1924 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 82 1929 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 85 1966 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 11 841 3 A41G34C35T37
A38G27C20T51 A35G37C31T46 A. baumannii 32 1415 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 45 1651 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 54 1697 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 58 1712 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 60 1725 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 66 1802 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 76 1883 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 78 1891 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 79 1892 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 83 1947 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 84 1964 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 53 1696 24 A40G35C34T38
A39G26C22T49 A35G37C33T44 A. baumannii 36 1458 49 A40G35C34T38
A39G26C22T49 A35G37C30T47 A. baumannii 59 1716 9 A40G35C32T40
A38G27C20T51 A36G35C31T47 A. baumannii 9 805 30 A40G35C32T40
A38G27C21T50 A35G36C29T49 A. baumannii 18 967 39 A40G35C33T39
A38G27C20T51 A35G37C30T47 A. baumannii 30 1322 48 A40G35C35T37
A38G27C21T50 A35G37C30T47 A. baumannii 26 1218 50 A40G35C34T38
A38G27C21T50 A35G37C33T44 A. sp. 13TU 15 875 A1 A41G39C31T36
A37G26C24T49 A34G38C31T46 A. sp. 13TU 17 895 A1 A41G39C31T36
A37G26C24T49 A34G38C31T46 A. sp. 3 12 853 B7 A43G37C30T37
A36G27C24T49 A34G37C31T47 A. johnsonii 25 1202 NEW1 A42G38C31T36
A40G27C19T50 A35G37C32T45 A. sp. 2082 87 2082 NEW2 A43G37C32T35
A37G26C21T52 A35G38C31T45
[0442] TABLE-US-00032 TABLE 18A Base Compositions Determined from
A. baumannii DNA Samples Obtained from Northwestern Medical Center
and Amplified with Speciating Primer Pair No. 2922 and
Triangulation Genotyping Analysis Primer Pair Nos. 1151 and 1156 PP
No: 2922 PP No: 1151 PP No: 1156 Species Ibis# Isolate ST efp trpE
adk A. baumannii 54 536 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A.
baumannii 87 665 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A.
baumannii 8 80 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 9 91 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 10 92 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 11 131 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 12 137 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 21 218 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 26 242 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 94 678 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 1 9 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 2 13 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 3 19 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 4 24 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 5 36 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 6 39 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 13 139 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 15 165 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 16 170 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 17 186 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 20 202 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 22 221 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 24 234 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 25 239 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 33 370 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 34 389 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A.
baumannii 19 201 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A.
baumannii 27 257 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 29 301 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 31 354 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 36 422 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 37 424 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 38 434 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 39 473 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 40 482 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 44 512 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 45 516 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 47 522 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 48 526 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 50 528 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 52 531 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 53 533 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 56 542 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 59 550 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 62 556 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 64 557 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 70 588 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 73 603 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 74 605 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 75 606 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 77 611 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 79 622 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 83 643 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 85 653 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 89 669 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 93 674 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 23 228 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 32 369 52 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 35 393 52 A44G35C25T43 A43G36C20T43 A44G32C26T38 A.
baumannii 30 339 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 41 485 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 42 493 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 43 502 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 46 520 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 49 527 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 51 529 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 65 562 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 68 579 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 57 546 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 58 548 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 60 552 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 61 555 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 63 557 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 66 570 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 67 578 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 69 584 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 71 593 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 72 602 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 76 609 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 78 621 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 80 625 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 81 628 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 82 632 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 84 649 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 86 655 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 88 668 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 90 671 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 91 672 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 92 673 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A.
baumannii 18 196 55 A44G35C25T43 A44G35C20T43 A44G32C27T37 A.
baumannii 55 537 27 A44G35C25T43 A44G35C19T44 A44G32C27T37 A.
baumannii 28 263 27 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. sp. 3
14 164 B7 A46G35C24T42 A42G34C20T46 A43G33C24T40 mixture 7 71 ?
mixture ND ND
[0443] TABLE-US-00033 TABLE 18B Base Compositions Determined from
A. baumannii DNA Samples Obtained from Northwestern Medical Center
and Amplified with Triangulation Genotyping Analysis Primer Pair
Nos. 1158, 1160 and 1165 PP No: 1158 PP No: 1160 PP No: 1165
Species Ibis# Isolate ST mutY mutY fumC A. baumannii 54 536 3
A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 87 665 3
A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 8 80 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 9 91 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 10 92 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 11 131 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 12 137 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 21 218 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 26 242 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 94 678 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 1 9 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 2 13 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 3 19 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 4 24 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 5 36 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 6 39 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 13 139 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 15 165 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 16 170 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 17 186 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 20 202 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 22 221 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 24 234 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 25 239 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 33 370 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 34 389 10
A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 19 201 14
A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 27 257 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 29 301 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 31 354 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 36 422 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 37 424 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 38 434 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 39 473 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 40 482 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 44 512 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 45 516 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 47 522 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 48 526 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 50 528 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 52 531 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 53 533 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 56 542 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 59 550 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 62 556 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 64 557 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 70 588 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 73 603 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 74 605 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 75 606 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 77 611 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 79 622 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 83 643 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 85 653 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 89 669 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 93 674 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 23 228 51
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 32 369 52
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 35 393 52
A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 30 339 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 41 485 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 42 493 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 43 502 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 46 520 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 49 527 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 51 529 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 65 562 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 68 579 53
A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 57 546 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 58 548 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 60 552 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 61 555 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 63 557 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 66 570 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 67 578 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 69 584 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 71 593 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 72 602 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 76 609 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 78 621 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 80 625 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 81 628 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 82 632 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 84 649 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 86 655 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 88 668 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 90 671 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 91 672 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 92 673 54
A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 18 196 55
A27G21C25T22 A31G36C27T35 A40G33C29T37 A. baumannii 55 537 27
A27G21C25T22 A32G35C28T34 A40G33C30T36 A. baumannii 28 263 27
A27G21C25T22 A32G35C28T34 A40G33C30T36 A. sp. 3 14 164 B7
A26G23C23T23 A30G36C27T36 A39G37C26T37 mixture 7 71 ? ND ND ND
[0444] TABLE-US-00034 TABLE 18C Base Compositions Determined from
A. baumannii DNA Samples Obtained from Northwestern Medical Center
and Amplified with Triangulation Genotyping Analysis Primer Pair
Nos. 1167, 1170 and 1171 PP No: 1167 PP No: 1170 PP No: 1171
Species Ibis# Isolate ST fumC fumC ppa A. baumannii 54 536 3
A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 87 665 3
A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 8 80 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 9 91 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 10 92 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 11 131 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 12 137 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 21 218 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 26 242 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 94 678 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 1 9 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 2 13 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 3 19 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 4 24 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 5 36 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 6 39 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 13 139 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 15 165 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 16 170 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 17 186 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 20 202 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 22 221 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 24 234 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 25 239 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 33 370 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 34 389 10
A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 19 201 14
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 27 257 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 29 301 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 31 354 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 36 422 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 37 424 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 38 434 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 39 473 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 40 482 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 44 512 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 45 516 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 47 522 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 48 526 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 50 528 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 52 531 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 53 533 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 56 542 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 59 550 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 62 556 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 64 557 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 70 588 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 73 603 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 74 605 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 75 606 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 77 611 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 79 622 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 83 643 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 85 653 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 89 669 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 93 674 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 23 228 51
A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 32 369 52
A40G35C34T38 A38G27C21T50 A35G37C31T46 A. baumannii 35 393 52
A40G35C34T38 A38G27C21T50 A35G37C31T46 A. baumannii 30 339 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 41 485 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 42 493 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 43 502 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 46 520 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 49 527 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 51 529 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 65 562 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 68 579 53
A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 57 546 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 58 548 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 60 552 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 61 555 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 63 557 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 66 570 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 67 578 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 69 584 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 71 593 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 72 602 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 76 609 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 78 621 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 80 625 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 81 628 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 82 632 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 84 649 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 86 655 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 88 668 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 90 671 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 91 672 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 92 673 54
A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 18 196 55
A42G34C33T38 A38G27C20T51 A35G37C31T46 A. baumannii 55 537 27
A40G35C33T39 A38G27C20T51 A35G37C33T44 A. baumannii 28 263 27
A40G35C33T39 A38G27C20T51 A35G37C33T44 A. sp. 3 14 164 B7
A43G37C30T37 A36G27C24T49 A34G37C31T47 mixture 7 71 -- ND ND ND
[0445] Base composition analysis of the samples obtained from
Walter Reed hospital indicated that a majority of the strain types
identified were the same strain types already characterized by the
OIF study of Example 12. This is not surprising since at least some
patients from which clinical samples were obtained in OIF were
transferred to the Walter Reed Hospital (WRAIR). Examples of these
common strain types include: ST10, ST11, ST12, ST14, ST15, ST16 and
ST46. A strong correlation was noted between these strain types and
the presence of mutations in the gyrA and parC which confer
quinolone drug resistance.
[0446] In contrast, the results of base composition analysis of
samples obtained from Northwestern Medical Center indicate the
presence of 4 major strain types: ST10, ST51, ST53 and ST54. All of
these strain types have the gyrA quinolone resistance mutation and
most also have the parC quinolone resistance mutation, with the
exception of ST35. This observation is consistent with the current
understanding that the gyrA mutation generally appears before the
parC mutation and suggests that the acquisition of these drug
resistance mutations is rather recent and that resistant isolates
are taking over the wild-type isolates. Another interesting
observation was that a single isolate of ST3 (isolate 841) displays
a triangulation genotyping analysis pattern similar to other
isolates of ST3, but the codon analysis amplification product base
compositions indicate that this isolate has not yet undergone the
quinolone resistance mutations in gyrA and parC.
[0447] The six isolates that represent species other than
Acinetobacter baumannii in the samples obtained from the Walter
Reed Hospital were each found to not carry the drug resistance
mutations.
[0448] The results described above involved analysis of 183 samples
using the methods and compositions of the present invention.
Results were provided to collaborators at the Walter Reed hospital
and Northwestern Medical center within a week of obtaining samples.
This example highlights the rapid throughout characteristics of the
analysis platform and the resolving power of triangulation
genotyping analysis and codon analysis for identification of and
determination of drug resistance in bacteria.
Example 14: Identification of Drug Resistance Genes and Virulence
Factors in Staphylococcus aureus
[0449] An eight primer pair panel was designed for identification
of drug resistance genes and virulence factors of Staphylococcus
aureus and is shown in Table 19. The primer sequences are found in
Table 2 and are cross-referenced by the primer pair numbers, primer
pair names or SEQ ID NOs listed in Table 19. TABLE-US-00035 TABLE
19 Primer Pairs for Identification of Drug Resistance Genes and
Virulence Factors in Staphylococcus aureus Forward Reverse Primer
Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name
NO:) Reverse Primer Name NO:) Gene 879 MECA_Y14051_4507_4530_F 288
MECA_Y14051_4555_4581_R 1269 mecA 2056 MECI-R_NC003923-41798- 698
MECI-R_NC003923-41798- 1420 MecI-R 41609_33_60_F 41609_86_113_R
2081 ERMA_NC002952-55890- 217 ERMA_NC002952-55890- 1167 ermA
56621_366_395_F 56621_438_465_R 2086 ERMC_NC005908-2004- 399
ERMC_NC005908-2004- 1041 ermC 2738_85_116_F 2738_173_206_R 2095
PVLUK_NC003923-1529595- 456 PVLUK_NC003923-1529595- 1261 Pv-luk
1531285_688_713_F 1531285_775_804_R 2249 TUFB_NC002758-615038- 430
TUFB_NC002758-615038- 1321 tufB 616222_696_725_F 616222_793_820_R
2256 NUC_NC002758-894288- 174 NUC_NC002758-894288- 853 Nuc
894974_316_345_F 894974_396_421_R 2313 MUPR_X75439_2486_2516_F 172
MUPR_X75439_2548_2574_R 1360 mupR
[0450] Primer pair numbers 2256 and 2249 are confirmation primers
designed with the aim of high level identification of
Staphylococcus aureus. The nuc gene is a Staphylococcus
aureus-specific marker gene. The tufB gene is a universal
housekeeping gene but the bioagent identifying amplicon defined by
primer pair number 2249 provides a unique base composition (A43 G28
C19 T35) which distinguishes Staphylococcus aureus from other
members of the genus Staphylococcus.
[0451] High level methicillin resistance in a given strain of
Staphylococcus aureus is indicated by bioagent identifying
amplicons defined by primer pair numbers 879 and 2056. Analyses
have indicated that primer pair number 879 is not expected to prime
S. sciuri homolog or Enterococcus faecalis/faciem
ampicillin-resistant PBP5 homologs.
[0452] Macrolide and erythromycin resistance in a given strain of
Staphylococcus aureus is indicated by bioagent identifying
amplicons defined by primer pair numbers 2081 and 2086.
[0453] Resistance to mupriocin in a given strain of Staphylococcus
aureus is indicated by bioagent identifying amplicons defined by
primer pair number 2313.
[0454] Virulence in a given strain of Staphylococcus aureus is
indicated by bioagent identifying amplicons defined by primer pair
number 2095. This primer pair can simultaneously and identify the
pvl (lukS-PV) gene and the lukD gene which encodes a homologous
enterotoxin. A bioagent identifying amplicon of the lukD gene has a
six nucleobase length difference relative to the lukS-PV gene.
[0455] A total of 32 blinded samples of different strains of
Staphylococcus aureus were provided by the Center for Disease
Control (CDC). Each sample was analyzed by PCR amplification with
the eight primer pair panel, followed by purification and
measurement of molecular masses of the amplification products by
mass spectrometry. Base compositions for the amplification products
were calculated. The base compositions provide the information
summarized above for each primer pair. The results are shown in
Tables 20A and B. One result noted upon un-blinding of the samples
is that each of the PVL+ identifications agreed with PVL+
identified in the same samples by standard PCR assays. These
results indicate that the panel of eight primer pairs is useful for
identification of drug resistance and virulence sub-species
characteristics for Staphylococcus aureus. It is expected that a
kit comprising one or more of the members of this panel will be a
useful embodiment of the present invention. TABLE-US-00036 TABLE
20A Drug Resistance and Virulence Identified in Blinded Samples of
Various Strains of Staphylococcus aureus with Primer Pair Nos.
2081, 2086, 2095 and 2256 Primer Primer Primer Sample Primer Pair
No. Pair No. Pair No. Pair No. Index No. 2081 (ermA) 2086 (ermC)
2095 (pv-luk) 2256 (nuc) CDC0010 - - PVL-/lukD+ + CDC0015 - -
PVL+/lukD+ + CDC0019 - + PVL-/lukD+ + CDC0026 + - PVL-/lukD+ +
CDC0030 + - PVL-/lukD+ + CDC004 - - PVL+/lukD+ + CDC0014 - +
PVL+/lukD+ + CDC008 - - PVL-/lukD+ + CDC001 + - PVL-/lukD+ +
CDC0022 + - PVL-/lukD+ + CDC006 + - PVL-/lukD+ + CDC007 - -
PVL-/lukD+ + CDCVRSA1 + - PVL-/lukD+ + CDCVRSA2 + + PVL-/lukD+ +
CDC0011 + - PVL-/lukD+ + CDC0012 - - PVL+/lukD- + CDC0021 + -
PVL-/lukD+ + CDC0023 + - PVL-/lukD+ + CDC0025 + - PVL-/lukD+ +
CDC005 - - PVL-/lukD+ + CDC0018 + - PVL+/lukD- + CDC002 - -
PVL-/lukD+ + CDC0028 + - PVL-/lukD+ + CDC003 - - PVL-/lukD+ +
CDC0013 - - PVL+/lukD+ + CDC0016 - - PVL-/lukD+ + CDC0027 + -
PVL-/lukD+ + CDC0029 - - PVL+/lukD+ + CDC0020 - + PVL-/lukD+ +
CDC0024 - - PVL-/lukD+ + CDC0031 - - PVL-/lukD+ +
[0456] TABLE-US-00037 TABLE 20B Drug Resistance and Virulence
Identified in Blinded Samples of Various Strains of Staphylococcus
aureus with Primer Pair Nos. 2249, 879, 2056, and 2313 Sample
Primer Pair No. 2249 Primer Pair No. Primer Pair No. Primer Pair
No. Index No. (tufB) 879 (mecA) 2056 (mecI-R) 2313 (mupR) CDC0010
Staphylococcus aureus + + - CDC0015 Staphylococcus aureus - - -
CDC0019 Staphylococcus aureus + + - CDC0026 Staphylococcus aureus +
+ - CDC0030 Staphylococcus aureus + + - CDC004 Staphylococcus
aureus + + - CDC0014 Staphylococcus aureus + + - CDC008
Staphylococcus aureus + + - CDC001 Staphylococcus aureus + + -
CDC0022 Staphylococcus aureus + + - CDC006 Staphylococcus aureus +
+ + CDC007 Staphylococcus aureus + + - CDCVRSA1 Staphylococcus
aureus + + - CDCVRSA2 Staphylococcus aureus + + - CDC0011
Staphylococcus aureus - - - CDC0012 Staphylococcus aureus + + -
CDC0021 Staphylococcus aureus + + - CDC0023 Staphylococcus aureus +
+ - CDC0025 Staphylococcus aureus + + - CDC005 Staphylococcus
aureus + + - CDC0018 Staphylococcus aureus + + - CDC002
Staphylococcus aureus + + - CDC0028 Staphylococcus aureus + + -
CDC003 Staphylococcus aureus + + - CDC0013 Staphylococcus aureus +
+ - CDC0016 Staphylococcus aureus + + - CDC0027 Staphylococcus
aureus + + - CDC0029 Staphylococcus aureus + + - CDC0020
Staphylococcus aureus - - - CDC0024 Staphylococcus aureus + + -
CDC0031 Staphylococcus scleiferi - - -
Example 15
Selection and Use of Triangulation Genotyping Analysis Primer Pairs
for Staphylococcus aureus
[0457] To combine the power of high-throughput mass spectrometric
analysis of bioagent identifying amplicons with the sub-species
characteristic resolving power provided by triangulation genotyping
analysis, a panel of eight triangulation genotyping analysis primer
pairs was selected. The primer pairs are designed to produce
bioagent identifying amplicons within six different housekeeping
genes which are listed in Table 21. The primer sequences are found
in Table 2 and are cross-referenced by the primer pair numbers,
primer pair names or SEQ ID NOs listed in Table 21. TABLE-US-00038
TABLE 21 Primer Pairs for Triangulation Genotyping Analysis of
Staphylococcus aureus Forward Reverse Primer Primer Primer Pair
(SEQ ID (SEQ ID Target No. Forward Primer Name NO:) Reverse Primer
Name NO:) Gene 2146 ARCC_NC003923-2725050- 437
ARCC_NC003923-2725050- 1137 arcC 2724595_131_161_F
2724595_214_245_R 2149 AROE_NC003923-1674726- 530
AROE_NC003923-1674726- 891 aroE 1674277_30_62_F 1674277_155_181_R
2150 AROE_NC003923-1674726- 474 AROE_NC003923-1674726- 869 aroE
1674277_204_232_F 1674277_308_335_R 2156 GMK_NC003923-1190906- 268
GMK_NC003923-1190906- 1284 gmk 1191334_301_329_F 1191334_403_432_R
2157 PTA_NC003923-628885- 418 PTA_NC003923-628885- 1301 pta
629355_237_263_F 629355_314_345_R 2161 TPI_NC003923-830671- 318
TPI_NC003923-830671- 1300 tpi 831072_1_34_F 831072_97_129_R 2163
YQI_NC003923-378916- 440 YQI_NC003923-378916- 1076 yqi
379431_142_167_F 379431_259_284_R 2166 YQI_NC003923-378916- 219
YQI_NC003923-378916- 1013 yqi 379431_275_300_F 379431_364_396_R
[0458] The same samples analyzed for drug resistance and virulence
in Example 14 were subjected to triangulation genotyping analysis.
The primer pairs of Table 21 were used to produce amplification
products by PCR, which were subsequently purified and measured by
mass spectrometry. Base compositions were calculated from the
molecular masses and are shown in Tables 22A and 22B.
TABLE-US-00039 TABLE 22A Triangulation Genotyping Analysis of
Blinded Samples of Various Strains of Staphylococcus aureus with
Primer Pair Nos. 2146, 2149, 2150 and 2156 Sample Primer Pair No.
Primer Pair No. Primer Pair No. Primer Pair No. Index No. Strain
2146 (arcC) 2149(aroE) 2150 (aroE) 2156 (gmk) CDC0010 COL A44 G24
C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0015 COL
A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32
CDC0019 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30
C20 T32 CDC0026 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43
A50 G30 C20 T32 CDC0030 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36
C13 T43 A50 G30 C20 T32 CDC004 COL A44 G24 C18 T29 A59 G24 C18 T51
A40 G36 C13 T43 A50 G30 C20 T32 CDC0014 COL A44 G24 C18 T29 A59 G24
C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC008 ???? A44 G24 C18 T29
A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC001 Mu50 A45 G23
C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC0022
Mu50 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21
T31 CDC006 Mu50 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51
G29 C21 T31 CDC0011 MRSA252 A45 G24 C18 T28 A58 G24 C19 T51 A41 G36
C12 T43 A51 G29 C21 T31 CDC0012 MRSA252 A45 G24 C18 T28 A58 G24 C19
T51 A41 G36 C12 T43 A51 G29 C21 T31 CDC0021 MRSA252 A45 G24 C18 T28
A58 G24 C19 T51 A41 G36 C12 T43 A51 G29 C21 T31 CDC0023 ST:110 A45
G24 C18 T28 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0025
ST:110 A45 G24 C18 T28 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20
T32 CDC005 ST:338 A44 G24 C18 T29 A59 G23 C19 T51 A40 G36 C14 T42
A51 G29 C21 T31 CDC0018 ST:338 A44 G24 C18 T29 A59 G23 C19 T51 A40
G36 C14 T42 A51 G29 C21 T31 CDC002 ST:108 A46 G23 C20 T26 A58 G24
C19 T51 A42 G36 C12 T42 A51 G29 C20 T32 CDC0028 ST:108 A46 G23 C20
T26 A58 G24 C19 T51 A42 G36 C12 T42 A51 G29 C20 T32 CDC003 ST:107
A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31
CDC0013 ST:12 ND A59 G24 C18 T51 A40 G36 C13 T43 A51 G29 C21 T31
CDC0016 ST:120 A45 G23 C18 T29 A58 G24 C19 T51 A40 G37 C13 T42 A51
G29 C21 T31 CDC0027 ST:105 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36
C13 T43 A51 G29 C21 T31 CDC0029 MSSA476 A45 G23 C20 T27 A58 G24 C19
T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0020 ST:15 A44 G23 C21 T27
A59 G23 C18 T52 A40 G36 C13 T43 A50 G30 C20 T32 CDC0024 ST:137 A45
G23 C20 T27 A57 G25 C19 T51 A40 G36 C13 T43 A51 G29 C22 T30 CDC0031
*** No product No product No product No product
[0459] TABLE-US-00040 TABLE 22B Triangulation Genotyping Analysis
of Blinded Samples of Various Strains of Staphylococcus aureus with
Primer Pair Nos. 2146, 2149, 2150 and 2156 Sample Primer Pair No.
Primer Pair No. Primer Pair No. Primer Pair No. Index No. Strain
2157 (pta) 2161 (tpi) 2163 (yqi) 2166 (yqi) CDC0010 COL A32 G25 C23
T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0015 COL A32
G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0019
COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37
CDC0026 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30
C18 T37 CDC0030 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43
A37 G30 C18 T37 CDC004 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37
C22 T43 A37 G30 C18 T37 CDC0014 COL A32 G25 C23 T29 A51 G28 C22 T28
A41 G37 C22 T43 A37 G30 C18 T37 CDC008 unknown A32 G25 C23 T29 A51
G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC001 Mu50 A33 G25 C22
T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC0022 Mu50
A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36
CDC006 Mu50 A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31
C19 T36 CDC0011 MRSA252 A32 G25 C23 T29 A50 G28 C22 T29 A42 G36 C22
T43 A37 G30 C18 T37 CDC0012 MRSA252 A32 G25 C23 T29 A50 G28 C22 T29
A42 G36 C22 T43 A37 G30 C18 T37 CDC0021 MRSA252 A32 G25 C23 T29 A50
G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0023 ST:110 A32 G25
C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0025
ST:110 A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18
T37 CDC005 ST:338 A32 G25 C24 T28 A51 G27 C21 T30 A42 G36 C22 T43
A37 G30 C18 T37 CDC0018 ST:338 A32 G25 C24 T28 A51 G27 C21 T30 A42
G36 C22 T43 A37 G30 C18 T37 CDC002 ST:108 A33 G25 C23 T28 A50 G28
C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0028 ST:108 A33 G25 C23
T28 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC003 ST:107
A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37
CDC0013 ST:12 A32 G25 C23 T29 A51 G28 C22 T28 A42 G36 C22 T43 A37
G30 C18 T37 CDC0016 ST:120 A32 G25 C24 T28 A50 G28 C21 T30 A42 G36
C22 T43 A37 G30 C18 T37 CDC0027 ST:105 A33 G25 C22 T29 A50 G28 C22
T29 A43 G36 C21 T43 A36 G31 C19 T36 CDC0029 MSSA476 A33 G25 C22 T29
A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC0020 ST:15 A33
G25 C22 T29 A50 G28 C21 T30 A42 G36 C22 T43 A36 G31 C18 T37 CDC0024
ST:137 A33 G25 C22 T29 A51 G28 C22 T28 A42 G36 C22 T43 A37 G30 C18
T37 CDC0031 *** A34 G25 C25 T25 A51 G27 C24 T27 No product No
product Note: *** The sample CDC0031 was identified as
Staphylococcus scleiferi as indicated in Example 14. Thus, the
triangulation genotyping primers designed for Staphylococcus aureus
would generally not be expected to prime and produce amplification
products of this organism. Tables 22A and 22B indicate that
amplification products are obtained for this organism only with
primer pair numbers 2157 and 2161.
[0460] A total of thirteen different genotypes of Staphylococcus
aureus were identified according to the unique combinations of base
compositions across the eight different bioagent identifying
amplicons obtained with the eight primer pairs. These results
indicate that this eight primer pair panel is useful for analysis
of unknown or newly emerging strains of Staphylococcus aureus. It
is expected that a kit comprising one or more of the members of
this panel will be a useful embodiment of the present
invention.
Example 16
Selection and Use of Triangulation Genotyping Analysis Primer Pairs
for Members of the Bacterial Genus Vibrio
[0461] To combine the power of high-throughput mass spectrometric
analysis of bioagent identifying amplicons with the sub-species
characteristic resolving power provided by triangulation genotyping
analysis, a panel of eight triangulation genotyping analysis primer
pairs was selected. The primer pairs are designed to produce
bioagent identifying amplicons within seven different housekeeping
genes which are listed in Table 23. The primer sequences are found
in Table 2 and are cross-referenced by the primer pair numbers,
primer pair names or SEQ ID NOs listed in Table 23. TABLE-US-00041
TABLE 23 Primer Pairs for Triangulation Genotyping Analysis of
Members of the Bacterial Genus Vibrio Forward Reverse Primer Primer
Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name NO:)
Reverse Primer Name NO:) Gene 1098 RNASEP_VBC_331_349_F 325
RNASEP_VBC_388_414_R 1163 RNAse P 2000 CTXB_NC002505_46_70_F 278
CTXB_NC002505_132_162_R 1039 ctxB 2001 FUR_NC002505_87_113_F 465
FUR_NC002505_205_228_R 1037 fur 2011 GYRB_NC002505_1161_1190_F 148
GYRB_NC002505_1255_1284_R 1172 gyrB 2012 OMPU_NC002505_85_110_F 190
OMPU_NC002505_154_180_R 1254 ompU 2014 OMPU_NC002505_431_455_F 266
OMPU_NC002505_544_567_R 1094 ompU 2323 CTXA_NC002505-1568114- 508
CTXA_NC002505-1568114- 1297 ctxA 1567341_122_149_F
1567341_186_214_R 2927 GAPA_NC002505_694_721_F 259
GAPA_NC_002505_29_58_R 1060 gapA
[0462] A group of 50 bacterial isolates containing multiple strains
of both environmental and clinical isolates of Vibrio cholerae, 9
other Vibrio species, and 3 species of Photobacteria were tested
using this panel of primer pairs. Base compositions of
amplification products obtained with these 8 primer pairs were used
to distinguish amongst various species tested, including
sub-species differentiation within Vibrio cholerae isolates. For
instance, the non-O1/non-O139 isolates were clearly resolved from
the O1 and the O139 isolates, as were several of the environmental
isolates of Vibrio cholerae from the clinical isolates.
[0463] It is expected that a kit comprising one or more of the
members of this panel will be a useful embodiment of the present
invention.
Example 17
Selection and Use of Triangulation Genotyping Analysis Primer Pairs
for Members of the Bacterial Genus Pseudomonas
[0464] To combine the power of high-throughput mass spectrometric
analysis of bioagent identifying amplicons with the sub-species
characteristic resolving power provided by triangulation genotyping
analysis, a panel of twelve triangulation genotyping analysis
primer pairs was selected. The primer pairs are designed to produce
bioagent identifying amplicons within seven different housekeeping
genes which are listed in Table 24. The primer sequences are found
in Table 2 and are cross-referenced by the primer pair numbers,
primer pair names or SEQ ID NOs listed in Table 24. TABLE-US-00042
TABLE 24 Primer Pairs for Triangulation Genotyping Analysis of
Members of the Bacterial Genus Pseudomonas Forward Reverse Primer
Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name
NO:) Reverse Primer Name NO:) Gene 2949 ACS_NC002516-970624- 376
ACS_NC002516-970624- 1265 acsA 971013_299_316_F 971013_364_383_R
2950 ARO_NC002516-26883- 267 ARO_NC002516-26883- 1341 aroE
27380_4_26_F 27380_111_128_R 2951 ARO_NC002516-26883- 705
ARO_NC002516-26883- 1056 aroE 27380_356_377_F 27380_459_484_R 2954
GUA_NC002516-4226546- 710 GUA_NC002516-4226546- 1259 guaA
4226174_155_178_F 4226174_265_287_R 2956 GUA_NC002516-4226546- 374
GUA_NC002516-4226546- 1111 guaA 4226174_242_263_F 4226174_355_371_R
2957 MUT_NC002516-5551158- 545 MUT_NC002516-5551158- 978 mutL
5550717_5_26_F 5550717_99_116_R 2959 NUO_NC002516-2984589- 249
NUO_NC002516-2984589- 1095 nuoD 2984954_8_26_F 2984954_97_117_R
2960 NUO_NC002516-2984589- 195 NUO_NC002516-2984589- 1376 nuoD
2984954_218_239_F 2984954_301_326_R 2961 PPS_NC002516-1915014- 311
PPS_NC002516-1915014- 1014 pps 1915383_44_63_F 1915383_140_165_R
2962 PPS_NC002516-1915014- 365 PPS_NC002516-1915014- 1052 pps
1915383_240_258_F 1915383_341_360_R 2963 TRP_NC002516-671831- 527
TRP_NC002516-671831- 1071 trpE 672273_24_42_F 672273_131_150_R 2964
TRP_NC002516-671831- 490 TRP_NC002516-671831- 1182 trpE
672273_261_282_F 672273_362_383_R
[0465] It is expected that a kit comprising one or more of the
members of this panel will be a useful embodiment of the present
invention.
[0466] The present invention includes any combination of the
various species and subgeneric groupings falling within the generic
disclosure. This invention therefore includes the generic
description of the invention with a proviso or negative limitation
removing any subject matter from the genus, regardless of whether
or not the excised material is specifically recited herein.
[0467] While in accordance with the patent statutes, description of
the various embodiments and examples have been provided, the scope
of the invention is not to be limited thereto or thereby.
Modifications and alterations of the present invention will be
apparent to those skilled in the art without departing from the
scope and spirit of the present invention.
[0468] Therefore, it will be appreciated that the scope of this
invention is to be defined by the appended claims, rather than by
the specific examples which have been presented by way of
example.
[0469] Each reference (including, but not limited to, journal
articles, U.S. and non-U.S. patents, patent application
publications, international patent application publications, gene
bank gi or accession numbers, internet web sites, and the like)
cited in the present application is incorporated herein by
reference in its entirety.
Sequence CWU 1
1
1464 1 24 DNA Artificial Sequence Primer 1 aaactagata acagtagaca
tcac 24 2 29 DNA Artificial Sequence Primer 2 aaccttaatt ggaaagaaac
ccaagaagt 29 3 17 DNA Artificial Sequence Primer 3 aacgcacaat
cagaagc 17 4 25 DNA Artificial Sequence Primer 4 aactaccgtc
cgcagttcta cttcc 25 5 25 DNA Artificial Sequence Primer 5
aactaccgtc ctcagttcta cttcc 25 6 18 DNA Artificial Sequence Primer
6 aagacgacct gcacgggc 18 7 18 DNA Artificial Sequence Primer 7
aagcggtgga gcatgtgg 18 8 26 DNA Artificial Sequence Primer 8
aaggaaggcg tgatcaccgt tgaaga 26 9 23 DNA Artificial Sequence Primer
9 aaggtactcc ggggataaca ggc 23 10 22 DNA Artificial Sequence Primer
10 aagtcggaat cgctagtaat cg 22 11 19 DNA Artificial Sequence Primer
11 aatctgctat ttggtcagg 19 12 22 DNA Artificial Sequence Primer 12
acaacgaagt acaatacaag ac 22 13 21 DNA Artificial Sequence Primer 13
acaatacaag acaaaagaag g 21 14 19 DNA Artificial Sequence Primer 14
accacgccgt aaacgatga 19 15 24 DNA Artificial Sequence Primer 15
accatgacag aaggcatttt gaca 24 16 22 DNA Artificial Sequence Primer
16 acccagtgct gctgaaccgt gc 22 17 19 DNA Artificial Sequence Primer
17 accgagcaag gagaccagc 19 18 19 DNA Artificial Sequence Primer 18
acctgcccag tgctggaag 19 19 17 DNA Artificial Sequence Primer 19
acgcgaagaa ccttacc 17 20 20 DNA Artificial Sequence Primer 20
actcgttttt aatcagcccg 20 21 20 DNA Artificial Sequence Primer 21
agaacaccga tggcgaaggc 20 22 23 DNA Artificial Sequence Primer 22
agaatcaagt tcccaggggt tac 23 23 20 DNA Artificial Sequence Primer
23 agagtttgat catggctcag 20 24 28 DNA Artificial Sequence Primer 24
agcaggtggt gaaatcggcc acatgatt 28 25 18 DNA Artificial Sequence
Primer 25 agcgtaaagg tgaacctt 18 26 26 DNA Artificial Sequence
Primer 26 agcttttgca tattatatcg agccac 26 27 28 DNA Artificial
Sequence Primer 27 aggacagagt gagtactttg accgaggt 28 28 22 DNA
Artificial Sequence Primer 28 agtctcaaga gtgaacacgt aa 22 29 32 DNA
Artificial Sequence Primer 29 agttataaac acggctttcc tatggcttat cc
32 30 21 DNA Artificial Sequence Primer 30 atactcctga ctgaccgata g
21 31 20 DNA Artificial Sequence Primer 31 atatcgacgg cggtgtttgg 20
32 25 DNA Artificial Sequence Primer 32 atcaatttgg tggccaagaa cctgg
25 33 29 DNA Artificial Sequence Primer 33 atgattacaa ttcaagaagg
tcgtcacgc 29 34 23 DNA Artificial Sequence Primer 34 atggacaagg
ttggcaagga agg 23 35 20 DNA Artificial Sequence Primer 35
atggccatgg cagaagctca 20 36 25 DNA Artificial Sequence Primer 36
atgtcgattg caatccgtac ttgtg 25 37 19 DNA Artificial Sequence Primer
37 atgttgggtt aagtcccgc 19 38 25 DNA Artificial Sequence Primer 38
atgttgggtt aagtcccgca acgag 25 39 28 DNA Artificial Sequence Primer
39 caaaacttat taggtaagcg tgttgact 28 40 27 DNA Artificial Sequence
Primer 40 caaaggtaag caaggacgtt tccgtca 27 41 27 DNA Artificial
Sequence Primer 41 caaaggtaag caaggtcgtt tccgtca 27 42 17 DNA
Artificial Sequence Primer 42 caacgagcgc aaccctt 17 43 17 DNA
Artificial Sequence Primer 43 caacggatgc tggcaag 17 44 31 DNA
Artificial Sequence Primer 44 caagaagaaa aagagcttct aaaaagaata c 31
45 23 DNA Artificial Sequence Primer 45 caagcaaacg cacaatcaga agc
23 46 19 DNA Artificial Sequence Primer 46 caagtcatca tggccctta 19
47 26 DNA Artificial Sequence Primer 47 caataccgca acagcggtgg
cttggg 26 48 19 DNA Artificial Sequence Primer 48 cactggaact
gagacacgg 19 49 20 DNA Artificial Sequence Primer 49 cagaatcaag
ttcccagggg 20 50 24 DNA Artificial Sequence Primer 50 cagagaccgt
tttatcctat cagc 24 51 20 DNA Artificial Sequence Primer 51
cagcgtttcg gcgaaatgga 20 52 29 DNA Artificial Sequence Primer 52
caggagtcgt tcaactcgat ctacatgat 29 53 24 DNA Artificial Sequence
Primer 53 caggtttagt accagaacat gcag 24 54 23 DNA Artificial
Sequence Primer 54 catccacacg gtggtggtga agg 23 55 23 DNA
Artificial Sequence Primer 55 ccacacgccg ttcttcaaca act 23 56 28
DNA Artificial Sequence Primer 56 ccacagttct acttccgtac tactgacg 28
57 19 DNA Artificial Sequence Primer 57 ccagcagccg cggtaatac 19 58
19 DNA Artificial Sequence Primer 58 ccgtaacttc gggagaagg 19 59 20
DNA Artificial Sequence Primer 59 ccgtggtatt ggagttattg 20 60 29
DNA Artificial Sequence Primer 60 cctatattaa tcgtttacag aaactggct
29 61 19 DNA Artificial Sequence Primer 61 cctgataagg gtgaggtcg 19
62 30 DNA Artificial Sequence Primer 62 ccttacttcg aactatgaat
cttttggaag 30 63 14 DNA Artificial Sequence Primer 63 cgaagaacct
tacc 14 64 27 DNA Artificial Sequence Primer 64 cgaagtacaa
tacaagacaa aagaagg 27 65 18 DNA Artificial Sequence Primer 65
cgacgcgctg cgcttcac 18 66 22 DNA Artificial Sequence Primer 66
cgagagggaa acaacccaga cc 22 67 30 DNA Artificial Sequence Primer 67
cgagtatagc taaaaaaata gtttatgaca 30 68 23 DNA Artificial Sequence
Primer 68 cgcaaaaaaa tccagctatt agc 23 69 20 DNA Artificial
Sequence Primer 69 cgccgacttc gacggtgacc 20 70 20 DNA Artificial
Sequence Primer 70 cggaattact gggcgtaaag 20 71 21 DNA Artificial
Sequence Primer 71 cggattggag tctgcaactc g 21 72 22 DNA Artificial
Sequence Primer 72 cggcgtactt caacgacagc ca 22 73 24 DNA Artificial
Sequence Primer 73 cgtaactata acggtcctaa ggta 24 74 26 DNA
Artificial Sequence Primer 74 cgtcagggta aattccgtga agttaa 26 75 26
DNA Artificial Sequence Primer 75 cgtcgggtga ttaaccgtaa caaccg 26
76 26 DNA Artificial Sequence Primer 76 cgtcgtgtaa ttaaccgtaa
caaccg 26 77 20 DNA Artificial Sequence Primer 77 cgtggcggcg
tggttatcga 20 78 25 DNA Artificial Sequence Primer 78 cgtgttgact
attcggggcg ttcag 25 79 18 DNA Artificial Sequence Primer 79
ctagtacgag aggaccgg 18 80 18 DNA Artificial Sequence Primer 80
ctgacacctg cccggtgc 18 81 24 DNA Artificial Sequence Primer 81
ctggcaggta tgcgtggtct gatg 24 82 23 DNA Artificial Sequence Primer
82 ctggctaaaa ctttggcaac ggt 23 83 24 DNA Artificial Sequence
Primer 83 ctgtccctag tacgagagga ccgg 24 84 22 DNA Artificial
Sequence Primer 84 ctgttcttag tacgagagga cc 22 85 24 DNA Artificial
Sequence Primer 85 cttctgcaac aagctgtgga acgc 24 86 24 DNA
Artificial Sequence Primer 86 cttgctggta tgcgtggtct gatg 24 87 29
DNA Artificial Sequence Primer 87 cttggaggta agtctcattt tggtgggca
29 88 19 DNA Artificial Sequence Primer 88 cttgtacaca ccgcccgtc 19
89 30 DNA Artificial Sequence Primer 89 cttgtacttg tggctcacac
ggctgtttgg 30 90 21 DNA Artificial Sequence Primer 90 cttttgcata
ttatatcgag c 21 91 20 DNA Artificial Sequence Primer 91 gaatagcaat
taatccaaat 20 92 18 DNA Artificial Sequence Primer 92 gaaagagttc
ggattggg 18 93 21 DNA Artificial Sequence Primer 93 gaaggatata
cggttgatgt c 21 94 20 DNA Artificial Sequence Primer 94 gaatagcaat
taatccaaat 20 95 20 DNA Artificial Sequence Primer 95 gacacggtcc
agactcctac 20 96 18 DNA Artificial Sequence Primer 96 gacagttcgg
tccctatc 18 97 18 DNA Artificial Sequence Primer 97 gaccacctcg
gcaaccgt 18 98 30 DNA Artificial Sequence Primer 98 gacctacagt
aagaggttct gtaatgaacc 30 99 16 DNA Artificial Sequence Primer 99
gacgcctgcc cggtgc 16 100 20 DNA Artificial Sequence Primer 100
gacttaccaa cccgatgcaa 20 101 20 DNA Artificial Sequence Primer 101
gagagcaagc ggacctcata 20 102 27 DNA Artificial Sequence Primer 102
gagagtttga tcctggctca gaacgaa 27 103 19 DNA Artificial Sequence
Primer 103 gaggaaagtc catgctcac 19 104 19 DNA Artificial Sequence
Primer 104 gaggaaagtc catgctcgc 19 105 17 DNA Artificial Sequence
Primer 105 gaggaaagtc cgggctc 17 106 22 DNA Artificial Sequence
Primer 106 gataccctgg tagtccacac cg 22 107 20 DNA Artificial
Sequence Primer 107 gatctggagg aataccggtg 20 108 29 DNA Artificial
Sequence Primer 108 gatgactttt tagctaatgg tcaggcagc 29 109 30 DNA
Artificial Sequence Primer 109 gattattgtt atcctgttat gccatttgag 30
110 18 DNA Artificial Sequence Primer 110 gcacaacctg cggctgcg 18
111 27 DNA Artificial Sequence Primer 111 gcactatgca cacgtagatt
gtcctgg 27 112 21 DNA Artificial Sequence Primer 112 gccttgtaca
cacctcccgt c 21 113 20 DNA Artificial Sequence Primer 113
gcgaagaacc ttaccaggtc 20 114 20 DNA Artificial Sequence Primer 114
gctacacacg tgctacaatg 20 115 30 DNA Artificial Sequence Primer 115
gctggtgaaa ataacccaga tgtcgtcttc 30 116 25 DNA Artificial Sequence
Primer 116 gcttcaggaa tcaatgatgg agcag 25 117 19 DNA Artificial
Sequence Primer 117 ggacggagaa ggctatgtt 19 118 22 DNA Artificial
Sequence Primer 118 ggattagaga ccctggtagt cc 22 119 26 DNA
Artificial Sequence Primer 119 ggattagata ccctggtagt ccacgc 26 120
25 DNA Artificial Sequence Primer 120 ggctcagcca tttagttacc gctat
25 121 21 DNA Artificial Sequence Primer 121 gggaactgaa acatctaagt
a 21 122 22 DNA Artificial Sequence Primer 122 gggagcaaac
aggattagat ac 22 123 29 DNA Artificial Sequence Primer 123
gggcaacagc agcggattgc gattgcgcg 29 124 23 DNA Artificial Sequence
Primer 124 gggcagcgtt tcggcgaaat gga 23 125 26 DNA Artificial
Sequence Primer 125 ggggagtgaa agagatcctg aaaccg 26 126 30 DNA
Artificial Sequence Primer 126 ggggattcag ccatcaaagc agctattgac 30
127 27 DNA Artificial Sequence Primer 127 ggggattgat atcaccgata
agaagaa 27 128 24 DNA Artificial Sequence Primer 128 ggtgaaagaa
gttgcctcta aagc 24 129 15 DNA Artificial Sequence Primer 129
ggtggatgcc ttggc 15 130 20 DNA Artificial Sequence Primer 130
ggtgttaaat agcctggcag 20 131 20 DNA Artificial Sequence Primer 131
ggtttagtac cagaacatgc 20 132 23 DNA Artificial Sequence Primer 132
gtcaaagtgg cacgtttact ggc 23 133 22 DNA Artificial Sequence Primer
133 gtcgtgaaaa cgagctggaa ga 22 134 30 DNA Artificial Sequence
Primer 134 gtgagatgtt gggttaagtc ccgtaacgag 30 135 23 DNA
Artificial Sequence Primer 135 gtgcatgcgg atacagagca gag 23 136 26
DNA Artificial Sequence Primer 136 gtggcatgcc taatacatgc aagtcg 26
137 18 DNA Artificial Sequence Primer 137 gtgtagcggt gaaatgcg 18
138 21 DNA Artificial Sequence Primer 138 gttatcctgt tatgccattt g
21 139 28 DNA Artificial Sequence Primer 139 gttatttagc actcgttttt
aatcagcc 28 140 22 DNA Artificial Sequence Primer 140 gttgtgaggt
taagcgacta ag 22 141 22 DNA Artificial Sequence Primer 141
gttgtgaggt taagcgacta ag 22 142 24 DNA Artificial Sequence Primer
142 tctagtaata ataggaccct cagc 24 143 15 DNA Artificial Sequence
Primer 143 tatggctcta ctcaa 15 144 29 DNA Artificial Sequence
Primer 144 taaaacaaac tacggtaaca ttgatcgca 29 145 33 DNA Artificial
Sequence Primer 145 taaaactttt gccgtaatga tgggtgaaga tat 33 146 31
DNA Artificial Sequence Primer 146 taaacacggc tttcctatgg cttatccaaa
t 31 147 28 DNA Artificial Sequence Primer 147 taaaccccat
cgggagcaag accgaata 28 148 30 DNA Artificial Sequence Primer 148
taaagcccgt gaaatgactc gtcgtaaagg 30 149 28 DNA Artificial Sequence
Primer 149 taaagttggt tttattggtt ggcgcgga 28 150 25 DNA Artificial
Sequence Primer 150 taaatctgcc cgtgtcgttg gtgac 25 151 29 DNA
Artificial Sequence Primer 151 taacaactcg ccttatgaaa cgggatata 29
152 20 DNA Artificial Sequence Primer 152 taacacatgc aagtcgaacg 20
153 29 DNA Artificial Sequence Primer 153 taaccattca agaactagat
cttcaggca 29 154 30 DNA Artificial Sequence Primer 154 taaccttaat
tggaaagaaa cccaagaagt 30 155 25 DNA Artificial Sequence Primer 155
taacggttat catggcccag atggg 25 156 27 DNA Artificial Sequence
Primer 156 taactctgat gtttttgatg ggaaggt 27 157 27 DNA Artificial
Sequence Primer 157 taactgcatg gaacccttct ttactag 27 158 27 DNA
Artificial Sequence Primer 158 taagaagccg gaaaccatca actaccg 27 159
22 DNA Artificial Sequence Primer 159 taagagcgca ccggtaagtt gg
22 160 28 DNA Artificial Sequence Primer 160 taagcatgct gtggcttatc
gtgaaatg 28 161 23 DNA Artificial Sequence Primer 161 taagctgcca
gcggaatgct ttc 23 162 29 DNA Artificial Sequence Primer 162
taaggatagt gcaacagaga tataccgcc 29 163 30 DNA Artificial Sequence
Primer 163 taaggtatga caccggataa atcatataaa 30 164 33 DNA
Artificial Sequence Primer 164 taaggtttat tgtctttgtg gagatgggga ttt
33 165 31 DNA Artificial Sequence Primer 165 taatcaagca ttggaagatg
aaatgcatac c 31 166 29 DNA Artificial Sequence Primer 166
taatcggtaa atatcacccg catggtgac 29 167 29 DNA Artificial Sequence
Primer 167 taatcggtaa gtatcaccct catggtgat 29 168 24 DNA Artificial
Sequence Primer 168 taatcgtgga atacgggttt gcta 24 169 30 DNA
Artificial Sequence Primer 169 taatgaaccc taatgaccat ccacacggtg 30
170 27 DNA Artificial Sequence Primer 170 taatgatgaa ttaggtgcgg
gttcttt 27 171 29 DNA Artificial Sequence Primer 171 taatgggtaa
atatcaccct catggtgac 29 172 31 DNA Artificial Sequence Primer 172
taattgggct ctttctcgct taaacacctt a 31 173 25 DNA Artificial
Sequence Primer 173 tacaaagcaa gacactggct cacta 25 174 30 DNA
Artificial Sequence Primer 174 tacaaaggtc aaccaatgac attcagacta 30
175 34 DNA Artificial Sequence Primer 175 tacaacatat tattaaagag
acgggtttga atcc 34 176 20 DNA Artificial Sequence Primer 176
tacaagcact cccagctgca 20 177 29 DNA Artificial Sequence Primer 177
tacaatgctt gtttatgctg gtaaagcag 29 178 25 DNA Artificial Sequence
Primer 178 tacacaacaa tggcggtaaa gatgg 25 179 15 DNA Artificial
Sequence Primer 179 tacagagttt gcgac 15 180 21 DNA Artificial
Sequence Primer 180 tacaggccgt gttgaacgtg g 21 181 21 DNA
Artificial Sequence Primer 181 tacatgctag ccgcgtctta c 21 182 27
DNA Artificial Sequence Primer 182 taccactatt aatgtcgctg gtgcttc 27
183 25 DNA Artificial Sequence Primer 183 taccatgaca gaaggcattt
tgaca 25 184 19 DNA Artificial Sequence Primer 184 taccccaaac
cgacacagg 19 185 23 DNA Artificial Sequence Primer 185 taccccaggg
aaagtgccac aga 23 186 25 DNA Artificial Sequence Primer 186
taccggcgca aaaagtcgag attgg 25 187 21 DNA Artificial Sequence
Primer 187 tacctatatg cgccagaccg c 21 188 26 DNA Artificial
Sequence Primer 188 tacgatttca cttccgcagc cagatt 26 189 27 DNA
Artificial Sequence Primer 189 tacgcgtctt gaagcgtttc gttatga 27 190
26 DNA Artificial Sequence Primer 190 tacgctgacg gaatcaacca aagcgg
26 191 21 DNA Artificial Sequence Primer 191 tacggtgaat acgttcccgg
g 21 192 15 DNA Artificial Sequence Primer 192 tacagagttt gcgac 15
193 23 DNA Artificial Sequence Primer 193 tactacttca agccgaactt ccg
23 194 28 DNA Artificial Sequence Primer 194 tactagcggt aagcttaaac
aagattgc 28 195 22 DNA Artificial Sequence Primer 195 tactctcggt
ggagaagctc gc 22 196 22 DNA Artificial Sequence Primer 196
tactggaaca aagtctgcga cc 22 197 27 DNA Artificial Sequence Primer
197 tacttactac ttcaagccga acttccg 27 198 28 DNA Artificial Sequence
Primer 198 tacttacttg agaatccaca agctgcaa 28 199 28 DNA Artificial
Sequence Primer 199 tacttggtaa ataccaccca catggtga 28 200 32 DNA
Artificial Sequence Primer 200 tactttttta aaactaggga tgcgtttgaa gc
32 201 27 DNA Artificial Sequence Primer 201 tagaaatcaa ggtgatagtg
gcaatga 27 202 21 DNA Artificial Sequence Primer 202 tagaacaccg
atggcgaagg c 21 203 22 DNA Artificial Sequence Primer 203
tagaacgtcg cgagacagtt cg 22 204 21 DNA Artificial Sequence Primer
204 tagactgccc aggacacgct g 21 205 29 DNA Artificial Sequence
Primer 205 tagataattg ggctctttct cgcttaaac 29 206 22 DNA Artificial
Sequence Primer 206 tagataccct ggtagtccac gc 22 207 28 DNA
Artificial Sequence Primer 207 tagatgaaaa aggcgaagtg gctaatgg 28
208 28 DNA Artificial Sequence Primer 208 tagatgaaaa gggcgaagtg
gctaatgg 28 209 30 DNA Artificial Sequence Primer 209 tagcaacaaa
tatatctgaa gcagcgtact 30 210 29 DNA Artificial Sequence Primer 210
tagcaggtgg tgaaatcggc cacatgatt 29 211 26 DNA Artificial Sequence
Primer 211 tagcatcaga actgttgttc cgctag 26 212 24 DNA Artificial
Sequence Primer 212 tagcccagca caatttgtga ttca 24 213 34 DNA
Artificial Sequence Primer 213 tagcctttaa cgaaaatgta aaaatgcgtt
ttga 34 214 27 DNA Artificial Sequence Primer 214 tagcgaatgt
ggctttactt cacaatt 27 215 19 DNA Artificial Sequence Primer 215
tagcgtaaag gtgaacctt 19 216 20 DNA Artificial Sequence Primer 216
tagctaatgg tcaggcagcc 20 217 30 DNA Artificial Sequence Primer 217
tagctatctt atcgttgaga agggatttgc 30 218 22 DNA Artificial Sequence
Primer 218 tagctggcgc gaaattaggt gt 22 219 26 DNA Artificial
Sequence Primer 219 tagctggcgg tatggagaat atgtct 26 220 27 DNA
Artificial Sequence Primer 220 tagcttttgc atattatatc gagccac 27 221
29 DNA Artificial Sequence Primer 221 taggaattac ggctgataaa
gcgtataaa 29 222 35 DNA Artificial Sequence Primer 222 taggcgaaga
tatacaaaga gtattagaag ctaga 35 223 25 DNA Artificial Sequence
Primer 223 taggcgtgaa agcaagctac cgttt 25 224 25 DNA Artificial
Sequence Primer 224 taggtgctgg ttacgcagat caaga 25 225 30 DNA
Artificial Sequence Primer 225 taggtttacg tcagtatggc gtgattatgg 30
226 23 DNA Artificial Sequence Primer 226 tagtaccgaa gctggtcata cga
23 227 17 DNA Artificial Sequence Primer 227 tagtacgaga ggaccgg 17
228 18 DNA Artificial Sequence Primer 228 tagtcccgca acgagcgc 18
229 27 DNA Artificial Sequence Primer 229 tagtgataga actgtaggca
caatcgt 27 230 22 DNA Artificial Sequence Primer 230 tagttgctca
aacagctggg ct 22 231 29 DNA Artificial Sequence Primer 231
tataagtggg taaaccgtga atatcgtgt 29 232 24 DNA Artificial Sequence
Primer 232 tatacttcaa cgcctgctgc tttc 24 233 22 DNA Artificial
Sequence Primer 233 tatcgctcag gcgaactcca ac 22 234 23 DNA
Artificial Sequence Primer 234 tatgaccaaa ctcatcagac gag 23 235 30
DNA Artificial Sequence Primer 235 tatgattaca attcaagaag gtcgtcacgc
30 236 27 DNA Artificial Sequence Primer 236 tatgcagtgg aacgatggtt
tccaaga 27 237 24 DNA Artificial Sequence Primer 237 tatgctgacc
gaccagtggt acgt 24 238 21 DNA Artificial Sequence Primer 238
tatggccatg gcagaagctc a 21 239 15 DNA Artificial Sequence Primer
239 tatggctcta ctcaa 15 240 31 DNA Artificial Sequence Primer 240
tatgtccaag aagcatagca aaaaaagcaa t 31 241 27 DNA Artificial
Sequence Primer 241 tattcaaggt ggtcctttga tgcatgt 27 242 22 DNA
Artificial Sequence Primer 242 tattggacaa cggtcgtcgc gg 22 243 30
DNA Artificial Sequence Primer 243 tattgtttca aatgtacaag gtgaagtgcg
30 244 30 DNA Artificial Sequence Primer 244 tatttcacat gtaattttga
tattcgcact 30 245 32 DNA Artificial Sequence Primer 245 tcaaaaagcc
ctaggtaaag agattccata tc 32 246 29 DNA Artificial Sequence Primer
246 tcaaactggg caatcggaac tggtaaatc 29 247 26 DNA Artificial
Sequence Primer 247 tcaaatgtac aaggtgaagt gcgtga 26 248 29 DNA
Artificial Sequence Primer 248 tcaacaacct cttggaggta aagctcagt 29
249 19 DNA Artificial Sequence Primer 249 tcaacctcgg cccgaacca 19
250 25 DNA Artificial Sequence Primer 250 tcaacctgac tgcgtgaatg
gttgt 25 251 27 DNA Artificial Sequence Primer 251 tcaacgaagg
taaaaaccat ctcaacg 27 252 27 DNA Artificial Sequence Primer 252
tcaacggtaa cttctatgtt acttctg 27 253 26 DNA Artificial Sequence
Primer 253 tcaactcgaa ttttcaacag gtacca 26 254 17 DNA Artificial
Sequence Primer 254 tcaagaagaa aaagagc 17 255 24 DNA Artificial
Sequence Primer 255 tcaagcaaac gcacaatcag aagc 24 256 27 DNA
Artificial Sequence Primer 256 tcaagcagaa gctttggaag aagaagg 27 257
27 DNA Artificial Sequence Primer 257 tcaagccgta cgtattatta ggtgctg
27 258 27 DNA Artificial Sequence Primer 258 tcaataccgc aacagcggtg
gcttggg 27 259 28 DNA Artificial Sequence Primer 259 tcaatgaacg
accaacaagt gattgatg 28 260 28 DNA Artificial Sequence Primer 260
tcaatgaacg atcaacaagt gattgatg 28 261 24 DNA Artificial Sequence
Primer 261 tcacatatcg tgagcaatga actg 24 262 30 DNA Artificial
Sequence Primer 262 tcaccaggtt caactcaaaa aatattaaca 30 263 25 DNA
Artificial Sequence Primer 263 tcaccagttt gccacgtatc ttcaa 25 264
28 DNA Artificial Sequence Primer 264 tcaccctcat ggtgactcat
ctatttat 28 265 28 DNA Artificial Sequence Primer 265 tcaccctcat
ggtgattcag ctgtttat 28 266 25 DNA Artificial Sequence Primer 266
tcaccgatat catggcttac cacgg 25 267 23 DNA Artificial Sequence
Primer 267 tcaccgtgcc gttcaaggaa gag 23 268 29 DNA Artificial
Sequence Primer 268 tcacctccaa gtttagatca cttgagaga 29 269 26 DNA
Artificial Sequence Primer 269 tcacgataag aaaaccggtc aagagg 26 270
27 DNA Artificial Sequence Primer 270 tcactcttac atataaggaa ggcgctc
27 271 25 DNA Artificial Sequence Primer 271 tcagaccatg ctcgcagaga
aactt 25 272 25 DNA Artificial Sequence Primer 272 tcagagaccg
ttttatccta tcagc 25 273 26 DNA Artificial Sequence Primer 273
tcagcaaatg catcacaaac agataa 26 274 25 DNA Artificial Sequence
Primer 274 tcagcatatg cacatggaac acctc 25 275 26 DNA Artificial
Sequence Primer 275 tcagcatatg cacatggaac acctca 26 276 22 DNA
Artificial Sequence Primer 276 tcagccatca aagcagctat tg 22 277 21
DNA Artificial Sequence Primer 277 tcagcgcgta cagtgggtga t 21 278
25 DNA Artificial Sequence Primer 278 tcagcgtatg cacatggaac tcctc
25 279 23 DNA Artificial Sequence Primer 279 tcagctacat cgactatgcg
atg 23 280 30 DNA Artificial Sequence Primer 280 tcagctagac
cttttaggta aagctaagct 30 281 29 DNA Artificial Sequence Primer 281
tcagctattt ttccaggtat ccaaggtgg 29 282 23 DNA Artificial Sequence
Primer 282 tcagctgtcg cagttcatgg acc 23 283 25 DNA Artificial
Sequence Primer 283 tcaggaaaag ggcattttac ccttg 25 284 30 DNA
Artificial Sequence Primer 284 tcaggagtcg ttcaactcga tctacatgat 30
285 31 DNA Artificial Sequence Primer 285 tcaggagtcg ttcaactcga
tctacatgat g 31 286 30 DNA Artificial Sequence Primer 286
tcaggatgga aataaccacc aattcactac 30 287 23 DNA Artificial Sequence
Primer 287 tcaggcattg cggttgggat ggc 23 288 24 DNA Artificial
Sequence Primer 288 tcaggtactg ctatccaccc tcaa 24 289 22 DNA
Artificial Sequence Primer 289 tcaggtggct tacacggcgt ag 22 290 26
DNA Artificial Sequence Primer 290 tcagtatgta tccaccgtag ccagtc 26
291 23 DNA Artificial Sequence Primer 291 tcagttccgt tatcgccatt gca
23 292 24 DNA Artificial Sequence Primer 292 tcagttccgt tatcgccatt
gcat 24 293 25 DNA Artificial Sequence Primer 293 tcagttccgt
tatcgccatt gcatt 25 294 24 DNA Artificial Sequence Primer 294
tcagttcggc ggtcagcgct tcgg 24 295 34 DNA Artificial Sequence Primer
295 tcagttttaa tgtctcgtat gatcgaatca aaag 34 296 24 DNA Artificial
Sequence Primer 296 tcatccacac ggtggtggtg aagg 24 297 28 DNA
Artificial Sequence Primer 297 tcatcctaag ccaagtgtag actctgta 28
298 31 DNA Artificial Sequence Primer 298 tcatgataat atctttgaaa
tcggctcagg a 31 299 33 DNA Artificial Sequence Primer 299
tcatgttgag cttaaaccta tagaagtaaa agc 33 300 27 DNA Artificial
Sequence Primer 300 tcattatcat gcgccaatga gtgcaga 27 301 28 DNA
Artificial Sequence Primer 301 tcattcaaga actagatctt caggcaag 28
302 26 DNA Artificial Sequence Primer 302 tccaaaaaaa tcagcgcgta
cagtgg 26 303 29 DNA Artificial Sequence Primer 303 tccaaaccag
gtgtatcaag aacatcagg 29 304 29 DNA Artificial Sequence Primer 304
tccaaataag tggcgttaca aatactgaa 29 305 32 DNA Artificial Sequence
Primer 305 tccaacgaag tacaatacaa gacaaaagaa gg 32 306 32 DNA
Artificial Sequence Primer 306 tccaaggtac actaaactta cttgagctaa tg
32 307 24 DNA Artificial Sequence Primer 307 tccaatgcca caaactcgtg
aaca 24 308 24 DNA Artificial Sequence Primer 308 tccacacgcc
gttcttcaac aact 24 309 21 DNA Artificial Sequence Primer 309
tccacacggt ggtggtgaag g 21 310 26 DNA Artificial Sequence Primer
310 tccaccaaga gcaagatcaa ataggc 26 311 20 DNA Artificial Sequence
Primer 311 tccacggtca tggagcgcta 20 312 30 DNA Artificial Sequence
Primer 312 tccacttatc gcaaatggaa aattaagcaa 30 313 33 DNA
Artificial Sequence Primer 313 tccagatgga caaattttct tagaaactga ttt
33 314 26 DNA Artificial Sequence Primer 314 tccagcacga attgctgcta
tgaaag 26 315 33 DNA Artificial Sequence Primer 315 tccaggacaa
atgtatgaaa aatgtccaag aag 33 316 25 DNA Artificial Sequence Primer
316 tccattgttc gtatggctca agact
25 317 31 DNA Artificial Sequence Primer 317 tcccaattaa ttctgccatt
tttccaggta t 31 318 34 DNA Artificial Sequence Primer 318
tcccacgaaa cagatgaaga aattaacaaa aaag 34 319 30 DNA Artificial
Sequence Primer 319 tcccagctag accttttagg taaagctaag 30 320 26 DNA
Artificial Sequence Primer 320 tcccaggtga cgatgtacct gtaatc 26 321
26 DNA Artificial Sequence Primer 321 tccccaggac accctgaaat ttcaac
26 322 34 DNA Artificial Sequence Primer 322 tcccccacgc tttaattgtt
tatgatgatt tgag 34 323 31 DNA Artificial Sequence Primer 323
tcccggactt aatatcaatg aaaattgtgg a 31 324 28 DNA Artificial
Sequence Primer 324 tcccggagct tttatgacta aagcagat 28 325 19 DNA
Artificial Sequence Primer 325 tccgcggagt tgactgggt 19 326 20 DNA
Artificial Sequence Primer 326 tccgctgaat ctgtcgccgc 20 327 23 DNA
Artificial Sequence Primer 327 tccggctcac gttattatgg tac 23 328 27
DNA Artificial Sequence Primer 328 tccgtacgta ttattaggtg ctggtca 27
329 30 DNA Artificial Sequence Primer 329 tccgttatcg ccattgcatt
atttggaact 30 330 33 DNA Artificial Sequence Primer 330 tccgttctta
caaatagcaa tagaacttga agc 33 331 36 DNA Artificial Sequence Primer
331 tccgttgatt attgttatcc tgttatgcca tttgag 36 332 34 DNA
Artificial Sequence Primer 332 tcctaatgga cttaatatca atgaaaattg
tgga 34 333 22 DNA Artificial Sequence Primer 333 tcctagagga
atggctgcca cg 22 334 30 DNA Artificial Sequence Primer 334
tcctatatta atcgtttaca gaaactggct 30 335 31 DNA Artificial Sequence
Primer modified_base (15)...(15) I 335 tcctcaatga acgatcaaca
agtgattgat g 31 336 31 DNA Artificial Sequence Primer 336
tcctcaatga atgatcaaca agtgattgat g 31 337 31 DNA Artificial
Sequence Primer modified_base (15)...(15) I modified_base
(24)...(24) I 337 tcctcgatga acgatcaaca agtgattgat g 31 338 31 DNA
Artificial Sequence Primer modified_base (15)...(15) I
modified_base (24)...(24) I 338 tcctcgatga atgatcaaca agtgattgat g
31 339 31 DNA Artificial Sequence Primer modified_base (6)...(6) I
modified_base (15)...(15) I 339 tcctcgatga acgatcaaca agtgattgat g
31 340 31 DNA Artificial Sequence Primer modified_base (6)...(6) I
modified_base (12)...(12) I modified_base (15)...(15) I
modified_base (24)...(24) I 340 tcctcgatga acgatcaaca agtgattgat g
31 341 20 DNA Artificial Sequence Primer 341 tcctgaaaaa tggagcacgg
20 342 23 DNA Artificial Sequence Primer 342 tcctgaagca agtgcattta
cga 23 343 28 DNA Artificial Sequence Primer 343 tcctgaccga
cccattattc cctttatc 28 344 33 DNA Artificial Sequence Primer 344
tcctgatgct caaagtgctt ttttagatcc ttt 33 345 34 DNA Artificial
Sequence Primer 345 tcctgttatc cctgaagtag ttaatcaagt ttgt 34 346 35
DNA Artificial Sequence Primer 346 tcctgttatc cctgaagtag ttaatcaagt
ttgtt 35 347 36 DNA Artificial Sequence Primer 347 tcctgttatt
cctgaagtag ttaatcaagt ttgtta 36 348 31 DNA Artificial Sequence
Primer 348 tccttacttc gaactatgaa tcttttggaa g 31 349 29 DNA
Artificial Sequence Primer 349 tccttatagg gatggctatc agtaatgtt 29
350 22 DNA Artificial Sequence Primer 350 tccttgaccg cctttccgat ac
22 351 33 DNA Artificial Sequence Primer 351 tccttgcttt agttttaagt
gcatgtaatt caa 33 352 32 DNA Artificial Sequence Primer 352
tcctttgata tattatgcga tggaaggttg gt 32 353 30 DNA Artificial
Sequence Primer 353 tcctttgatg catgtaattg ctgcaaaagc 30 354 31 DNA
Artificial Sequence Primer 354 tcgaaagctt ttgcatatta tatcgagcca c
31 355 28 DNA Artificial Sequence Primer 355 tcgaagtaca atacaagaca
aaagaagg 28 356 28 DNA Artificial Sequence Primer 356 tcgacaacac
cattatctat ggtgtgaa 28 357 23 DNA Artificial Sequence Primer 357
tcgacctttg gcaggaacta gac 23 358 17 DNA Artificial Sequence Primer
358 tcgagcaggc gctgccg 17 359 31 DNA Artificial Sequence Primer 359
tcgagtatag ctaaaaaaat agtttatgac a 31 360 26 DNA Artificial
Sequence Primer 360 tcgatctggt ttcatgctgt ttcagt 26 361 28 DNA
Artificial Sequence Primer 361 tcgatgaacg accaacaagt gattgatg 28
362 24 DNA Artificial Sequence Primer 362 tcgattaggc agcaacgaaa
gccg 24 363 24 DNA Artificial Sequence Primer 363 tcgcaaaaaa
atccagctat tagc 24 364 26 DNA Artificial Sequence Primer 364
tcgccaatca aaactaaggg aatggc 26 365 19 DNA Artificial Sequence
Primer 365 tcgccatcgt caccaaccg 19 366 16 DNA Artificial Sequence
Primer 366 tcgcccgcga ggacgt 16 367 21 DNA Artificial Sequence
Primer 367 tcgccgactt cgacggtgac c 21 368 22 DNA Artificial
Sequence Primer 368 tcgccggcaa tgccattgga ta 22 369 23 DNA
Artificial Sequence Primer 369 tcgccgtgga aaaatcctac gct 23 370 31
DNA Artificial Sequence Primer 370 tcgcgttgca acaaaacttt ctaaagtatg
t 31 371 24 DNA Artificial Sequence Primer 371 tcgctacagg
ccctttagga caag 24 372 27 DNA Artificial Sequence Primer 372
tcgctatctt atcgttgaga agggatt 27 373 24 DNA Artificial Sequence
Primer 373 tcggaatctg atgttgcagt tgtt 24 374 22 DNA Artificial
Sequence Primer 374 tcggccgcac cttcatcgaa gt 22 375 28 DNA
Artificial Sequence Primer 375 tcggcgaaat ccgtattcct gaaaatga 28
376 18 DNA Artificial Sequence Primer 376 tcggcgcctg cctgatga 18
377 23 DNA Artificial Sequence Primer 377 tcgggtgatg atgcgcgtga agg
23 378 31 DNA Artificial Sequence Primer 378 tcggtttagt aaaagaacgt
attgctcaac c 31 379 28 DNA Artificial Sequence Primer 379
tcgtacgtat tattaggtgc tggtcact 28 380 21 DNA Artificial Sequence
Primer 380 tcgtatggct caatggtgga g 21 381 30 DNA Artificial
Sequence Primer 381 tcgtcttttt gattctttcc ctgataatgc 30 382 32 DNA
Artificial Sequence Primer 382 tcgtcttttt gattctttcc ctgataatgc tc
32 383 25 DNA Artificial Sequence Primer 383 tcgtgattat ggatggcaac
gtgaa 25 384 24 DNA Artificial Sequence Primer 384 tcgtgcccgc
aatttgcata aagc 24 385 21 DNA Artificial Sequence Primer 385
tcgtggcggc gtggttatcg a 21 386 27 DNA Artificial Sequence Primer
386 tcgtgttgaa cgtggtcaaa tcaaagt 27 387 23 DNA Artificial Sequence
Primer 387 tcgttcctgg aacacgatga cgc 23 388 27 DNA Artificial
Sequence Primer 388 tcgtttggtg gtggtagatg aaaaagg 27 389 11 DNA
Artificial Sequence Primer 389 tccaccctca a 11 390 25 DNA
Artificial Sequence Primer 390 tctaaaacac caggtcaccc agaag 25 391
24 DNA Artificial Sequence Primer 391 tctaaatggt cgtgcagttg cgtg 24
392 30 DNA Artificial Sequence Primer 392 tctactgatt ttggtaatct
tgcagcacag 30 393 24 DNA Artificial Sequence Primer 393 tctagtaata
ataggaccct cagc 24 394 31 DNA Artificial Sequence Primer 394
tctcaaggtg atattggtgt aggtaactta a 31 395 24 DNA Artificial
Sequence Primer 395 tctcattacg ttgcatcgga aaca 24 396 30 DNA
Artificial Sequence Primer 396 tctcgatgaa cgaccaacaa gtgattgatg 30
397 28 DNA Artificial Sequence Primer 397 tctcgtggtg cacaagtaac
ggatatta 28 398 32 DNA Artificial Sequence Primer 398 tctgaaatga
atagtgatag aactgtaggc ac 32 399 32 DNA Artificial Sequence Primer
399 tctgaacatg ataatatctt tgaaatcggc tc 32 400 30 DNA Artificial
Sequence Primer 400 tctgaatgtc tatatggagg tacaacacta 30 401 19 DNA
Artificial Sequence Primer 401 tctgacacct gcccggtgc 19 402 20 DNA
Artificial Sequence Primer 402 tctgcccgtg tcgttggtga 20 403 24 DNA
Artificial Sequence Primer 403 tctggaggca caccaaataa aaca 24 404 21
DNA Artificial Sequence Primer 404 tctggataac ggtcgtcgcg g 21 405
25 DNA Artificial Sequence Primer 405 tctggcaggt atgcgtggtc tgatg
25 406 24 DNA Artificial Sequence Primer 406 tctggctaaa actttggcaa
cggt 24 407 29 DNA Artificial Sequence Primer 407 tctggtccaa
caaaaggaac gattacagg 29 408 25 DNA Artificial Sequence Primer 408
tctgtcccta gtacgagagg accgg 25 409 23 DNA Artificial Sequence
Primer 409 tctgttctta gtacgagagg acc 23 410 26 DNA Artificial
Sequence Primer 410 tcttatgcca agaggacaga gtgagt 26 411 29 DNA
Artificial Sequence Primer 411 tcttatgcca agaggacaga gtgagtact 29
412 31 DNA Artificial Sequence Primer 412 tcttattcca acttcaaacc
gaactatgac g 31 413 29 DNA Artificial Sequence Primer 413
tcttctcatc ctatggctat tatgcttgc 29 414 33 DNA Artificial Sequence
Primer 414 tcttgatact tgtaatgtgg gcgataaata tgt 33 415 32 DNA
Artificial Sequence Primer 415 tcttgcagca gtttatttga tgaacctaaa gt
32 416 28 DNA Artificial Sequence Primer 416 tcttgctctt tcgtgagttc
agtaaatg 28 417 31 DNA Artificial Sequence Primer 417 tcttgtactt
gtggctcaca cggctgtttg g 31 418 27 DNA Artificial Sequence Primer
418 tcttgtttat gctggtaaag cagatgg 27 419 28 DNA Artificial Sequence
Primer 419 tctttatggt ggagatgact gaaaccga 28 420 28 DNA Artificial
Sequence Primer 420 tctttcttga atgctggtgt acgtatcg 28 421 25 DNA
Artificial Sequence Primer 421 tctttgaaat cggctcagga aaagg 25 422
26 DNA Artificial Sequence Primer 422 tctttgccat tgaagatgac ttaagc
26 423 29 DNA Artificial Sequence Primer 423 tcttttacaa aaggggaaaa
agttgactt 29 424 34 DNA Artificial Sequence Primer 424 tgaaaaatgt
ccaagaagca tagcaaaaaa agca 34 425 30 DNA Artificial Sequence Primer
425 tgaaaagggt gaagtagcaa atggagatag 30 426 32 DNA Artificial
Sequence Primer 426 tgaaaagtat ggatttgaac aactcgtgaa ta 32 427 27
DNA Artificial Sequence Primer 427 tgaaatctca ttacgttgca tcggaaa 27
428 30 DNA Artificial Sequence Primer 428 tgaaattgct acaggccctt
taggacaagg 30 429 25 DNA Artificial Sequence Primer 429 tgaacgctgg
tggcatgctt aacac 25 430 30 DNA Artificial Sequence Primer 430
tgaacgtggt caaatcaaag ttggtgaaga 30 431 31 DNA Artificial Sequence
Primer 431 tgaacgtggt caaatcaaag ttggtgaaga a 31 432 27 DNA
Artificial Sequence Primer 432 tgaagcttgt tctttagcag gacttca 27 433
28 DNA Artificial Sequence Primer 433 tgaaggtgga cgtcacactc
cattcttc 28 434 26 DNA Artificial Sequence Primer 434 tgaagtagaa
atgactgaac gtccga 26 435 28 DNA Artificial Sequence Primer 435
tgaagtagaa ggtgcaaagc aagttaga 28 436 34 DNA Artificial Sequence
Primer 436 tgaagtgcgt gatgatatcg atgcacttga tgta 34 437 31 DNA
Artificial Sequence Primer 437 tgaatagtga tagaactgta ggcacaatcg t
31 438 31 DNA Artificial Sequence Primer 438 tgaatgctta tttacctgca
ctcccacaac t 31 439 31 DNA Artificial Sequence Primer 439
tgaattagtt caatcatttg ttgaacgacg t 31 440 26 DNA Artificial
Sequence Primer 440 tgaattgctg ctatgaaagg tggctt 26 441 27 DNA
Artificial Sequence Primer 441 tgacagcgaa gaaggttaga cttgtcc 27 442
26 DNA Artificial Sequence Primer 442 tgacatccgg ctcacgttat tatggt
26 443 27 DNA Artificial Sequence Primer 443 tgacatccgg ctcacgttat
tatggta 27 444 28 DNA Artificial Sequence Primer 444 tgacatccgg
ctcacgttat tatggtac 28 445 29 DNA Artificial Sequence Primer 445
tgacatgata ataaccgatt gaccgaaga 29 446 22 DNA Artificial Sequence
Primer 446 tgacatgctt gtccgttcag gc 22 447 31 DNA Artificial
Sequence Primer 447 tgacatggac tccccctata taactcttga g 31 448 23
DNA Artificial Sequence Primer 448 tgaccaggtg atggccatgt tcg 23 449
31 DNA Artificial Sequence Primer 449 tgacctacag taagaggttc
tgtaatgaac c 31 450 23 DNA Artificial Sequence Primer 450
tgacgatctt cgcggtgact agt 23 451 26 DNA Artificial Sequence Primer
451 tgacggccta tacggtgttg gtttct 26 452 24 DNA Artificial Sequence
Primer 452 tgacgtcatc ggtaagtacc accc 24 453 27 DNA Artificial
Sequence Primer 453 tgagatggat ttaaacctgt tcaccgc 27 454 30 DNA
Artificial Sequence Primer 454 tgagattgct gaacatttaa tgctgattga 30
455 32 DNA Artificial Sequence Primer 455 tgagcaatgg ggctttgaaa
gaatttttaa at 32 456 26 DNA Artificial Sequence Primer 456
tgagctgcat caactgtatt ggatag 26 457 28 DNA Artificial Sequence
Primer 457 tgagctttta gttgactttt tcaacagc 28 458 20 DNA Artificial
Sequence Primer 458 tgaggaccgt gtcgcgctca 20 459 35 DNA Artificial
Sequence Primer 459 tgagggtttt atgcttaaag ttggttttat tggtt 35 460
30 DNA Artificial Sequence Primer 460 tgaggtggtg gataactcaa
ttgatgaagc 30 461 29 DNA Artificial Sequence Primer 461 tgagtaacat
ccatatttct gccatacgt 29 462 22 DNA Artificial Sequence Primer 462
tgagtaagtt ccacccgcac gg 22 463 30 DNA Artificial Sequence Primer
463 tgagtcactt gaagttgata caaatcctct 30 464 28 DNA Artificial
Sequence Primer 464 tgagtgatga aggccttagg gttgtaaa 28 465 27 DNA
Artificial Sequence Primer 465 tgagtgccaa catatcagtg ctgaaga 27 466
30 DNA Artificial Sequence Primer 466 tgagtttaac agttcaccat
atgaaacagg 30 467 25 DNA Artificial Sequence Primer 467 tgatacttca
acgcctgctg ctttc 25 468 25 DNA Artificial Sequence Primer 468
tgatcactgg tgctgctcag atgga 25 469 30 DNA Artificial Sequence
Primer 469 tgatcatccg tggtataacg atttattagt 30 470 29 DNA
Artificial Sequence Primer 470 tgatcgttga gaagggattt gcgaaaaga
29 471 29 DNA Artificial Sequence Primer 471 tgatctcaga atctaataat
tgggacgaa 29 472 30 DNA Artificial Sequence Primer 472 tgatcttaaa
aatttccgcc aacttcattc 30 473 30 DNA Artificial Sequence Primer 473
tgatgacttt ttagctaatg gtcaggcagc 30 474 29 DNA Artificial Sequence
Primer 474 tgatggcaag tggatagggt ataatacag 29 475 24 DNA Artificial
Sequence Primer 475 tgattaccat gagtggcaag caag 24 476 31 DNA
Artificial Sequence Primer 476 tgattattgt tatcctgtta tgccatttga g
31 477 19 DNA Artificial Sequence Primer 477 tgattccggt gcccgtggt
19 478 19 DNA Artificial Sequence Primer 478 tgattctggt gcccgtggt
19 479 34 DNA Artificial Sequence Primer 479 tgattttgct aaatttagag
aaattgcgga tgaa 34 480 24 DNA Artificial Sequence Primer 480
tgcaaaatct gcaacgagct ttgg 24 481 23 DNA Artificial Sequence Primer
481 tgcaaaggag gtactcagac cat 23 482 25 DNA Artificial Sequence
Primer 482 tgcaagcaaa cgcacaatca gaagc 25 483 20 DNA Artificial
Sequence Primer 483 tgcaagcgcg accacatacg 20 484 23 DNA Artificial
Sequence Primer 484 tgcaagcttc tggtgctagc att 23 485 24 DNA
Artificial Sequence Primer 485 tgcaagtggt acttcaacat gggg 24 486 30
DNA Artificial Sequence Primer 486 tgcaagttaa gaaagctgtt gcaggtttat
30 487 33 DNA Artificial Sequence Primer 487 tgcaattgct ttagttttaa
gtgcatgtaa ttc 33 488 31 DNA Artificial Sequence Primer 488
tgcacaatca gaagctaaga aagcgcaagc t 31 489 24 DNA Artificial
Sequence Primer 489 tgcacacgcc gttcttcaac aact 24 490 22 DNA
Artificial Sequence Primer 490 tgcacatcgt gtccaacgtc ac 22 491 32
DNA Artificial Sequence Primer 491 tgcaccggct attaagaatt actttgccaa
ct 32 492 23 DNA Artificial Sequence Primer 492 tgcacgatgc
ggaatggttc aca 23 493 28 DNA Artificial Sequence Primer 493
tgcacgccga ctatgttaag aacatgat 28 494 30 DNA Artificial Sequence
Primer 494 tgcacttatc gcaaatggaa aattaagcaa 30 495 21 DNA
Artificial Sequence Primer 495 tgcagggaac agctttaggc a 21 496 22
DNA Artificial Sequence Primer 496 tgcatacaaa cagtcggagc ct 22 497
23 DNA Artificial Sequence Primer 497 tgcataccgg taagttggca aca 23
498 27 DNA Artificial Sequence Primer 498 tgcatattat atcgagccac
agcatcg 27 499 33 DNA Artificial Sequence Primer 499 tgcattattt
ggaactattg caactgctaa tgc 33 500 28 DNA Artificial Sequence Primer
500 tgccaagagg acagagtgag tactttga 28 501 31 DNA Artificial
Sequence Primer 501 tgccggacaa ttacgattca tcgagtatta a 31 502 33
DNA Artificial Sequence Primer 502 tgccgtaatg ataggtgaag atatacaaag
agt 33 503 23 DNA Artificial Sequence Primer 503 tgccgtgttg
aacgtggtca aat 23 504 33 DNA Artificial Sequence Primer 504
tgcctagaag atcttaaaaa tttccgccaa ctt 33 505 33 DNA Artificial
Sequence Primer 505 tgcctatctt tttgctgata tagcacatat tgc 33 506 27
DNA Artificial Sequence Primer 506 tgcctcgaag ctgaatataa ccaagtt 27
507 22 DNA Artificial Sequence Primer 507 tgcctgtagg gaatcctgct ga
22 508 25 DNA Artificial Sequence Primer 508 tgcctgttct tagtacgaga
ggacc 25 509 23 DNA Artificial Sequence Primer 509 tgcgcagctc
ttggtatcga gtt 23 510 20 DNA Artificial Sequence Primer 510
tgcgcggaag atgtaacggg 20 511 30 DNA Artificial Sequence Primer 511
tgcggatcgt ttggtggttg tagatgaaaa 30 512 20 DNA Artificial Sequence
Primer 512 tgcgggtagg gagcttgagc 20 513 31 DNA Artificial Sequence
Primer 513 tgcgtacaat acgctttatg aaattttaac a 31 514 27 DNA
Artificial Sequence Primer 514 tgcgtataaa aaacacagat ggcagca 27 515
21 DNA Artificial Sequence Primer 515 tgcgtttacc gcaatgcgtg c 21
516 29 DNA Artificial Sequence Primer 516 tgctacggta ggatctcctt
atcctattg 29 517 30 DNA Artificial Sequence Primer 517 tgctagtcaa
tctatcattc cggttgatac 30 518 27 DNA Artificial Sequence Primer 518
tgctagttat ggtacagagt ttgcgac 27 519 26 DNA Artificial Sequence
Primer 519 tgctatggtg ttaccttccc tatgca 26 520 27 DNA Artificial
Sequence Primer 520 tgctcaaccc gatcctaaat tagacga 27 521 27 DNA
Artificial Sequence Primer 521 tgctcaatct aaacctaaag tcgaaga 27 522
33 DNA Artificial Sequence Primer 522 tgctcgagtg attgactttg
ctaaatttag aga 33 523 24 DNA Artificial Sequence Primer 523
tgctcgtaag ggtctggcgg atac 24 524 29 DNA Artificial Sequence Primer
524 tgctcgtggt gcacaagtaa cggatatta 29 525 26 DNA Artificial
Sequence Primer 525 tgctgaggcc tggaccgatt atttac 26 526 27 DNA
Artificial Sequence Primer 526 tgctggtaac agagccttat aggcgca 27 527
19 DNA Artificial Sequence Primer 527 tgctggtacg ggtcgagga 19 528
31 DNA Artificial Sequence Primer 528 tgctggtgaa aataacccag
atgtcgtctt c 31 529 32 DNA Artificial Sequence Primer 529
tgctgtagct tatcgcgaaa tgtctttgat tt 32 530 28 DNA Artificial
Sequence Primer 530 tgcttattta cctgcactcc cacaactg 28 531 26 DNA
Artificial Sequence Primer 531 tgcttcagga atcaatgatg gagcag 26 532
27 DNA Artificial Sequence Primer 532 tgcttcggat ccagcagcac ttcaata
27 533 19 DNA Artificial Sequence Primer 533 tgcttctggt gctagcatt
19 534 32 DNA Artificial Sequence Primer 534 tgctttccta tggcttatcc
aaatttagat cg 32 535 29 DNA Artificial Sequence Primer 535
tgcttttgat ggtgatgcag atcgtttgg 29 536 24 DNA Artificial Sequence
Primer 536 tggaaagcca tgcgtctgac atct 24 537 23 DNA Artificial
Sequence Primer 537 tggaaaggtg ttgcagctac tca 23 538 31 DNA
Artificial Sequence Primer 538 tggaaatggc agctagaata gtagctaaaa t
31 539 30 DNA Artificial Sequence Primer 539 tggaacaaaa tagtctctcg
gattttgact 30 540 33 DNA Artificial Sequence Primer 540 tggaacagga
attaattctc atcctgatta tcc 33 541 30 DNA Artificial Sequence Primer
541 tggaacgtta tcaggtgccc caaaaattcg 30 542 23 DNA Artificial
Sequence Primer 542 tggaactatt gcaactgcta atg 23 543 30 DNA
Artificial Sequence Primer 543 tggaacttga agctctcgct cttaaagatg 30
544 19 DNA Artificial Sequence Primer 544 tggaagatct gggtcaggc 19
545 22 DNA Artificial Sequence Primer 545 tggaagtcat caagcgcctg gc
22 546 30 DNA Artificial Sequence Primer 546 tggaataaca aaacatgaag
gaaaccactt 30 547 32 DNA Artificial Sequence Primer 547 tggaatgatg
ataaagattt cgcagatagc ta 32 548 29 DNA Artificial Sequence Primer
548 tggacaatag acaatcactt ggatttaca 29 549 28 DNA Artificial
Sequence Primer 549 tggacacata tcgtgagcaa tgaactga 28 550 23 DNA
Artificial Sequence Primer 550 tggacggcat cacgattctc tac 23 551 19
DNA Artificial Sequence Primer 551 tggactcctc ggtggtcgc 19 552 19
DNA Artificial Sequence Primer 552 tggagcacgg cttctgatc 19 553 30
DNA Artificial Sequence Primer 553 tggagcttga agctatcgct cttaaagatg
30 554 22 DNA Artificial Sequence Primer 554 tggaggtgtc actccacacg
aa 22 555 25 DNA Artificial Sequence Primer 555 tggaggttgt
tgtatgtatg gtggt 25 556 26 DNA Artificial Sequence Primer 556
tggatattca ccgaacacta gggttg 26 557 27 DNA Artificial Sequence
Primer 557 tggatggcat ggtgaaatgg atatgtc 27 558 25 DNA Artificial
Sequence Primer 558 tggatgggga ttagcggtta caatg 25 559 26 DNA
Artificial Sequence Primer 559 tggatgttaa gggtgatttt cccgaa 26 560
23 DNA Artificial Sequence Primer 560 tggattagag accctggtag tcc 23
561 19 DNA Artificial Sequence Primer 561 tggcacggcc atctccgtg 19
562 34 DNA Artificial Sequence Primer 562 tggcactctt gcctttaata
ttagtaaact atca 34 563 31 DNA Artificial Sequence Primer 563
tggcagctag aatagtagct aaaatcccta c 31 564 28 DNA Artificial
Sequence Primer 564 tggcagtttt acaaggtgct gtttcatc 28 565 31 DNA
Artificial Sequence Primer 565 tggcatttct tatgaagctt gttctttagc a
31 566 24 DNA Artificial Sequence Primer 566 tggccagcgc ttcggtgaaa
tgga 24 567 21 DNA Artificial Sequence Primer 567 tggcccgaaa
gaagctgagc g 21 568 32 DNA Artificial Sequence Primer 568
tggcctaatg ggcttaatat caatgaaaat tg 32 569 22 DNA Artificial
Sequence Primer 569 tggcgaacct ggtgaacgaa gc 22 570 26 DNA
Artificial Sequence Primer 570 tggcgagtgg atagggtata atacag 26 571
27 DNA Artificial Sequence Primer 571 tggcgtagta gagctattta cagacac
27 572 26 DNA Artificial Sequence Primer 572 tggcaagtgg atagggtata
atacag 26 573 25 DNA Artificial Sequence Primer 573 tggctccttg
gtatgactct gcttc 25 574 25 DNA Artificial Sequence Primer 574
tggctgacat cctacatgac tgtga 25 575 31 DNA Artificial Sequence
Primer 575 tggcttatcc aaatttagat cgtggtttta c 31 576 30 DNA
Artificial Sequence Primer 576 tgggacttga agctatcgct cttaaagatg 30
577 30 DNA Artificial Sequence Primer 577 tgggatgaaa aagcgttctt
ttatccatga 30 578 34 DNA Artificial Sequence Primer 578 tgggattatt
gttatcctgt tatgccattt gaga 34 579 32 DNA Artificial Sequence Primer
579 tgggatttta aaaaacattg gtaacatcgc ag 32 580 30 DNA Artificial
Sequence Primer 580 tgggcaacag cagcggattg cgattgcgcg 30 581 24 DNA
Artificial Sequence Primer 581 tgggcagcgt ttcggcgaaa tgga 24 582 33
DNA Artificial Sequence Primer 582 tgggcctaat gggcttaata tcaatgaaaa
ttg 33 583 28 DNA Artificial Sequence Primer 583 tgggcgatgc
tgcgaaatgg ttaaaaga 28 584 27 DNA Artificial Sequence Primer 584
tgggcgtgag caatgaactg attatac 27 585 18 DNA Artificial Sequence
Primer 585 tgggcgtgga acgtccac 18 586 24 DNA Artificial Sequence
Primer 586 tgggctcttt ctcgcttaaa cacc 24 587 25 DNA Artificial
Sequence Primer 587 tgggctcttt ctcgcttaaa cacct 25 588 31 DNA
Artificial Sequence Primer 588 tggggattca gccatcaaag cagctattga c
31 589 28 DNA Artificial Sequence Primer 589 tggggattga tatcaccgat
aagaagaa 28 590 33 DNA Artificial Sequence Primer 590 tggggcttta
aatattccaa ttgaagattt tca 33 591 33 DNA Artificial Sequence Primer
591 tggggctttg ctttatagtt ttttacattt aag 33 592 28 DNA Artificial
Sequence Primer modified_base (5)...(5) I modified_base (14)...(14)
I 592 tgggtgatgc tgctaaatgg ttaaaaga 28 593 35 DNA Artificial
Sequence Primer 593 tgggtcgtgg ttttacagaa aatttcttat atatg 35 594
28 DNA Artificial Sequence Primer 594 tgggtgacat tcatcaattt
catcgttc 28 595 32 DNA Artificial Sequence Primer 595 tgggtttaca
catatcgtga gcaatgaact ga 32 596 25 DNA Artificial Sequence Primer
596 tggtaaatac cacccacatg gtgac 25 597 24 DNA Artificial Sequence
Primer 597 tggtaacaga gccttatagg cgca 24 598 28 DNA Artificial
Sequence Primer 598 tggtaacaga gccttatagg cgcatatg 28 599 30 DNA
Artificial Sequence Primer 599 tggtaagagc gcaccggtaa gttggtaaca 30
600 18 DNA Artificial Sequence Primer 600 tggtacagag tttgcgac 18
601 26 DNA Artificial Sequence Primer 601 tggtacatgt gccttcattg
atgctg 26 602 18 DNA Artificial Sequence Primer 602 tggtacagag
tttgcgac 18 603 24 DNA Artificial Sequence Primer 603 tggtactcac
ttagcgggtt tccg 24 604 24 DNA Artificial Sequence Primer 604
tggtatgata tgatgcctgc acca 24 605 21 DNA Artificial Sequence Primer
605 tggtatgcgt ggtctgatgg c 21 606 31 DNA Artificial Sequence
Primer 606 tggtattcta ttttgctgat aatgacctcg c 31 607 25 DNA
Artificial Sequence Primer 607 tggtcaaatc aaagttggtg aagaa 25 608
29 DNA Artificial Sequence Primer 608 tggtcttatg ccaagaggac
agagtgagt 29 609 24 DNA Artificial Sequence Primer 609 tggtgactcg
gcatgttatg aagc 24 610 30 DNA Artificial Sequence Primer 610
tggtgacttc ataatggatg aagttgaagt 30 611 27 DNA Artificial Sequence
Primer 611 tggtgcgagt gcttatgctc gtattat 27 612 13 DNA Artificial
Sequence Primer 612 tggtgctagc att 13 613 24 DNA Artificial
Sequence Primer 613 tggtgctttc tggcgcttaa acga 24 614 27 DNA
Artificial Sequence Primer 614 tggtggacat ttaacacatg gtgcaaa 27 615
26 DNA Artificial Sequence Primer 615 tggtggtgaa atagatagga ctgctt
26 616 13 DNA Artificial Sequence Primer 616 tggtgctagc att 13 617
26 DNA Artificial Sequence Primer 617 tggttatcgc tcaggcgaac tccaac
26 618 33 DNA Artificial Sequence Primer 618 tggttatgta ccaaatactt
tgtctgaaga tgg 33 619 31 DNA Artificial Sequence Primer 619
tggtttagat aattccttag gatctatgcg t 31 620 31 DNA Artificial
Sequence Primer modified_base (3)...(3) I modified_base (6)...(6) I
modified_base (9)...(9) I modified_base (12)...(13) I modified_base
(15)...(15) I 620 tgtcctactg tttgtggttc tgtaatgaac c 31 621 24 DNA
Artificial Sequence Primer 621 tgtaactatc acccgcacgg tgat 24 622 30
DNA Artificial Sequence Primer 622 tgtaagctct acaacccaca aaaccttacg
30 623 30 DNA Artificial Sequence Primer 623 tgtaatgaac cctaatgacc
atccacacgg 30 624 31 DNA Artificial Sequence Primer 624 tgtacccgct
gaattaacga atttatacga c 31 625 24 DNA Artificial Sequence Primer
625 tgtactcggt aagtatcacc cgca
24 626 21 DNA Artificial Sequence Primer 626 tgtactgcta tccaccctca
a 21 627 24 DNA Artificial Sequence Primer 627 tgtagccgct
aagcactacc atcc 24 628 30 DNA Artificial Sequence Primer 628
tgtagcttat cgcgaaatgt ctttgatttt 30 629 33 DNA Artificial Sequence
Primer 629 tgtatggtgg tgtaacgtta catgataata atc 33 630 27 DNA
Artificial Sequence Primer 630 tgtattaggg gcatacagtc ctcatcc 27 631
24 DNA Artificial Sequence Primer 631 tgtcaaagtg gcacgtttac tggc 24
632 24 DNA Artificial Sequence Primer 632 tgtcatgggt aaatatcacc
ctca 24 633 28 DNA Artificial Sequence Primer 633 tgtccaagaa
gcatagcaaa aaaagcaa 28 634 23 DNA Artificial Sequence Primer 634
tgtcgatgca acgcgaagaa cct 23 635 25 DNA Artificial Sequence Primer
635 tgtcggtaca cgatattctt cacga 25 636 27 DNA Artificial Sequence
Primer 636 tgtgaataaa tcacgattga ttgagca 27 637 26 DNA Artificial
Sequence Primer 637 tgtggagtaa cactgcatga aaacaa 26 638 27 DNA
Artificial Sequence Primer 638 tgtggtcaaa tcaaagttgg tgaagaa 27 639
25 DNA Artificial Sequence Primer 639 tgttcaagag ctagatcttc aggca
25 640 26 DNA Artificial Sequence Primer 640 tgttcaagag ctagatcttc
aggcaa 26 641 28 DNA Artificial Sequence Primer 641 tgttcgctgt
ttcacaaaca acattcca 28 642 32 DNA Artificial Sequence Primer 642
tgttctttag caggacttca caaacttgat aa 32 643 29 DNA Artificial
Sequence Primer 643 tgttgaacgt ggtcaaatca aagttggtg 29 644 31 DNA
Artificial Sequence Primer 644 tgttgggagt attccttacc atttaagcac a
31 645 23 DNA Artificial Sequence Primer 645 tgttggtgct ttctggcgct
taa 23 646 38 DNA Artificial Sequence Primer 646 tccttgttgt
cctactgttt gtggttctgt aatgaacc 38 647 29 DNA Artificial Sequence
Primer modified_base (7)...(7) I modified_base (10)...(10) I
modified_base (13)...(13) I modified_base (16)...(16) I
modified_base (19)...(20) I modified_base (22)...(22) I 647
ttaaagttgg ttttattggt tggcgcgga 29 648 30 DNA Artificial Sequence
Primer 648 ttaacatgaa ggaaaccact ttgataatgg 30 649 26 DNA
Artificial Sequence Primer 649 ttaacggtta tcatggccca gatggg 26 650
22 DNA Artificial Sequence Primer 650 ttaagtcccg caacgagcgc aa 22
651 22 DNA Artificial Sequence Primer 651 ttaagtcccg caacgatcgc aa
22 652 28 DNA Artificial Sequence Primer 652 ttaatttgcc aaaaatgcaa
ccaggtag 28 653 27 DNA Artificial Sequence Primer 653 ttacacatat
cgtgagcaat gaactga 27 654 31 DNA Artificial Sequence Primer 654
ttacaggaag tttaggtggt aatctaaaag g 31 655 30 DNA Artificial
Sequence Primer 655 ttactccatt attgcttggt tacactttcc 30 656 35 DNA
Artificial Sequence Primer 656 ttataactta ctgcaatcta ttcagttgct
tggtg 35 657 26 DNA Artificial Sequence Primer 657 ttataccgga
aacttcccga aaggag 26 658 32 DNA Artificial Sequence Primer 658
ttatcagcta gaccttttag gtaaagctaa gc 32 659 23 DNA Artificial
Sequence Primer 659 ttatcgctca ggcgaactcc aac 23 660 28 DNA
Artificial Sequence Primer 660 ttatcgtttg tggagctagt gcttatgc 28
661 30 DNA Artificial Sequence Primer 661 ttatgaagcg tgttctttag
caggacttca 30 662 25 DNA Artificial Sequence Primer 662 ttatggatgg
caacgtgaaa cgcgt 25 663 21 DNA Artificial Sequence Primer 663
ttattgttat cctgttatgc c 21 664 25 DNA Artificial Sequence Primer
664 ttatttacct gcactcccac aactg 25 665 33 DNA Artificial Sequence
Primer 665 ttcaaaaact ccaggccatc ctgaaatttc aac 33 666 28 DNA
Artificial Sequence Primer 666 ttcaacaggt accaatgatt tgatctca 28
667 28 DNA Artificial Sequence Primer 667 ttcccaccga tatcatggct
taccacgg 28 668 25 DNA Artificial Sequence Primer 668 ttccgtaagt
cggctaaaac agtcg 25 669 24 DNA Artificial Sequence Primer 669
ttcctccttt tgaaagcgac ggtt 24 670 17 DNA Artificial Sequence Primer
670 ttcctcggcc gcctggc 17 671 29 DNA Artificial Sequence Primer 671
ttcctgaccg acccattatt ccctttatc 29 672 22 DNA Artificial Sequence
Primer 672 ttcgatgcaa cgcgaagaac ct 22 673 27 DNA Artificial
Sequence Primer 673 ttcgccaatc aaaactaagg gaatggc 27 674 20 DNA
Artificial Sequence Primer 674 ttcggcggtc agcgcttcgg 20 675 26 DNA
Artificial Sequence Primer 675 ttctaaaaca ccaggtcacc cagaag 26 676
27 DNA Artificial Sequence Primer 676 ttctatctcg ttggtttatt cggagtt
27 677 30 DNA Artificial Sequence Primer 677 ttctgaatgt ctatatggag
gtacaacact 30 678 21 DNA Artificial Sequence Primer 678 ttgactgccc
aggtcacgct g 21 679 22 DNA Artificial Sequence Primer 679
ttgactgcgg cacaacacgg at 22 680 33 DNA Artificial Sequence Primer
680 ttgagaagac atccggctca cgttattatg gta 33 681 31 DNA Artificial
Sequence Primer 681 ttgagggtat gcaccgtctt tttgattctt t 31 682 24
DNA Artificial Sequence Primer 682 ttgcaactgc tgatttagct caga 24
683 22 DNA Artificial Sequence Primer 683 ttgcacaagc aaggcgctat tt
22 684 28 DNA Artificial Sequence Primer 684 ttgccaatga tattcgttgg
ttagcaag 28 685 31 DNA Artificial Sequence Primer 685 ttgcccgcgg
tgcggaagta accgatatta c 31 686 23 DNA Artificial Sequence Primer
686 ttgcgaatag aacgatggct cgt 23 687 30 DNA Artificial Sequence
Primer 687 ttgctcgtgg tgcacaagta acggatatta 30 688 31 DNA
Artificial Sequence Primer 688 ttgctcgtgg tgcacaagta acggatatta c
31 689 31 DNA Artificial Sequence Primer modified_base (15)...(15)
I modified_base (29)...(29) I 689 ttgctcgtgg tgcacaagta acggatatta
c 31 690 29 DNA Artificial Sequence Primer 690 ttgcttaaag
ttggttttat tggttggcg 29 691 32 DNA Artificial Sequence Primer 691
ttggtccttt ttatacgaaa gaagaagttg aa 32 692 25 DNA Artificial
Sequence Primer 692 ttgtaaatgc cggtgcttca gatcc 25 693 22 DNA
Artificial Sequence Primer 693 ttgtacacac cgcccgtcat ac 22 694 31
DNA Artificial Sequence Primer 694 ttgtagcaca gcaaggcaaa tttcctgaaa
c 31 695 30 DNA Artificial Sequence Primer 695 ttgtatgtat
ggtggtgtaa cgttacatga 30 696 27 DNA Artificial Sequence Primer 696
ttgtatgtat ggtggtgtaa ctgagca 27 697 23 DNA Artificial Sequence
Primer 697 tttaagtccc gcaacgagcg caa 23 698 28 DNA Artificial
Sequence Primer 698 tttacacata tcgtgagcaa tgaactga 28 699 30 DNA
Artificial Sequence Primer 699 tttacactac ttttattcat tgccctaacg 30
700 19 DNA Artificial Sequence Primer 700 tttacagctt tatgcaccg 19
701 29 DNA Artificial Sequence Primer 701 tttcacacag cgtgtttata
gttctacca 29 702 30 DNA Artificial Sequence Primer 702 tttcacatgt
aattttgata ttcgcactga 30 703 28 DNA Artificial Sequence Primer 703
tttcatctta tcgaggaccc gaaatcga 28 704 25 DNA Artificial Sequence
Primer 704 tttcctcctt ttgaaagcga cggtt 25 705 22 DNA Artificial
Sequence Primer 705 tttcgaaggg cctttcgacc tg 22 706 23 DNA
Artificial Sequence Primer 706 tttcgatgca acgcgaagaa cct 23 707 27
DNA Artificial Sequence Primer 707 tttgatttta cgccgtcctc caggtcg 27
708 32 DNA Artificial Sequence Primer 708 tttgcggatg aagtaggtgc
ctatcttttt gc 32 709 32 DNA Artificial Sequence Primer 709
ttttatgctt aaagttggtt ttattggttg gc 32 710 24 DNA Artificial
Sequence Primer 710 ttttgaaggt gatccgtgcc aacg 24 711 29 DNA
Artificial Sequence Primer 711 aaactatttt tttagctata ctcgaacac 29
712 19 DNA Artificial Sequence Primer 712 aacatagcct tctccgtcc 19
713 21 DNA Artificial Sequence Primer 713 aacttcgcct tcggtcatgt t
21 714 17 DNA Artificial Sequence Primer 714 aaggaggtga tccagcc 17
715 29 DNA Artificial Sequence Primer 715 aatcgacgac catcttggaa
agatttctc 29 716 21 DNA Artificial Sequence Primer 716 acaaaaggca
cgccatcacc c 21 717 21 DNA Artificial Sequence Primer 717
acaaaaggta cgccgtcacc c 21 718 18 DNA Artificial Sequence Primer
modified_base (12)...(12) I 718 acaacacgag ctgacgac 18 719 18 DNA
Artificial Sequence Primer 719 acaacacgag ctgacgac 18 720 18 DNA
Artificial Sequence Primer modified_base (16)...(16) I 720
acaacacgag ctgacgac 18 721 18 DNA Artificial Sequence Primer
modified_base (14)...(14) I 721 acaacacgag ctgacgac 18 722 18 DNA
Artificial Sequence Primer modified_base (11)...(11) I 722
acaacacgag ctgacgac 18 723 18 DNA Artificial Sequence Primer
modified_base (10)...(10) I modified_base (13)...(13) I 723
acaacacgag ctgacgac 18 724 18 DNA Artificial Sequence Primer
modified_base (8)...(8) I modified_base (10)...(10) I modified_base
(13)...(13) I 724 acaacacgag ctgacgac 18 725 18 DNA Artificial
Sequence Primer modified_base (8)...(8) I modified_base (10)...(10)
I modified_base (13)...(13) I modified_base (16)...(16) I 725
acaacacgag ctgacgac 18 726 20 DNA Artificial Sequence Primer 726
acaaccatgc accacctgtc 20 727 12 DNA Artificial Sequence Primer 727
acacgagctg ac 12 728 28 DNA Artificial Sequence Primer 728
accactttta ataaggtttg tagctaac 28 729 27 DNA Artificial Sequence
Primer 729 acctgcaata tctaatgcac tcttacg 27 730 24 DNA Artificial
Sequence Primer 730 acctgcatcc ctaaacgtac ttgc 24 731 22 DNA
Artificial Sequence Primer 731 accttgttac gacttcaccc ca 22 732 20
DNA Artificial Sequence Primer 732 acgaactgga tgtcgccgtt 20 733 18
DNA Artificial Sequence Primer 733 acgacacgag ctgacgac 18 734 18
DNA Artificial Sequence Primer 734 acgacacgag ctgacgac 18 735 20
DNA Artificial Sequence Primer 735 acgagctgac gacagccatg 20 736 19
DNA Artificial Sequence Primer 736 acgccatcag gccacgcat 19 737 21
DNA Artificial Sequence Primer 737 acgcgggcat gcagagatgc c 21 738
18 DNA Artificial Sequence Primer 738 acggcacgag gtagtcgc 18 739 20
DNA Artificial Sequence Primer 739 acggttacct tgttacgact 20 740 20
DNA Artificial Sequence Primer 740 acgtccttca tcgcctctga 20 741 27
DNA Artificial Sequence Primer 741 acgtttttcg ttttgaacga taatgct 27
742 17 DNA Artificial Sequence Primer 742 actgctgcct cccgtag 17 743
20 DNA Artificial Sequence Primer 743 acttagatgc tttcagcggt 20 744
20 DNA Artificial Sequence Primer 744 agacctcctg cgtgcaaagc 20 745
31 DNA Artificial Sequence Primer 745 agataaagaa tcacgaatat
caatttgtag c 31 746 22 DNA Artificial Sequence Primer 746
agccgacatc gaggtgccaa ac 22 747 28 DNA Artificial Sequence Primer
747 agctgctaga tgagcttctg ccatggcc 28 748 23 DNA Artificial
Sequence Primer 748 aggatagatt tatttcttgt tcg 23 749 20 DNA
Artificial Sequence Primer 749 agtccatccc ggtcctctcg 20 750 22 DNA
Artificial Sequence Primer 750 ataagccatg ttctgttcca tc 22 751 18
DNA Artificial Sequence Primer 751 ataagccggg ttctgtcg 18 752 26
DNA Artificial Sequence Primer 752 atatgattat cattgaactg cggccg 26
753 19 DNA Artificial Sequence Primer 753 atcccctgct tctgctgcc 19
754 30 DNA Artificial Sequence Primer 754 attcaagagc catttctttt
ggtaaaccac 30 755 22 DNA Artificial Sequence Primer 755 attgcccaga
aatcaaatca tc 22 756 33 DNA Artificial Sequence Primer 756
attgcttctt acttgcttag cataaatttt cca 33 757 21 DNA Artificial
Sequence Primer 757 attgtagcac gtgtgtagcc c 21 758 24 DNA
Artificial Sequence Primer 758 caagcggttt gcctcaaata gtca 24 759 22
DNA Artificial Sequence Primer 759 caatctgctg acggatctga gc 22 760
15 DNA Artificial Sequence Primer 760 caccgggcag gcgtc 15 761 20
DNA Artificial Sequence Primer 761 cacggctacc ttgttacgac 20 762 20
DNA Artificial Sequence Primer 762 cagataaaga atcgctccag 20 763 25
DNA Artificial Sequence Primer 763 catgacagcc aagacctcac ccacc 25
764 18 DNA Artificial Sequence Primer 764 catgatggtc acaaccgg 18
765 20 DNA Artificial Sequence Primer 765 ccaaacaccg ccgtcgatat 20
766 26 DNA Artificial Sequence Primer 766 ccaacctttt ccacaacaga
atcagc 26 767 27 DNA Artificial Sequence Primer 767 ccaagtgctg
gtttacccca tggagta 27 768 23 DNA Artificial Sequence Primer 768
ccacttttaa taaggtttgt agc 23 769 27 DNA Artificial Sequence Primer
769 ccagcagtta ctgtcccctc atctttg 27 770 28 DNA Artificial Sequence
Primer 770 ccataaggtc accgtcacca ttcaaagc 28 771 18 DNA Artificial
Sequence Primer 771 ccatgcagca cctgtctc 18 772 29 DNA Artificial
Sequence Primer 772 cccatttttt cacgcatgct gaaaatatc 29 773 21 DNA
Artificial Sequence Primer 773 cccccgtcaa ttcctttgag t 21 774 24
DNA Artificial Sequence Primer 774 ccctgtagta gaagaggtaa ccac 24
775 21 DNA Artificial Sequence Primer 775 ccgacaagga atttcgctac c
21 776 23 DNA Artificial Sequence Primer 776 ccgcggtcga attgcatgcc
ttc 23 777 17 DNA Artificial Sequence Primer 777 ccggtcctct
cgtacta
17 778 18 DNA Artificial Sequence Primer 778 ccgtgctcca tttttcag 18
779 25 DNA Artificial Sequence Primer 779 cctacccaac gttcaccaag
ggcag 25 780 17 DNA Artificial Sequence Primer 780 cctcctgcgt
gcaaagc 17 781 20 DNA Artificial Sequence Primer 781 cctgtagtag
aagaggtaac 20 782 18 DNA Artificial Sequence Primer 782 ccttctcccg
aagttacg 18 783 20 DNA Artificial Sequence Primer 783 ccttgttacg
acttcacccc 20 784 24 DNA Artificial Sequence Primer 784 cgaacggcca
gagtagtcaa cacg 24 785 24 DNA Artificial Sequence Primer 785
cgaacggcct gagtagtcaa cacg 24 786 24 DNA Artificial Sequence Primer
786 cgacttgacg gttaacattt cctg 24 787 21 DNA Artificial Sequence
Primer 787 cgagttgcag actgcgatcc g 21 788 21 DNA Artificial
Sequence Primer 788 cgagttgcag actgcgatcc g 21 789 25 DNA
Artificial Sequence Primer 789 cgcaccatgc gtagagatga agtac 25 790
25 DNA Artificial Sequence Primer 790 cgcaccgtgg gttgagatga agtac
25 791 18 DNA Artificial Sequence Primer 791 cgcatttcac cgctacac 18
792 20 DNA Artificial Sequence Primer 792 cgcggtcggc tcgttgatga 20
793 21 DNA Artificial Sequence Primer 793 cggctgctgg cacgaagtta g
21 794 15 DNA Artificial Sequence Primer 794 cggcttcaag acccc 15
795 24 DNA Artificial Sequence Primer 795 cggtacgaac tggatgtcgc
cgtt 24 796 15 DNA Artificial Sequence Primer 796 cgtactcccc aggcg
15 797 30 DNA Artificial Sequence Primer 797 cgtataagct gcaccataag
cttgtaatgc 30 798 21 DNA Artificial Sequence Primer 798 cgtggactac
cagggtatct a 21 799 21 DNA Artificial Sequence Primer 799
ctatcggtca gtcaggagta t 21 800 22 DNA Artificial Sequence Primer
800 cttctacatt tttagccatc ac 22 801 20 DNA Artificial Sequence
Primer 801 ctttacgccc agtaattccg 20 802 25 DNA Artificial Sequence
Primer 802 ctttcgcttt ctcgaactca accat 25 803 17 DNA Artificial
Sequence Primer 803 gaatatcaat ttgtagc 17 804 27 DNA Artificial
Sequence Primer 804 gaccccaacc tggccttttg tcgttga 27 805 19 DNA
Artificial Sequence Primer 805 gaccgttata gttacggcc 19 806 19 DNA
Artificial Sequence Primer 806 gacgggcggt gtgtacaag 19 807 19 DNA
Artificial Sequence Primer 807 gacgggcggt gtgtacaag 19 808 19 DNA
Artificial Sequence Primer 808 gacgggcggt gtgtacaag 19 809 21 DNA
Artificial Sequence Primer 809 gacgtcatcc ccaccttcct c 21 810 22
DNA Artificial Sequence Primer 810 gacgtcatcc ccaccttcct cc 22 811
19 DNA Artificial Sequence Primer 811 gagcatcagc gtgcgtgct 19 812
25 DNA Artificial Sequence Primer 812 gagctgcgcc aacgaataaa tcgtc
25 813 29 DNA Artificial Sequence Primer 813 gattggcgat aaagtgatat
tttctaaaa 29 814 26 DNA Artificial Sequence Primer 814 gcccaccaga
aagactagca ggataa 26 815 21 DNA Artificial Sequence Primer 815
gccgtccatc tgagcagcac c 21 816 21 DNA Artificial Sequence Primer
816 gccgtccatt tgagcagcac c 21 817 19 DNA Artificial Sequence
Primer 817 gccttgcgac cgtactccc 19 818 18 DNA Artificial Sequence
Primer 818 gcgaccgtac tccccagg 18 819 19 DNA Artificial Sequence
Primer 819 gcgctccacg tcttcacgc 19 820 19 DNA Artificial Sequence
Primer 820 gcgtgacagg caggtattc 19 821 28 DNA Artificial Sequence
Primer 821 gcgtgacgac cttcttgaat tgtaatca 28 822 24 DNA Artificial
Sequence Primer 822 gcgttccaca gcttgttgca gaag 24 823 18 DNA
Artificial Sequence Primer 823 gctgctggca cggagtta 18 824 26 DNA
Artificial Sequence Primer 824 gctgctttga tggctgaatc cccttc 26 825
21 DNA Artificial Sequence Primer 825 gctggattcg cctttgctac g 21
826 20 DNA Artificial Sequence Primer 826 gcttacacac ccggcctatc 20
827 23 DNA Artificial Sequence Primer 827 ggaatttacc agcgatagac acc
23 828 30 DNA Artificial Sequence Primer 828 ggataattgg tcgtaacaag
ggatagtgag 30 829 25 DNA Artificial Sequence Primer 829 ggcatcacca
tttccttgtc cttcg 25 830 18 DNA Artificial Sequence Primer 830
ggccgtactc cccaggcg 18 831 20 DNA Artificial Sequence Primer 831
ggcgcttgta cttaccgcac 20 832 25 DNA Artificial Sequence Primer 832
gggtctacac ctgcacttgc ataac 25 833 16 DNA Artificial Sequence
Primer 833 gggtttcccc attcgg 16 834 20 DNA Artificial Sequence
Primer 834 ggtaaccctt gtctttgaat 20 835 19 DNA Artificial Sequence
Primer 835 ggtaaggttc ttcgcgttg 19 836 28 DNA Artificial Sequence
Primer 836 ggtataacgc atcgcagcaa aagattta 28 837 28 DNA Artificial
Sequence Primer 837 gtaacccttg tctttgaatt gtatttgc 28 838 22 DNA
Artificial Sequence Primer 838 gtaagccatg ttttgttcca tc 22 839 22
DNA Artificial Sequence Primer 839 gtatctaatc ctgtttgctc cc 22 840
27 DNA Artificial Sequence Primer 840 gtccgacttg acggtcaaca tttcctg
27 841 18 DNA Artificial Sequence Primer 841 gtgcgccctt tctaactt 18
842 22 DNA Artificial Sequence Primer 842 gtgctggttt accccatgga gt
22 843 21 DNA Artificial Sequence Primer 843 gttcaaatgc ctggataccc
a 21 844 24 DNA Artificial Sequence Primer 844 gttgtcacca
ggcattacca tttc 24 845 24 DNA Artificial Sequence Primer 845
gttgtcgcca ggcataacca tttc 24 846 24 DNA Artificial Sequence Primer
846 gtttcatgct tagatgcttt cagc 24 847 25 DNA Artificial Sequence
Primer 847 gtttttcgtt gcgtacgatg atgtc 25 848 27 DNA Artificial
Sequence Primer 848 taaacgtccg ataccaatgg ttcgctc 27 849 30 DNA
Artificial Sequence Primer 849 taaactattt ttttagctat actcgaacac 30
850 28 DNA Artificial Sequence Primer 850 taaagacacc gctgggttta
aatgtgca 28 851 27 DNA Artificial Sequence Primer 851 taaagagacg
tttggtagtt catttgc 27 852 33 DNA Artificial Sequence Primer 852
taaaggatag cggtaactaa atggctgagc cat 33 853 26 DNA Artificial
Sequence Primer 853 taaatgcact tgcttcaggg ccatat 26 854 31 DNA
Artificial Sequence Primer 854 taaattccgc aaagactttg gcattaggtg t
31 855 29 DNA Artificial Sequence Primer 855 taacaaatcc cgtctgagtt
cctcttgca 29 856 28 DNA Artificial Sequence Primer 856 taacaacgtt
accttcgcga tccactaa 28 857 23 DNA Artificial Sequence Primer 857
taaccatttc gcgtaagatt caa 23 858 29 DNA Artificial Sequence Primer
858 taaccacccc aagatttatc tttttgcca 29 859 23 DNA Artificial
Sequence Primer 859 taaccatttc gcgtaagatt caa 23 860 39 DNA
Artificial Sequence Primer 860 taacccttgt ctttgaattg tatttgcaat
taatcctgg 39 861 29 DNA Artificial Sequence Primer 861 taaccgtttc
caaaggtact gtattttgt 29 862 34 DNA Artificial Sequence Primer 862
taaccgtttc caaaggtact gtattttgtt tacc 34 863 26 DNA Artificial
Sequence Primer 863 taactcctct tccttcaaca ggtgga 26 864 29 DNA
Artificial Sequence Primer 864 taactgaccc aaagctgaaa gctttactg 29
865 33 DNA Artificial Sequence Primer 865 taagacaagg ttttgtggat
tttttagctt gtt 33 866 26 DNA Artificial Sequence Primer 866
taagagtgat gcgggctggt tcaaca 26 867 25 DNA Artificial Sequence
Primer 867 taagcaatac ctttacttgc accac 25 868 27 DNA Artificial
Sequence Primer 868 taagcaatac ctttacttgc accacct 27 869 28 DNA
Artificial Sequence Primer 869 taagcaatac ctttacttgc accacctg 28
870 31 DNA Artificial Sequence Primer 870 taagcaccat ataagtctac
ttttttccct t 31 871 27 DNA Artificial Sequence Primer 871
taagccagca agagctgtat agttcca 27 872 26 DNA Artificial Sequence
Primer 872 taagctcccg tatcttgagt cgcctc 26 873 23 DNA Artificial
Sequence Primer 873 taagttacct tgcccgtcaa cca 23 874 27 DNA
Artificial Sequence Primer 874 taagttcctt cgctagtatg ttggctt 27 875
30 DNA Artificial Sequence Primer 875 taatcgacga ccatcttgga
aagatttctc 30 876 23 DNA Artificial Sequence Primer 876 taatctggct
gcggaagtga aat 23 877 25 DNA Artificial Sequence Primer 877
taatctggct gcggaagtga aatcg 25 878 31 DNA Artificial Sequence
Primer 878 taatgccggg tagtgcaatc cattcttcta g 31 879 24 DNA
Artificial Sequence Primer 879 taatgcgata ctggcctgca agtc 24 880 33
DNA Artificial Sequence Primer 880 tacaaccttc ggataatcag gatgagaatt
aat 33 881 27 DNA Artificial Sequence Primer 881 tacaacgtga
taaacacgac cagaagc 27 882 35 DNA Artificial Sequence Primer 882
tacaactggt tcaaaaacat taagctgtaa ttgtc 35 883 32 DNA Artificial
Sequence Primer 883 tacagcttta aagccagcaa aatgaattac ag 32 884 22
DNA Artificial Sequence Primer 884 tacaggagca gcaggcttca ag 22 885
26 DNA Artificial Sequence Primer 885 tacatcgttt cgcccaagat caatca
26 886 33 DNA Artificial Sequence Primer 886 tacatctcct tcgatagaaa
tttcattgct atc 33 887 25 DNA Artificial Sequence Primer 887
taccaaagcg tgcacgatag ttgag 25 888 27 DNA Artificial Sequence
Primer 888 taccatctac ccaaacatta gcaccaa 27 889 22 DNA Artificial
Sequence Primer 889 taccccagtt cccctgacct tc 22 890 27 DNA
Artificial Sequence Primer 890 taccggaagc accagcgaca ttaatag 27 891
27 DNA Artificial Sequence Primer 891 tacctgcatt aatcgcttgt tcatcaa
27 892 22 DNA Artificial Sequence Primer 892 taccttaccg ccaaagctgt
ct 22 893 24 DNA Artificial Sequence Primer 893 taccttagga
ccgttatagt tacg 24 894 24 DNA Artificial Sequence Primer 894
taccttttcc acaacagaat cagc 24 895 21 DNA Artificial Sequence Primer
895 tacgagctga cgacagccat g 21 896 23 DNA Artificial Sequence
Primer 896 tacgagctga cgacagccat gca 23 897 22 DNA Artificial
Sequence Primer 897 tacgcattac tcacccgtcc gc 22 898 20 DNA
Artificial Sequence Primer 898 tacgccatca ggccacgcat 20 899 27 DNA
Artificial Sequence Primer 899 tacgctaagc cacgtccata tttatca 27 900
35 DNA Artificial Sequence Primer 900 tacgtatgta aattccgcaa
agactttggc attag 35 901 30 DNA Artificial Sequence Primer 901
tacgtcgcct ttaacttggt tatattcagc 30 902 31 DNA Artificial Sequence
Primer 902 tacgttctac gatttcttca tcaggtacat c 31 903 24 DNA
Artificial Sequence Primer 903 tacgtttgta tcttctgcag aacc 24 904 29
DNA Artificial Sequence Primer 904 tacacctggt ttcgttttga tgatttgta
29 905 24 DNA Artificial Sequence Primer 905 tactagacga cgggtcaggt
aacc 24 906 32 DNA Artificial Sequence Primer 906 tacttcagct
tcgtccaata aaaaatcaca at 32 907 31 DNA Artificial Sequence Primer
907 tactttaagg ggctatcttt accatgaacc t 31 908 27 DNA Artificial
Sequence Primer 908 tagagagtag ccatcttcac cgttgtc 27 909 23 DNA
Artificial Sequence Primer 909 tagcaccaat caccctttcc tgt 23 910 28
DNA Artificial Sequence Primer 910 tagcagcaaa agttatcaca cctgcagt
28 911 25 DNA Artificial Sequence Primer 911 tagcagctag ctcgtaacca
gtgta 25 912 31 DNA Artificial Sequence Primer 912 tagccatacg
taccattgct tcataaatag a 31 913 22 DNA Artificial Sequence Primer
913 tagcccagct gtttgagcaa ct 22 914 20 DNA Artificial Sequence
Primer 914 tagccgcggt cgaattgcat 20 915 25 DNA Artificial Sequence
Primer 915 tagccttggc aacatcagca aaact 25 916 24 DNA Artificial
Sequence Primer 916 tagccttttc tccggcgtag atct 24 917 34 DNA
Artificial Sequence Primer 917 tagcgatttc tactcctaga gttgaaattt
cagg 34 918 29 DNA Artificial Sequence Primer 918 tagctgctag
atgagcttct gccatggcc 29 919 23 DNA Artificial Sequence Primer 919
taggatgaaa gcattccgct ggc 23 920 28 DNA Artificial Sequence Primer
920 taggatgagc attatcaggg aaagaatc 28 921 23 DNA Artificial
Sequence Primer 921 taggattttt ccacggcggc atc 23 922 31 DNA
Artificial Sequence Primer 922 taggcataac catttcagta ccttctggta a
31 923 28 DNA Artificial Sequence Primer 923 tagtatcacc acgtacaccc
ggatcagt 28 924 28 DNA Artificial Sequence Primer modified_base
(17)...(17) I modified_base (20)...(20) I 924 tagtatcacc acgtacaccc
ggatcagt 28 925 32 DNA Artificial Sequence Primer 925 tagtcctttc
tgaattttac catcaaaggt ac 32 926 32 DNA Artificial Sequence Primer
926 tagtcttttg gaacaccgtc tttaattaaa gt 32 927 30 DNA Artificial
Sequence Primer 927 tagtgttgta cctccatata gacattcaga 30 928 29 DNA
Artificial Sequence Primer 928 tagttgaagt tgcactatat actgttgga 29
929 23 DNA Artificial Sequence Primer 929 tataacgcac atcgtcaggg tga
23 930 26 DNA Artificial Sequence Primer 930 tatagcacca tccatctgag
cggcac 26 931 29 DNA Artificial Sequence Primer 931 tatatgaaca
ataccagttc cttctgagt 29 932 27 DNA Artificial Sequence Primer 932
tatatgatta tcattgaact gcggccg 27 933 28 DNA Artificial Sequence
Primer 933 tatccattga accaaagtta ccttggcc
28 934 20 DNA Artificial Sequence Primer 934 tatcccctgc ttctgctgcc
20 935 28 DNA Artificial Sequence Primer 935 tatcgacaga tccaaagtta
ccatgccc 28 936 27 DNA Artificial Sequence Primer 936 tatggtctat
ttcaatggca gttacga 27 937 24 DNA Artificial Sequence Primer 937
tatgtgctca cgagtttgcg gcat 24 938 28 DNA Artificial Sequence Primer
938 tatgtgtagt tgagcttact acatgagc 28 939 25 DNA Artificial
Sequence Primer 939 tattcttcgt tactcatgcc ataca 25 940 23 DNA
Artificial Sequence Primer 940 tattgcccag aaatcaaatc atc 23 941 30
DNA Artificial Sequence Primer 941 tattgcggat caccatgatg atattcttgc
30 942 31 DNA Artificial Sequence Primer 942 tattgctttt tttgctatgc
ttcttggaca t 31 943 24 DNA Artificial Sequence Primer 943
tattggaaat accggcagca tctc 24 944 30 DNA Artificial Sequence Primer
944 tatttgggtt tcattccact cagattctgg 30 945 32 DNA Artificial
Sequence Primer 945 tcaaaaacaa agaattcatt ttctggtcca aa 32 946 34
DNA Artificial Sequence Primer 946 tcaaaacgca tttttacatc ttcgttaaag
gcta 34 947 29 DNA Artificial Sequence Primer 947 tcaaaacttg
ctctagacca tttaactcc 29 948 30 DNA Artificial Sequence Primer 948
tcaaaatctt ttgattcgat catacgagac 30 949 27 DNA Artificial Sequence
Primer 949 tcaaacgatc cgcatcacca tcaaaag 27 950 30 DNA Artificial
Sequence Primer 950 tcaaagaacc agcacctaat tcatcattta 30 951 30 DNA
Artificial Sequence Primer 951 tcaaagaacc cgcacctaat tcatcattta 30
952 26 DNA Artificial Sequence Primer 952 tcaacaacac ctccttattc
ccactc 26 953 29 DNA Artificial Sequence Primer 953 tcaacaatca
gatagatgtc agacgcatg 29 954 28 DNA Artificial Sequence Primer 954
tcaacaccag cgttacctaa agtacctt 28 955 35 DNA Artificial Sequence
Primer 955 tcaactggtt caaaaacatt aagttgtaat tgtcc 35 956 28 DNA
Artificial Sequence Primer 956 tcaacttctg ccattaaaag taatgcca 28
957 24 DNA Artificial Sequence Primer 957 tcaagcgatc tacccgcatt
acaa 24 958 30 DNA Artificial Sequence Primer 958 tcaagcgcca
tctctttcgg taatccacat 30 959 30 DNA Artificial Sequence Primer 959
tcaagcgcca tttcttttgg taaaccacat 30 960 31 DNA Artificial Sequence
Primer 960 tcaagctata tgctacaact ggttcaaaaa c 31 961 30 DNA
Artificial Sequence Primer 961 tcaagctcta caccataaaa aaagctctca 30
962 28 DNA Artificial Sequence Primer 962 tcaaggttct caccgtttac
cttaggag 28 963 32 DNA Artificial Sequence Primer 963 tcaagtgctt
ttacttctat aggtttaagc tc 32 964 30 DNA Artificial Sequence Primer
964 tcaatacaga gtctacactt ggcttaggat 30 965 25 DNA Artificial
Sequence Primer 965 tcaatctcga ctttttgtgc cggta 25 966 28 DNA
Artificial Sequence Primer 966 tcacaaggac cattataatc aatgccaa 28
967 23 DNA Artificial Sequence Primer 967 tcacaccaag tagtgcaagg atc
23 968 29 DNA Artificial Sequence Primer 968 tcacacctgt aagtgagaaa
aaggttgat 29 969 34 DNA Artificial Sequence Primer 969 tcacaggttc
tacttcatca ataatttcca ttgc 34 970 34 DNA Artificial Sequence Primer
970 tcaccagctt cagcgtagtc taataattta cgga 34 971 22 DNA Artificial
Sequence Primer 971 tcaccatgcg cccgttcaca ta 22 972 37 DNA
Artificial Sequence Primer 972 tcaccgataa ataaaatacc taaagttaat
gccattg 37 973 29 DNA Artificial Sequence Primer 973 tcacctacag
ctttaaagcc agcaaaatg 29 974 28 DNA Artificial Sequence Primer 974
tcacgatacc tgcatcatca aattggtt 28 975 32 DNA Artificial Sequence
Primer 975 tcacgatcta aatttggata agccatagga aa 32 976 24 DNA
Artificial Sequence Primer 976 tcacgcgacg agtgccatcc attg 24 977 22
DNA Artificial Sequence Primer 977 tcacgcgcat catcaccagt ca 22 978
18 DNA Artificial Sequence Primer 978 tcacgggcca gctcgtct 18 979 28
DNA Artificial Sequence Primer 979 tcacgtcgtc cgacttcacg gtcagcat
28 980 26 DNA Artificial Sequence Primer 980 tcagaatcga tgccaaatgc
gtcatc 26 981 30 DNA Artificial Sequence Primer 981 tcagatataa
atggaacaaa tggagccact 30 982 32 DNA Artificial Sequence Primer 982
tcagcgtagt ctaataattt acggaacatt tc 32 983 25 DNA Artificial
Sequence Primer 983 tcagctgtta acggcttcaa gaccc 25 984 29 DNA
Artificial Sequence Primer 984 tcaggtatga aacacgatta gtcctttct 29
985 29 DNA Artificial Sequence Primer 985 tcagtttgca cttcaaaaga
aattgtgtt 29 986 29 DNA Artificial Sequence Primer 986 tcataactag
catttgtgct ttgaatgct 29 987 31 DNA Artificial Sequence Primer 987
tcataagggt tgcgttgcag attatcttta c 31 988 26 DNA Artificial
Sequence Primer 988 tcatctggtt taggatctgg ttgact 26 989 25 DNA
Artificial Sequence Primer 989 tcatctgtgg tatggcgggt aagtt 25 990
26 DNA Artificial Sequence Primer 990 tcatgacagc caagacctca cccacc
26 991 31 DNA Artificial Sequence Primer 991 tcatgataga actacctggt
tgcatttttg g 31 992 28 DNA Artificial Sequence Primer 992
tcatgtgcta atgttactgc tggatctg 28 993 31 DNA Artificial Sequence
Primer 993 tcattaggta aaatgtctgg acatgatcca a 31 994 28 DNA
Artificial Sequence Primer 994 tcatttattt cttcgctttt ctcgctac 28
995 20 DNA Artificial Sequence Primer 995 tcatttgtgc tttgaatgct 20
996 28 DNA Artificial Sequence Primer 996 tccaaacgat ctgcatcacc
atcaaaag 28 997 29 DNA Artificial Sequence Primer 997 tccaacccag
aaccacatac tttattcac 29 998 27 DNA Artificial Sequence Primer 998
tccaaccttt tccacaacag aatcagc 27 999 24 DNA Artificial Sequence
Primer 999 tccaagtgct ggtttacccc atgg 24 1000 26 DNA Artificial
Sequence Primer 1000 tccaagtgct ggtttacccc atggag 26 1001 28 DNA
Artificial Sequence Primer 1001 tccaagtttg acttaaacgt accatcgc 28
1002 32 DNA Artificial Sequence Primer 1002 tccacactgg attgtaattt
accttgttct tt 32 1003 26 DNA Artificial Sequence Primer 1003
tccaccacct caaagaccat gtggtg 26 1004 23 DNA Artificial Sequence
Primer 1004 tccagcaggt tctgacggaa acg 23 1005 28 DNA Artificial
Sequence Primer 1005 tccagcagtt actgtcccct catctttg 28 1006 30 DNA
Artificial Sequence Primer 1006 tccaggcatt accatttcta ctccttctgg 30
1007 29 DNA Artificial Sequence Primer 1007 tccataaggt caccgtcacc
attcaaagc 29 1008 35 DNA Artificial Sequence Primer modified_base
(21)...(21) I modified_base (30)...(30) I 1008 tccatacctt
tatgcaactt tgtatcaact ggaat 35 1009 28 DNA Artificial Sequence
Primer 1009 tccatattgt tgcataaaac ctgttggc 28 1010 27 DNA
Artificial Sequence Primer 1010 tccatccata gaaccaaagt taccttg 27
1011 26 DNA Artificial Sequence Primer 1011 tccatcgcag tcacgtttac
tgttgg 26 1012 32 DNA Artificial Sequence Primer 1012 tccatcgcca
gtttttgcat aatcgctaaa aa 32 1013 33 DNA Artificial Sequence Primer
1013 tccatctgtt aaaccatcat ataccatgct atc 33 1014 26 DNA Artificial
Sequence Primer 1014 tccatttccg acacgtcgtt gatcac 26 1015 27 DNA
Artificial Sequence Primer 1015 tcccaatcta acttccacat accatct 27
1016 29 DNA Artificial Sequence Primer 1016 tcccaatctt ttgattcgat
catacgaga 29 1017 27 DNA Artificial Sequence Primer 1017 tcccatacct
atggcgataa ctgtcat 27 1018 30 DNA Artificial Sequence Primer 1018
tcccattttt tcacgcatgc tgaaaatatc 30 1019 15 DNA Artificial Sequence
Primer 1019 tccccacctt cctcc 15 1020 25 DNA Artificial Sequence
Primer 1020 tccccatctc cgcaaagaca ataaa 25 1021 33 DNA Artificial
Sequence Primer 1021 tccccattta ataattccac ctactatcac act 33 1022
33 DNA Artificial Sequence Primer 1022 tcccctcatg tttaaatgat
caggataaaa agc 33 1023 31 DNA Artificial Sequence Primer 1023
tcccctttaa agcaccatta ctcattatag t 31 1024 33 DNA Artificial
Sequence Primer 1024 tcccgaacaa tgagttgtat caactatttt tac 33 1025
21 DNA Artificial Sequence Primer 1025 tcccgctggc aaataaactc g 21
1026 25 DNA Artificial Sequence Primer 1026 tcccggctag agattctgta
tacga 25 1027 28 DNA Artificial Sequence Primer 1027 tcccgtctga
gttcctcttg catgatca 28 1028 32 DNA Artificial Sequence Primer 1028
tccctaatag tagaaataac tgcatcagta gc 32 1029 34 DNA Artificial
Sequence Primer 1029 tcccttattt ttctttctac taccttcgga taat 34 1030
30 DNA Artificial Sequence Primer 1030 tcccttcctt aatatgagaa
ggaaaccact 30 1031 32 DNA Artificial Sequence Primer 1031
tccgaaactt gttttgtagc tttaatttga gc 32 1032 21 DNA Artificial
Sequence Primer 1032 tccgaagttg ccctggccgt c 21 1033 24 DNA
Artificial Sequence Primer 1033 tccgagacca gcgtaggtgt aacg 24 1034
22 DNA Artificial Sequence Primer 1034 tccgataagc cggattctgt gc 22
1035 28 DNA Artificial Sequence Primer 1035 tccgcaaaga ctttggcatt
aggtgtga 28 1036 27 DNA Artificial Sequence Primer 1036 tccgccaaaa
actccccttt tcacagg 27 1037 24 DNA Artificial Sequence Primer 1037
tccgccttca aaatggtggc gagt 24 1038 31 DNA Artificial Sequence
Primer 1038 tccggctaga gattctgtat acgaaaatat c 31 1039 31 DNA
Artificial Sequence Primer 1039 tccggctaga gattctgtat acgacaatat c
31 1040 23 DNA Artificial Sequence Primer 1040 tccggtaact
gggtcagctc gaa 23 1041 34 DNA Artificial Sequence Primer 1041
tccgtagttt tgcataattt atggtctatt tcaa 34 1042 27 DNA Artificial
Sequence Primer 1042 tccgtcatcg ctgacagaaa ctgagtt 27 1043 28 DNA
Artificial Sequence Primer 1043 tccgtctatc cacaagttaa ttggtact 28
1044 26 DNA Artificial Sequence Primer 1044 tcctacccaa cgttcaccaa
gggcag 26 1045 29 DNA Artificial Sequence Primer 1045 tcctccttgt
gcctcaaaac gcattttta 29 1046 30 DNA Artificial Sequence Primer 1046
tcctctatgc aacttagtat caacaggaat 30 1047 24 DNA Artificial Sequence
Primer 1047 tcctcttggg ccacgcaaag tttt 24 1048 27 DNA Artificial
Sequence Primer 1048 tcctcttttc acaggctcta cttcatc 27 1049 30 DNA
Artificial Sequence Primer 1049 tcctgaagat ctagttcttg aatggttact 30
1050 27 DNA Artificial Sequence Primer 1050 tcctgcaata tctaatgcac
tcttacg 27 1051 25 DNA Artificial Sequence Primer 1051 tcctgcagct
ctacctgctc catta 25 1052 20 DNA Artificial Sequence Primer 1052
tcctggccat cctgcaggat 20 1053 27 DNA Artificial Sequence Primer
1053 tcctgtttta tagccgccaa gagtaag 27 1054 21 DNA Artificial
Sequence Primer 1054 tccttcacgc gcatcatcac c 21 1055 27 DNA
Artificial Sequence Primer 1055 tccttctgat gcctgatgga ccaggag 27
1056 26 DNA Artificial Sequence Primer 1056 tccttggcat acatcatgtc
gtagca 26 1057 33 DNA Artificial Sequence Primer 1057 tccttgtgct
tcaaaacgca tttttacatt ttc 33 1058 28 DNA Artificial Sequence Primer
1058 tcctttaaaa taaccgctag tagctcct 28 1059 30 DNA Artificial
Sequence Primer 1059 tcctttatgc aacttagtat caaccggaat 30 1060 30
DNA Artificial Sequence Primer 1060 tcctttatgc aacttggtat
caacaggaat 30 1061 30 DNA Artificial Sequence Primer 1061
tcctttatgc aacttggtat caaccggaat 30 1062 29 DNA Artificial Sequence
Primer 1062 tcctttcaat gttacagaaa actctacag 29 1063 24 DNA
Artificial Sequence Primer 1063 tcgaaccgaa gttaccctga ccat 24 1064
30 DNA Artificial Sequence Primer 1064 tcgaattcag ctaaatactt
ttcagcatct 30 1065 26 DNA Artificial Sequence Primer 1065
tcgacctgga ggacgacgta aaatca 26 1066 25 DNA Artificial Sequence
Primer 1066 tcgacgacca tcttggaaag atttc 25 1067 25 DNA Artificial
Sequence Primer 1067 tcgagccgaa gttaccctgt ccgtc 25 1068 27 DNA
Artificial Sequence Primer 1068 tcgatccgca tcaccatcaa aagcaaa 27
1069 26 DNA Artificial Sequence Primer 1069 tcgatcgaac cgaagttacc
ctgacc 26 1070 28 DNA Artificial Sequence Primer 1070 tcgatcgtga
ctctctttat tttcagtt 28 1071 20 DNA Artificial Sequence Primer 1071
tcgatctcct tggcgtccga 20 1072 26 DNA Artificial Sequence Primer
1072 tcgcaccgtg ggttgagatg aagtac 26 1073 18 DNA Artificial
Sequence Primer 1073 tcgcagcgtg cgtggcac 18 1074 26 DNA Artificial
Sequence Primer 1074 tcgcaggctt acagaacgct ctccta 26 1075 23 DNA
Artificial Sequence Primer 1075 tcgcagttca tcagcacgaa gcg 23 1076
26 DNA Artificial Sequence Primer 1076 tcgccagcta gcacgatgtc attttc
26 1077 31 DNA Artificial Sequence Primer 1077 tcgccatagc
taagttgttt attgtttcca t 31 1078 22 DNA Artificial Sequence Primer
1078 tcgcctggtg caggcatcat at 22 1079 24 DNA Artificial Sequence
Primer 1079 tcgcgctgta tttttcctcc gaga 24 1080 18 DNA Artificial
Sequence Primer 1080 tcgctacctt aggaccgt 18 1081 29 DNA Artificial
Sequence Primer 1081 tcgctcagca ataattcact ataagccga 29 1082 29 DNA
Artificial Sequence Primer 1082 tcgctctctc aagtgatcta aacttggag 29
1083 25 DNA Artificial Sequence Primer 1083 tcgcttgagt gtagtcatga
ttgcg 25 1084 32 DNA Artificial Sequence Primer 1084 tcggaaacaa
agaattcatt ttctggtcca aa 32 1085 33 DNA Artificial Sequence Primer
1085 tcggaaatat tctttcaata cctttatgca act 33 1086 34 DNA Artificial
Sequence Primer 1086 tcggaaatat tctttcaata cctttatgca actt
34 1087 34 DNA Artificial Sequence Primer modified_base (20)...(20)
I modified_base (26)...(26) I 1087 tcggaaatat tctttcaata cctttatgca
actt 34 1088 20 DNA Artificial Sequence Primer 1088 tcggactcgc
tttcgctacg 20 1089 20 DNA Artificial Sequence Primer 1089
tcggataagc tgccacaagg 20 1090 19 DNA Artificial Sequence Primer
1090 tcggcatcac gccgtcgtc 19 1091 20 DNA Artificial Sequence Primer
1091 tcggcgaaca tggccatcac 20 1092 33 DNA Artificial Sequence
Primer 1092 tcgggcgtag tttttagtaa ttaaatcaga agt 33 1093 25 DNA
Artificial Sequence Primer 1093 tcggtacgaa ctggatgtcg ccgtt 25 1094
24 DNA Artificial Sequence Primer 1094 tcggtcagca aaacggtagc ttgc
24 1095 21 DNA Artificial Sequence Primer 1095 tcggtggtgg
tagccgatct c 21 1096 31 DNA Artificial Sequence Primer 1096
tcggtttaag ctctacatga tcgtaaggat a 31 1097 29 DNA Artificial
Sequence Primer 1097 tcggtttcag tcatctccac cataaaggt 29 1098 26 DNA
Artificial Sequence Primer 1098 tcgtatgacc agcttcggta ctacta 26
1099 32 DNA Artificial Sequence Primer 1099 tcgtcaacac taccattatt
accatgcatc tc 32 1100 26 DNA Artificial Sequence Primer 1100
tcgtccgact taacggtcag catttc 26 1101 29 DNA Artificial Sequence
Primer 1101 tcgtccgact taacggtcag catttcctg 29 1102 31 DNA
Artificial Sequence Primer 1102 tcgtccgact taacggtcag catttcctgc a
31 1103 26 DNA Artificial Sequence Primer 1103 tcgtcctctc
gaatctccga tatacc 26 1104 20 DNA Artificial Sequence Primer 1104
tcgtcgcgga cttcgaagcc 20 1105 26 DNA Artificial Sequence Primer
1105 tcgtcggact taacggtcag catttc 26 1106 29 DNA Artificial
Sequence Primer 1106 tcgtcggact taacggtcag catttcctg 29 1107 31 DNA
Artificial Sequence Primer 1107 tcgtcggact taacggtcag catttcctgc a
31 1108 28 DNA Artificial Sequence Primer 1108 tcgtcgtatt
tatagtgacc agcaccta 28 1109 28 DNA Artificial Sequence Primer 1109
tcgtgcctaa caaatcccgt ctgagttc 28 1110 22 DNA Artificial Sequence
Primer 1110 tcgtggacta ccagggtatc ta 22 1111 17 DNA Artificial
Sequence Primer 1111 tcgtgggcct tgccggt 17 1112 28 DNA Artificial
Sequence Primer 1112 tcgttaatta atctggctgc ggaagtga 28 1113 27 DNA
Artificial Sequence Primer 1113 tcgttgagat ggtttttacc ttcgttg 27
1114 25 DNA Artificial Sequence Primer 1114 tcgtttaagc gccagaaagc
accaa 25 1115 21 DNA Artificial Sequence Primer 1115 tcgtttcacc
ctgtcatgcc g 21 1116 26 DNA Artificial Sequence Primer 1116
tctttcgtat aaaaaggacc aattgg 26 1117 35 DNA Artificial Sequence
Primer 1117 tctacaacac ttgattgtaa tttgccttgt tcttt 35 1118 24 DNA
Artificial Sequence Primer 1118 tctagcggaa caacagttct gatg 24 1119
27 DNA Artificial Sequence Primer 1119 tctatagagt ccggactttc
ctcgtga 27 1120 30 DNA Artificial Sequence Primer 1120 tctataggta
ctgtagtttg ttttccgtct 30 1121 27 DNA Artificial Sequence Primer
1121 tctcacctac agctttaaag ccagcaa 27 1122 31 DNA Artificial
Sequence Primer 1122 tctcacctac agctttaaag ccagcaaaat g 31 1123 25
DNA Artificial Sequence Primer 1123 tctcatcccg atattaccgc catga 25
1124 29 DNA Artificial Sequence Primer 1124 tctcatgaaa aaggctcagg
agatacaag 29 1125 27 DNA Artificial Sequence Primer 1125 tctcttaccc
caccctttca cccttac 27 1126 31 DNA Artificial Sequence Primer 1126
tctctttcaa agcaccattg ctcattatag t 31 1127 24 DNA Artificial
Sequence Primer 1127 tctgcatttt tgcgagcctg tcta 24 1128 28 DNA
Artificial Sequence Primer 1128 tctgcctgag atgtcgaaaa aaacgttg 28
1129 26 DNA Artificial Sequence Primer 1129 tctggcccct ccatacatgt
atttag 26 1130 23 DNA Artificial Sequence Primer 1130 tctggctgcg
gaagtgaaat cgt 23 1131 23 DNA Artificial Sequence Primer 1131
tctgggtgac ctggtgtttt aga 23 1132 20 DNA Artificial Sequence Primer
1132 tctgtttcag ttgcaaattc 20 1133 34 DNA Artificial Sequence
Primer 1133 tcttcacact tttagaatca accgttttat tgtc 34 1134 35 DNA
Artificial Sequence Primer 1134 tcttcagcgt agtctaataa tttacggaac
atttc 35 1135 30 DNA Artificial Sequence Primer 1135 tcttccaagg
atagatttat ttcttgttcg 30 1136 33 DNA Artificial Sequence Primer
1136 tcttctgtaa agggtggttt attattcatc cca 33 1137 32 DNA Artificial
Sequence Primer 1137 tcttcttctt tcgtataaaa aggaccaatt gg 32 1138 28
DNA Artificial Sequence Primer 1138 tcttcttgaa aaattgttgt cccgaaac
28 1139 31 DNA Artificial Sequence Primer 1139 tcttctttcg
tataaaaagg accaattggt t 31 1140 18 DNA Artificial Sequence Primer
1140 tcttgacagc atccgttg 18 1141 32 DNA Artificial Sequence Primer
1141 tcttgagcat tggttcttac ttgttttgca ta 32 1142 23 DNA Artificial
Sequence Primer 1142 tcttgagcca tacgtaccat tgc 23 1143 32 DNA
Artificial Sequence Primer 1143 tcttggctta ggatgaaaat atagtggtgg ta
32 1144 39 DNA Artificial Sequence Primer 1144 tctttaagtt
cttccaagga tagatttatt tcttgttcg 39 1145 31 DNA Artificial Sequence
Primer 1145 tcttttcttt gcttaatttt ccatttgcga t 31 1146 14 DNA
Artificial Sequence Primer 1146 tgttactgct ggat 14 1147 25 DNA
Artificial Sequence Primer 1147 tgaacatttg cgacggtata cccat 25 1148
31 DNA Artificial Sequence Primer 1148 tgaatatgta atgcaaacca
gtctttgtca t 31 1149 21 DNA Artificial Sequence Primer 1149
tgaatcttga aacaccatac g 21 1150 26 DNA Artificial Sequence Primer
1150 tgaatcttga aacaccatac gtaacg 26 1151 34 DNA Artificial
Sequence Primer 1151 tgaattatgc aagaagtgat caattttctc acga 34 1152
34 DNA Artificial Sequence Primer 1152 tgaattcttt caaagcacca
ttgctcatta tagt 34 1153 30 DNA Artificial Sequence Primer 1153
tgacaggaca caatctgcat gaagtctgag 30 1154 25 DNA Artificial Sequence
Primer 1154 tgacccaaag ctgaaagctt tactg 25 1155 28 DNA Artificial
Sequence Primer 1155 tgaccccaac ctggcctttt gtcgttga 28 1156 20 DNA
Artificial Sequence Primer 1156 tgaccgttat agttacggcc 20 1157 22
DNA Artificial Sequence Primer 1157 tgacggcatc gataccaccg tc 22
1158 20 DNA Artificial Sequence Primer 1158 tgacgtcatc cccaccttcc
20 1159 22 DNA Artificial Sequence Primer 1159 tgacgtcatc
cccaccttcc tc 22 1160 20 DNA Artificial Sequence Primer 1160
tgacgtcatg cccaccttcc 20 1161 20 DNA Artificial Sequence Primer
1161 tgacgtcatg gccaccttcc 20 1162 32 DNA Artificial Sequence
Primer 1162 tgacttaaac gtaccatcgc ttcatataca ga 32 1163 27 DNA
Artificial Sequence Primer 1163 tgactttcct cccccttatc agtctcc 27
1164 31 DNA Artificial Sequence Primer 1164 tgagatgtcg aaaaaaacgt
tggcaaaata c 31 1165 31 DNA Artificial Sequence Primer 1165
tgagatgttg atgatttacc agttccgatt g 31 1166 20 DNA Artificial
Sequence Primer 1166 tgagcatcag cgtgcgtgct 20 1167 28 DNA
Artificial Sequence Primer 1167 tgagcatttt tatatccatc tccaccat 28
1168 32 DNA Artificial Sequence Primer 1168 tgagccatac gaacaatggt
ttcataaaca gc 32 1169 32 DNA Artificial Sequence Primer 1169
tgagccatga gtaccatggc ttcataacat gc 32 1170 26 DNA Artificial
Sequence Primer 1170 tgagcgtgtg gaaaaggact tggatg 26 1171 29 DNA
Artificial Sequence Primer 1171 tgagctggtg ctatatgaac aataccagt 29
1172 30 DNA Artificial Sequence Primer 1172 tgagtcaccc tccacaatgt
atagttcaga 30 1173 25 DNA Artificial Sequence Primer 1173
tgagtcgggt tcactttacc tggca 25 1174 27 DNA Artificial Sequence
Primer 1174 tgagtctaca cttggcttag gatgaaa 27 1175 32 DNA Artificial
Sequence Primer 1175 tgagttaaaa tgcgattgat ttcagtttcc aa 32 1176 32
DNA Artificial Sequence Primer 1176 tgagtttgaa ccatttcaga
gcgaatatct ac 32 1177 28 DNA Artificial Sequence Primer 1177
tgagtttgca cttcaaaaga aattgtgt 28 1178 29 DNA Artificial Sequence
Primer 1178 tgataaaaag cactaagcga tgaaacagc 29 1179 27 DNA
Artificial Sequence Primer 1179 tgataatgaa gggaaacctt tttcacg 27
1180 32 DNA Artificial Sequence Primer 1180 tgatattgaa ctggtgtacc
ataatagttg cc 32 1181 30 DNA Artificial Sequence Primer 1181
tgatcctgaa tgtttatatc tttaacgcct 30 1182 22 DNA Artificial Sequence
Primer 1182 tgatctccat ggcgcggatc tt 22 1183 19 DNA Artificial
Sequence Primer 1183 tgatgcgggc tggttcaac 19 1184 24 DNA Artificial
Sequence Primer 1184 tgatgcgggc tggttcaaca agag 24 1185 30 DNA
Artificial Sequence Primer 1185 tgatggtcta tttcaatggc agttacgaaa 30
1186 19 DNA Artificial Sequence Primer 1186 tgattatcag cggaagtag 19
1187 28 DNA Artificial Sequence Primer 1187 tgattcaaat gcagaaccat
caaactcg 28 1188 31 DNA Artificial Sequence Primer 1188 tgattcgatc
atacgagaca ttaaaactga g 31 1189 30 DNA Artificial Sequence Primer
1189 tgattggcga taaagtgata ttttctaaaa 30 1190 22 DNA Artificial
Sequence Primer 1190 tgattgtttt gcagctgatt gt 22 1191 22 DNA
Artificial Sequence Primer 1191 tgattgtttt gcagctgatt gt 22 1192 30
DNA Artificial Sequence Primer 1192 tgcaaaagta acggttacat
ctgctccaat 30 1193 33 DNA Artificial Sequence Primer 1193
tgcaacaatt aatgctccga caattaaagg att 33 1194 24 DNA Artificial
Sequence Primer 1194 tgcaactcat ctggtttagg atct 24 1195 32 DNA
Artificial Sequence Primer 1195 tgcaactgaa tagattgcag taagttataa gc
32 1196 23 DNA Artificial Sequence Primer 1196 tgcaagagca
accctagtgt tcg 23 1197 29 DNA Artificial Sequence Primer 1197
tgcaagggaa acctagaatt acaaaccct 29 1198 29 DNA Artificial Sequence
Primer 1198 tgcaatgtgt gctatgtcag caaaaagat 29 1199 18 DNA
Artificial Sequence Primer 1199 tgcacctgcg gtcgagcg 18 1200 24 DNA
Artificial Sequence Primer 1200 tgcacgcaaa cgctttactt cagc 24 1201
26 DNA Artificial Sequence Primer 1201 tgcacgtctg tttcagttgc aaattc
26 1202 13 DNA Artificial Sequence Primer 1202 tgcagctgat tgt 13
1203 26 DNA Artificial Sequence Primer 1203 tgcataggga aggtaacacc
atagtt 26 1204 25 DNA Artificial Sequence Primer 1204 tgcatcacca
tttccttgtc cttcg 25 1205 35 DNA Artificial Sequence Primer 1205
tgcatgaagc ataaaaactg tatcaagtgc tttta 35 1206 36 DNA Artificial
Sequence Primer 1206 tgcatgctta ctcaaatcat cataaacaat taaagc 36
1207 29 DNA Artificial Sequence Primer 1207 tgcattgtac cgaagtagtt
cacattgtt 29 1208 25 DNA Artificial Sequence Primer 1208 tgccaagtgc
tggtttaccc catgg 25 1209 26 DNA Artificial Sequence Primer 1209
tgccactttg acaactcctg ttgctg 26 1210 21 DNA Artificial Sequence
Primer 1210 tgccagcgac agaccatcgt a 21 1211 24 DNA Artificial
Sequence Primer 1211 tgccagctta gtcatacgga cttc 24 1212 27 DNA
Artificial Sequence Primer 1212 tgccagtttc cacatttcac gttcgtg 27
1213 30 DNA Artificial Sequence Primer 1213 tgccatacgt accatcgttt
cataaacagc 30 1214 24 DNA Artificial Sequence Primer 1214
tgccatagca aagcctacag catt 24 1215 28 DNA Artificial Sequence
Primer 1215 tgccatccat aatcacgcca tactgacg 28 1216 30 DNA
Artificial Sequence Primer 1216 tgccatttcc atgtactctt ctctaacatt 30
1217 27 DNA Artificial Sequence Primer 1217 tgcccaccag aaagactagc
aggataa 27 1218 20 DNA Artificial Sequence Primer 1218 tgcccaggta
caacctgcat 20 1219 27 DNA Artificial Sequence Primer 1219
tgccccattg ctcatgatag tagctac 27 1220 30 DNA Artificial Sequence
Primer 1220 tgccctttct aaaagtcttg agtgaagata 30 1221 25 DNA
Artificial Sequence Primer 1221 tgcccttttg taaaagcagg gctat 25 1222
23 DNA Artificial Sequence Primer 1222 tgccgataag ccggattctg tgc 23
1223 28 DNA Artificial Sequence Primer 1223 tgccgtaaca tagaagttac
cgttgatt 28 1224 33 DNA Artificial Sequence Primer 1224 tgccgtaact
aacataagag aattatgcaa gaa 33 1225 33 DNA Artificial Sequence Primer
1225 tgccgtatac gaaaatatct tatcatttag cgt 33 1226 25 DNA Artificial
Sequence Primer 1226 tgcctaacaa atcccgtctg agttc 25 1227 20 DNA
Artificial Sequence Primer 1227 tgcctcgcgc aacctacccg 20 1228 20
DNA Artificial Sequence Primer 1228 tgcctcgtgc aacccacccg 20 1229
22 DNA Artificial Sequence Primer 1229 tgcgaggaac ttcacgtcct gc 22
1230 30 DNA Artificial Sequence Primer 1230 tgcgatggta ggtatcttag
caatcattct 30 1231 24 DNA Artificial Sequence Primer 1231
tgcgcgagct tttatttggg tttc 24 1232 29 DNA Artificial Sequence
Primer 1232 tgcgctaatt cttcaacttc ttctttcgt 29 1233 32 DNA
Artificial Sequence Primer 1233 tgcgctatca acgattttga caatatatgt ga
32 1234 23 DNA Artificial Sequence Primer 1234 tgcggcagca
ctatcaccat cca 23 1235 21 DNA Artificial Sequence Primer 1235
tgcgggctgg ttcaacaaga g 21 1236 23 DNA Artificial Sequence Primer
1236 tgcgggtgat acttaccgag tac 23
1237 22 DNA Artificial Sequence Primer 1237 tgcggtctgg cgcatatagg
ta 22 1238 30 DNA Artificial Sequence Primer 1238 tgcgtagtct
aataatttac ggaacatttc 30 1239 29 DNA Artificial Sequence Primer
1239 tgcgtgacga ccttcttgaa ttgtaatca 29 1240 23 DNA Artificial
Sequence Primer 1240 tgcgtggact accagggtat cta 23 1241 13 DNA
Artificial Sequence Primer 1241 tgcagctgat tgt 13 1242 30 DNA
Artificial Sequence Primer 1242 tgctaaagtc ttgagccata cgaacaatgg 30
1243 24 DNA Artificial Sequence Primer 1243 tgctagacct ttacgtgcac
cgtg 24 1244 23 DNA Artificial Sequence Primer 1244 tgctaggcca
tcaggccacg cat 23 1245 34 DNA Artificial Sequence Primer 1245
tgctatatgc tacaactggt tcaaaaacat taag 34 1246 29 DNA Artificial
Sequence Primer 1246 tgctcacctg ctacaacaag tccagcaat 29 1247 29 DNA
Artificial Sequence Primer 1247 tgctcttacc tcaccgttcc acccttacc 29
1248 29 DNA Artificial Sequence Primer 1248 tgctgctttc gcatggttaa
ttgcttcaa 29 1249 27 DNA Artificial Sequence Primer 1249 tgctgctttg
atggctgaat ccccttc 27 1250 22 DNA Artificial Sequence Primer 1250
tgctggattc gcctttgcta cg 22 1251 21 DNA Artificial Sequence Primer
1251 tgctgtaggg aaatcagggc c 21 1252 18 DNA Artificial Sequence
Primer 1252 tgcttagatg ctttcagc 18 1253 34 DNA Artificial Sequence
Primer 1253 tgcttcaaaa cgcattttta cattttcgtt aaag 34 1254 27 DNA
Artificial Sequence Primer 1254 tgcttcagca cggccaccaa cttctag 27
1255 31 DNA Artificial Sequence Primer 1255 tgcttcagcg tagtctaata
atttacggaa c 31 1256 20 DNA Artificial Sequence Primer 1256
tgcttctctt ccgggtcggc 20 1257 32 DNA Artificial Sequence Primer
1257 tgcttgctca aatcatcata aacaattaaa gc 32 1258 31 DNA Artificial
Sequence Primer 1258 tgcttgctct ttcaagcagt cttgaatgaa g 31 1259 23
DNA Artificial Sequence Primer 1259 tgcttggtgg cttcttcgtc gaa 23
1260 32 DNA Artificial Sequence Primer 1260 tgctttgtaa tctagttcct
gaatagtaac ca 32 1261 30 DNA Artificial Sequence Primer 1261
tggaaaactc atgaaattaa agtgaaagga 30 1262 29 DNA Artificial Sequence
Primer 1262 tggaaaccgg ctaagtgagt accaccatc 29 1263 30 DNA
Artificial Sequence Primer 1263 tggaacaccg tctttaatta aagtatctcc 30
1264 24 DNA Artificial Sequence Primer 1264 tggaatttac cagcgataga
cacc 24 1265 20 DNA Artificial Sequence Primer 1265 tggaccacgc
cgaagaacgg 20 1266 30 DNA Artificial Sequence Primer 1266
tggacgatat tcacggttta cccacttata 30 1267 31 DNA Artificial Sequence
Primer 1267 tggactaata acaatgagct cattgtactg a 31 1268 31 DNA
Artificial Sequence Primer 1268 tggataattg gtcgtaacaa gggatagtga g
31 1269 27 DNA Artificial Sequence Primer 1269 tggatagacg
tcatatgaag gtgtgct 27 1270 27 DNA Artificial Sequence Primer 1270
tggatcactg cttacgaact cagcttc 27 1271 26 DNA Artificial Sequence
Primer 1271 tggatgtgct cacgagtctg tggcat 26 1272 23 DNA Artificial
Sequence Primer 1272 tggcaacagc tcaacacctt tgg 23 1273 26 DNA
Artificial Sequence Primer 1273 tggcaccgtg ggttgagatg aagtac 26
1274 19 DNA Artificial Sequence Primer 1274 tggcacgagc ctgacctgt 19
1275 34 DNA Artificial Sequence Primer 1275 tggcagcaat agtttgacgt
acaaatgcac acat 34 1276 26 DNA Artificial Sequence Primer 1276
tggcatcacc atttccttgt ccttcg 26 1277 29 DNA Artificial Sequence
Primer 1277 tggccacttt tatcagcaac cttacagtc 29 1278 19 DNA
Artificial Sequence Primer 1278 tggccgtact ccccaggcg 19 1279 20 DNA
Artificial Sequence Primer 1279 tggcgatgca ctggcttgag 20 1280 24
DNA Artificial Sequence Primer 1280 tggctcataa gacgcgcttg taga 24
1281 22 DNA Artificial Sequence Primer 1281 tggctgcgga agtgaaatcg
ta 22 1282 19 DNA Artificial Sequence Primer 1282 tggctgcttc
taagccaac 19 1283 26 DNA Artificial Sequence Primer 1283 tggcttgaga
atttaggatc cggcac 26 1284 30 DNA Artificial Sequence Primer 1284
tgggacgtaa tcgtataaat tcatcatttc 30 1285 36 DNA Artificial Sequence
Primer 1285 tgggataaca ttggttggaa tataagcaga aacatc 36 1286 30 DNA
Artificial Sequence Primer 1286 tgggatggag gtgtagaagg tgttatcatc 30
1287 30 DNA Artificial Sequence Primer 1287 tgggatggag gtgtagaagg
tgttatcatc 30 1288 32 DNA Artificial Sequence Primer 1288
tgggcaccat ttatccacaa attgattggt at 32 1289 31 DNA Artificial
Sequence Primer 1289 tggggacttc cttaccactt ttagtatcta a 31 1290 33
DNA Artificial Sequence Primer 1290 tggggatatg gaggtgtaga
aggtgttatc atc 33 1291 27 DNA Artificial Sequence Primer 1291
tggggtaaga cgcggctagc atgtatt 27 1292 25 DNA Artificial Sequence
Primer 1292 tgggtacgaa ctggatgtcg ccgtt 25 1293 27 DNA Artificial
Sequence Primer 1293 tgggtaggtt tttatctgtg acgcctt 27 1294 26 DNA
Artificial Sequence Primer 1294 tgggtctaca cctgcacttg cataac 26
1295 24 DNA Artificial Sequence Primer 1295 tgggtgctgg tttaccccat
ggag 24 1296 29 DNA Artificial Sequence Primer 1296 tgggttgcgt
tgcagattat ctttaccaa 29 1297 25 DNA Artificial Sequence Primer 1297
tgggtttcgc gcttagatgc tttca 25 1298 18 DNA Artificial Sequence
Primer 1298 tggtaaccct tgtctttg 18 1299 31 DNA Artificial Sequence
Primer 1299 tggtaaccct tgtctttgaa ttgtatttgc a 31 1300 33 DNA
Artificial Sequence Primer 1300 tggtacaaca tcgttagctt taccactttc
acg 33 1301 32 DNA Artificial Sequence Primer 1301 tggtacacct
ggtttcgttt tgatgatttg ta 32 1302 30 DNA Artificial Sequence Primer
1302 tggtacttca acttcatcca ttatgaagtc 30 1303 31 DNA Artificial
Sequence Primer 1303 tggtatattc gttaattaat ctggctgcgg a 31 1304 21
DNA Artificial Sequence Primer 1304 tggtctgagt acctcctttg c 21 1305
31 DNA Artificial Sequence Primer 1305 tggtgggtat cttagcaatc
attctaatag c 31 1306 32 DNA Artificial Sequence Primer 1306
tggtgttcta gtatagattg aggtagtggt ga 32 1307 24 DNA Artificial
Sequence Primer 1307 tggttagaag tcgtaacgtg gacc 24 1308 25 DNA
Artificial Sequence Primer 1308 tggttcaaca agagttgccg ttgca 25 1309
31 DNA Artificial Sequence Primer 1309 tggttcttac ttgctttgca
taaactttcc a 31 1310 31 DNA Artificial Sequence Primer 1310
tggttgtagt tcctgtagtt gttgcattaa c 31 1311 30 DNA Artificial
Sequence Primer 1311 tggtttgtca gaatcacgtt ctggagttgg 30 1312 28
DNA Artificial Sequence Primer 1312 tgtaaaagca gggctataat aaggactc
28 1313 29 DNA Artificial Sequence Primer 1313 tgtaaattcc
gcaaagactt tggcattag 29 1314 29 DNA Artificial Sequence Primer 1314
tgtaaccctt gtctttgaat tgtatttgc 29 1315 31 DNA Artificial Sequence
Primer 1315 tgtaattaac cgaaggttct gtagaagtat g 31 1316 28 DNA
Artificial Sequence Primer 1316 tgtacaagga ccattataat caatgcca 28
1317 31 DNA Artificial Sequence Primer 1317 tgtacaataa ggagtcacct
tatgtccctt a 31 1318 30 DNA Artificial Sequence Primer 1318
tgtacaccat ttatccacaa attgattggt 30 1319 29 DNA Artificial Sequence
Primer 1319 tgtaggcaag tgcataagaa attgataca 29 1320 27 DNA
Artificial Sequence Primer 1320 tgtcaatatg aaggtgctct gtggata 27
1321 28 DNA Artificial Sequence Primer 1321 tgtcaccagc ttcagcgtag
tctaataa 28 1322 19 DNA Artificial Sequence Primer 1322 tgtcactccc
gacacgcca 19 1323 29 DNA Artificial Sequence Primer 1323 tgtcagctaa
gctaataacg tttgtagag 29 1324 26 DNA Artificial Sequence Primer 1324
tgtcatcaag caccccaaaa tgaact 26 1325 28 DNA Artificial Sequence
Primer 1325 tgtccgactt gacggtcaac atttcctg 28 1326 28 DNA
Artificial Sequence Primer 1326 tgtccgactt gacggtcagc atttcctg 28
1327 28 DNA Artificial Sequence Primer 1327 tgtccgactt gacggttagc
atttcctg 28 1328 21 DNA Artificial Sequence Primer 1328 tgtcgcagca
tctgttcctg c 21 1329 29 DNA Artificial Sequence Primer 1329
tgtctattgt cgattgttac ctgtacagt 29 1330 27 DNA Artificial Sequence
Primer 1330 tgtgaacatt tgcgacggta tacccat 27 1331 29 DNA Artificial
Sequence Primer 1331 tgtgaagaac tttcaaatct gtgaatcca 29 1332 24 DNA
Artificial Sequence Primer 1332 tgtgatatgg aggtgtagaa ggtg 24 1333
27 DNA Artificial Sequence Primer 1333 tgtgatatgg aggtgtagaa
ggtgtta 27 1334 24 DNA Artificial Sequence Primer 1334 tgtgcaggca
tcatgtcata ccaa 24 1335 31 DNA Artificial Sequence Primer 1335
tgtgctgctt tcgcatggtt aattgcttca a 31 1336 22 DNA Artificial
Sequence Primer 1336 tgtgctggtt taccccatgg ag 22 1337 23 DNA
Artificial Sequence Primer 1337 tgtgctggtt taccccatgg agt 23 1338
15 DNA Artificial Sequence Primer 1338 tgtgctttga atgct 15 1339 28
DNA Artificial Sequence Primer 1339 tgtgcttttt ttgctgccat agcaaagc
28 1340 26 DNA Artificial Sequence Primer 1340 tgtggccgat
ttcaccacct gctcct 26 1341 18 DNA Artificial Sequence Primer 1341
tgtgttgtcg ccgcgcag 18 1342 20 DNA Artificial Sequence Primer 1342
tgttaacggc ttcaagaccc 20 1343 28 DNA Artificial Sequence Primer
1343 tgttaagtgt gttgcggctg tctttatt 28 1344 36 DNA Artificial
Sequence Primer 1344 tgttaatggt aacccttgtc tttgaattgt atttgc 36
1345 22 DNA Artificial Sequence Primer 1345 tgttactcac ccgtctgcca
ct 22 1346 14 DNA Artificial Sequence Primer 1346 tgttactgct ggat
14 1347 34 DNA Artificial Sequence Primer 1347 tgttcatgtt
taaatgatca ggataaaaag cact 34 1348 30 DNA Artificial Sequence
Primer 1348 tgttccaata gcagttccgc ccaaattgat 30 1349 30 DNA
Artificial Sequence Primer 1349 tgttctggat tgattgcaca atcaccaaag 30
1350 30 DNA Artificial Sequence Primer 1350 tgttcttgat acacctggtt
tcgttttgat 30 1351 30 DNA Artificial Sequence Primer 1351
tgttgaagct gtacttgacc tgattttacg 30 1352 19 DNA Artificial Sequence
Primer 1352 tgttgaccat gcttcttag 19 1353 28 DNA Artificial Sequence
Primer 1353 tgttgtgccg cagtcaaata tctaaata 28 1354 25 DNA
Artificial Sequence Primer 1354 tgtttgtgat gcatttgctg agcta 25 1355
33 DNA Artificial Sequence Primer 1355 tgttttatgt gtagttgagc
ttactacatg agc 33 1356 29 DNA Artificial Sequence Primer 1356
tgttttgtat ccaagtgctg gtttacccc 29 1357 11 DNA Artificial Sequence
Primer 1357 tactcatgcc a 11 1358 11 DNA Artificial Sequence Primer
1358 tattcttcgt t 11 1359 17 DNA Artificial Sequence Primer 1359
ttacttctaa cccactc 17 1360 27 DNA Artificial Sequence Primer 1360
ttaatctggc tgcggaagtg aaatcgt 27 1361 28 DNA Artificial Sequence
Primer 1361 ttaccatctt caaatacccg aacagtaa 28 1362 26 DNA
Artificial Sequence Primer 1362 ttaccgagca ggttctgacg gaaacg 26
1363 20 DNA Artificial Sequence Primer 1363 ttacgccatc aggccacgca
20 1364 17 DNA Artificial Sequence Primer 1364 ttactcaccc gtccgcc
17 1365 20 DNA Artificial Sequence Primer 1365 ttactcaccc
gtccgccgct 20 1366 34 DNA Artificial Sequence Primer 1366
ttacttcctt accactttta gtatctaaag cata 34 1367 17 DNA Artificial
Sequence Primer 1367 ttacttctaa cccactc 17 1368 21 DNA Artificial
Sequence Primer 1368 ttagaagtcg taacgtggac c 21 1369 22 DNA
Artificial Sequence Primer 1369 ttagatgctt tcagcactta tc 22 1370 26
DNA Artificial Sequence Primer 1370 ttcaaaacct tgctctcgcc aaacaa 26
1371 24 DNA Artificial Sequence Primer 1371 ttcaaaagtt gctcgagacc
attg 24 1372 23 DNA Artificial Sequence Primer 1372 ttcaaaatgc
ggaggcgtat gtg 23 1373 22 DNA Artificial Sequence Primer 1373
ttcaacaaga gttgccgttg ca 22 1374 28 DNA Artificial Sequence Primer
1374 ttcaacactc tcacctacag ctttaaag 28 1375 24 DNA Artificial
Sequence Primer 1375 ttcaagtgct tgctcaccat tgtc 24 1376 26 DNA
Artificial Sequence Primer 1376 ttcaggtaca gcaggtggtt caggat 26
1377 23 DNA Artificial Sequence Primer 1377 ttcaggtcca tcgggttcat
gcc 23 1378 29 DNA Artificial Sequence Primer 1378 ttcataagca
atacctttac ttgcaccac 29 1379 30 DNA Artificial Sequence Primer 1379
ttcattttct ggtccaaagt aagcagtatc 30 1380 25 DNA Artificial Sequence
Primer 1380 ttccaagtgc tggtttaccc catgg 25 1381 33 DNA Artificial
Sequence Primer 1381 ttccaccttg gatacctgga aaaatagctg aat 33 1382
36 DNA Artificial Sequence Primer 1382 ttccatttca actaattcta
ataattcttc atcgtc 36 1383 28 DNA Artificial Sequence Primer 1383
ttcccctgac cttcgattaa aggatagc 28 1384 27 DNA Artificial Sequence
Primer 1384 ttcgcgcatc caggagaagt acatgtt 27 1385 15 DNA Artificial
Sequence Primer 1385 ttcgctcgcc gctac 15 1386 18 DNA Artificial
Sequence Primer 1386 ttcgctctcg gcctggcc 18 1387 22 DNA Artificial
Sequence Primer 1387 ttcggtataa cgcatcgcag ca
22 1388 26 DNA Artificial Sequence Primer 1388 ttcgtgctgg
attttgtcct tgtcct 26 1389 21 DNA Artificial Sequence Primer 1389
ttcgtgctta gatgctttca g 21 1390 24 DNA Artificial Sequence Primer
1390 ttctgagcta aatcagcagt tgca 24 1391 23 DNA Artificial Sequence
Primer 1391 ttctgcgaat caatcgcacg ctg 23 1392 24 DNA Artificial
Sequence Primer 1392 ttctgcttga ggaatagtgc gtgg 24 1393 24 DNA
Artificial Sequence Primer 1393 ttctgggtga cctggtgttt taga 24 1394
31 DNA Artificial Sequence Primer 1394 ttcttccaag gatagattta
tttcttgttc g 31 1395 24 DNA Artificial Sequence Primer 1395
ttcttgaacg cgaggtttcg attg 24 1396 22 DNA Artificial Sequence
Primer 1396 ttgacatcgt ccctcttcac ag 22 1397 26 DNA Artificial
Sequence Primer 1397 ttgacatttg catgcttcaa agcctg 26 1398 23 DNA
Artificial Sequence Primer 1398 ttgacgtcat ccccaccttc ctc 23 1399
24 DNA Artificial Sequence Primer 1399 ttgacgttgc atgttcgagc ccat
24 1400 30 DNA Artificial Sequence Primer 1400 ttgcaatcga
catatccatt tcaccatgcc 30 1401 27 DNA Artificial Sequence Primer
1401 ttgcacgtct gtttcagttg caaattc 27 1402 27 DNA Artificial
Sequence Primer 1402 ttgcacgtct gtttcagttg caaattc 27 1403 20 DNA
Artificial Sequence Primer 1403 ttgcatcggg ttggtaagtc 20 1404 27
DNA Artificial Sequence Primer 1404 ttgccacttt gacaactcct gttgctg
27 1405 25 DNA Artificial Sequence Primer 1405 ttgccatagc
aaagcctaca gcatt 25 1406 30 DNA Artificial Sequence Primer 1406
ttgccattca tggtatttaa gtgtagcaga 30 1407 21 DNA Artificial Sequence
Primer 1407 ttgcgccata cgtaccatcg t 21 1408 25 DNA Artificial
Sequence Primer 1408 ttgcgttgca gattatcttt accaa 25 1409 25 DNA
Artificial Sequence Primer 1409 ttgctgccat agcaaagcct acagc 25 1410
30 DNA Artificial Sequence Primer 1410 ttgctgcttt cgcatggtta
atcgcttcaa 30 1411 30 DNA Artificial Sequence Primer 1411
ttgctgcttt cgcatggtta attgcttcaa 30 1412 27 DNA Artificial Sequence
Primer 1412 ttggacctgt aatcagctga atactgg 27 1413 22 DNA Artificial
Sequence Primer 1413 ttggccatca gaccacgcat ac 22 1414 22 DNA
Artificial Sequence Primer 1414 ttggccatca ggccacgcat ac 22 1415 28
DNA Artificial Sequence Primer 1415 ttggcgacgg tatacccata gctttata
28 1416 17 DNA Artificial Sequence Primer 1416 ttggtgcgct tggcgta
17 1417 32 DNA Artificial Sequence Primer 1417 ttggttctta
cttgttttgc ataaactttc ca 32 1418 35 DNA Artificial Sequence Primer
1418 ttgtacattt gaaacaatat gcatgacatg tgaat 35 1419 23 DNA
Artificial Sequence Primer 1419 ttgtcagact catcgcgaac atc 23 1420
28 DNA Artificial Sequence Primer 1420 ttgtgatatg gaggtgtaga
aggtgtta 28 1421 26 DNA Artificial Sequence Primer 1421 ttgtgattgt
tttgcagctg attgtg 26 1422 27 DNA Artificial Sequence Primer 1422
ttgtggccga tttcaccacc tgctcct 27 1423 21 DNA Artificial Sequence
Primer 1423 ttgttaacgg cttcaagacc c 21 1424 32 DNA Artificial
Sequence Primer 1424 ttgtttattg tttccatatg ctacacactt tc 32 1425 23
DNA Artificial Sequence Primer 1425 tttaagcgcc agaaagcacc aac 23
1426 25 DNA Artificial Sequence Primer 1426 tttacctcgc ctttccaccc
ttacc 25 1427 29 DNA Artificial Sequence Primer 1427 tttagctact
attctagctg ccatttcca 29 1428 27 DNA Artificial Sequence Primer 1428
tttatgacca gcttcggtac tactaaa 27 1429 30 DNA Artificial Sequence
Primer 1429 tttatggtct atttcaatgg cagttacgaa 30 1430 37 DNA
Artificial Sequence Primer modified_base (23)...(23) I
modified_base (32)...(32) I 1430 tttcaatacc tttatgcaac tttgtatcaa
ctggaat 37 1431 30 DNA Artificial Sequence Primer 1431 tttcacagca
tgcacgtctg tttcagttgc 30 1432 35 DNA Artificial Sequence Primer
1432 tttccccgat ctaaatttgg ataagccata ggaaa 35 1433 27 DNA
Artificial Sequence Primer 1433 tttccgatgc aacgtaatga gatttca 27
1434 22 DNA Artificial Sequence Primer 1434 tttcgtgctt agatgctttc
ag 22 1435 30 DNA Artificial Sequence Primer 1435 tttcttgaag
agtatgagct gctccgtaag 30 1436 22 DNA Artificial Sequence Primer
1436 tttgcacctt accgccaaag ct 22 1437 28 DNA Artificial Sequence
Primer 1437 tttgctcatg atctgcatga agcataaa 28 1438 24 DNA
Artificial Sequence Primer 1438 tttgctctcc gccaaagttt ccac 24 1439
28 DNA Artificial Sequence Primer 1439 tttggacctg taatcagctg
aatactgg 28 1440 29 DNA Artificial Sequence Primer 1440 tttgtgaaac
agcgaacatt ttcttggta 29 1441 20 DNA Artificial Sequence Primer 1441
ttttccagcc atgcagcgac 20 1442 34 DNA Artificial Sequence Primer
modified_base (29)...(29) I 1442 ttttcccttt atgcaactta gtatcaactg
gaat 34 1443 29 DNA Artificial Sequence Primer 1443 ttttgctcat
gatctgcatg aagcataaa 29 1444 2118 DNA Artificial Sequence
Concatenation of A. baumannii genes misc_feature 447-486, 778-817,
1162-1201, 1495-1534, 1928-1967, 2115-2118 n = A,T,C or G 1444
cgcgcggtaa aactaaagaa gaagatatag cattagaaaa agatttgctg tctgatgaaa
60 aagagattgc tgaacattta atgctgattg atcttgggcg aaacgatgta
gggcgtgtat 120 cgaaaatagg taaagtccaa gtcacggatc aaatggtgat
cgagcgttat tcacatgtca 180 tgcatattgt ttcaaatgta caaggtgaag
tgcgtgatga tatcgatgca cttgatgtat 240 ttaaagccac ctttccagca
ggaacgttat caggtgcccc aaaaattcgt gcaatggaaa 300 ttattgatga
agtagaacct gtgaaaaggg gagtttttgg cggggctgtt ggttatttgg 360
gatggcatgg tgaaatggat atgtcgattg caatccgtac ttgtgttatc cgtgataaaa
420 aggtgtatgt acaggctggt gcagggnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnnnn 480 nnnnnnggaa tctggcggtt tagtttcaga tgaactcatt
atcggtttag taaaagaacg 540 tattgctcaa cctgactgcg tgaatggttg
tattttcgac ggcttcccac gcactattcc 600 tcaagcagaa gctttggaaa
aagaagggat cagcattgat catgtaattg aaattgatgt 660 acctgatgaa
gaaatcgtaa aacgtctttc tggtcgtcgt cagcatcctg cttctggtcg 720
tgtttatcac gttgtataca atccacctaa agtggaaggt aaagatgatg tcacaggnnn
780 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnncgt tcaaccgtgt
aaaattacgt 840 aaccttaaaa ctggtaaagt tttagaaaaa acttttaaat
ctggtgatac tttagaagct 900 gctgacatcg tagaagtaga aatgaactac
ctatacaacg atggcgaaat gtggcacttc 960 atggacccag aaagcttcga
acaaattgca gctgacaaaa ctgcaatggg tgatgctgct 1020 aaatggttaa
aagacgactc aaatgaaaca tgtacaatca tgttattcaa cggcgttcct 1080
ttaaacgtaa atgcacctaa cttcgttgta ttgaaagttg ttgaaactga tccgggcgta
1140 cgtggtgata cttctggtgg tnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnnnn 1200 ntcgtgcccg yaatttgcat aaagctgccg gccttgtagc
acagcaaggc aaatttcctg 1260 aaactctaga agaatggatt gcactacccg
gcattggtcg ctcgaccgca ggtgcactca 1320 tgtctttagg tttacgtcag
tatggcgtga ttatggatgg caacgtgaaa cgcgttttag 1380 cccgtttctt
tgccattgaa gatgacttaa gcaaaccaca gcacgaacgt gaaatgtgga 1440
aactggctga agagctttgt cccacccaac gcaatcatga ctacactcaa gcgannnnnn
1500 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnttaaaa acactagcgg
taagcttaaa 1560 caagattgcc aatgatattc gttggttagc aagtggtcca
cgttgcggct tcggcgaaat 1620 ccgtattcct gaaaatgaac ctggttcaag
tatcatgcca ggtaaagtga acccgactca 1680 aagtgaagcc atgaccatgg
ttgttgctca agtacttggc aacgatacca ctattaatgt 1740 cgctggtgct
tctggtaact tcgagctcaa tgtatttatg ccagtgattg cttataactt 1800
actgcaatct attcagttgc ttggtgatgc atgtaatagt tttaatgatc actgtgcagt
1860 agggatcgag ccaaatcgtg agaaaattga tcatttcttg cataattctc
ttatgttagt 1920 tacggcannn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnccc ggttatgtac 1980 caaatacttt gtctgaagat ggtgacccat
tagacgtact tgttgtaact ccacatcctg 2040 ttgctgccgg ttctgtaatt
cgttgccgcc cagtgggcaa attaaacatg gaagacgacg 2100 gtggtatcga
tgccnnnn 2118 1445 102 DNA Artificial Sequence Calibration
Polynucleotide 1445 tttaagtccc gcaacgagcg caacccttga tcttagttgt
ttagttgggc actctaagg t 60 gactgccggt gacaaaccgg aggaaggtgg
ggatgacgtc aa 102 1446 94 DNA Artificial Sequence Calibration
Polynucleotide 1446 tagaacaccg atggcgaagg cgactttctg gtctgtaact
gacactgaga aagcgtgggg 60 agcaaacagg attagatacc ctggtagtcc acga 94
1447 108 DNA Artificial Sequence Calibration Polynucleotide 1447
tggattagag accctggtag tccacgccgt aaacgatgag tgctaagtgt tagaggcctt
60 tagtgctgaa gttaacgcat taagcactcc gcctggggag tacggcca 108 1448
108 DNA Artificial Sequence Calibration Polynucleotide 1448
tttcgatgca acgcgaagaa ccttaccagg tcttgacatc ctctgacaac cctagcttct
60 ccttcgggag cagagtgaca ggtggtgcat ggctgtcgtc agctcgta 108 1449 95
DNA Artificial Sequence Calibration Polynucleotide 1449 tctgacacct
gcccggtgct ggaaggttaa ggagaggggt tagcgtaact ctgaactgaa 60
gccccagtaa acggcggccg taactataac ggtca 95 1450 117 DNA Artificial
Sequence Calibration Polynucleotide 1450 tctgttctta gtacgagagg
accgggatgg acgcaccggt accagttgtt ctgccaaggg 60 catagctggg
tagctatgtg cggaagggat aagtgctgaa agcatctaag cacgaaa 117 1451 100
DNA Artificial Sequence Calibration Polynucleotide 1451 tgattattgt
tatcctgtta tgccatttga gatttttgag tggtattgga gttattgttc 60
caggattaat tgcaaataca attcaaagac aagggttaca 100 1452 112 DNA
Artificial Sequence Calibration Polynucleotide 1452 tcgaagtaca
atacaagaca aaagaaggta aaattactgt tttaggggaa aaattcaaga 60
aatatagaag tgatggctaa aaatgtagaa ggggtcttga agccgttaac aa 112 1453
100 DNA Artificial Sequence Calibration Polynucleotide 1453
ttgctcgtgg tgcacaagta acggatatta caatcattgt tgttgcagct gatgacggcg
60 taataaacag ttgaagcaat taaccatgcg aaagcagcaa 100 1454 114 DNA
Artificial Sequence Calibration Polynucleotide 1454 tagcttttgc
atattatatc gagccacagc atcgtgatgt tttacagctt tatgcaccgg 60
aagcttttaa tggataaatt taacgaacaa gaaataaatc tatccttgga agaa 114
1455 116 DNA Artificial Sequence Calibration Polynucleotide 1455
tgacctacag taagaggttc tgtaatgaac cctaatgacc atccacacgg tggtggtgaa
60 ggtagatctc ctatcggaaa gtccacgtac tccatggggt aaaccagcac ttggaa
116 1456 70 DNA Artificial Sequence Calibration Polynucleotide 1456
tccacacggt ggtggtgaag gtagatctcc tatcggaaag tccacgtact ccatggggta
60 aaccagcaca 70 1457 82 DNA Artificial Sequence Calibration
Polynucleotide 1457 ttatcgctca ggcgaactcc aacctggatg atgaaggccg
ctttttagaa ggtgacttgt 60 cgtagcaaag gcgaatccag ca 82 1458 87 DNA
Artificial Sequence Calibration Polynucleotide 1458 tgggcagcgt
ttcggcgaaa tggaagtggc tcgaagcgta tggcgcttcg tacgtgctgc 60
aggaaatgtt gaccgtcaag tcggaca 87 1459 97 DNA Artificial Sequence
Calibration Polynucleotide 1459 tcaggagtcg ttcaactcga tctacatgat
ggccgaccgc ccggggttcg gcggtgcaga 60 ttcgtcagct ggccggcatg
cgtggcctga tggcgta 97 1460 117 DNA Artificial Sequence Calibration
Polynucleotide 1460 tctggcaggt atgcgtggtc tgatggccaa tccatctggt
cgtatcatcg aacttccaat 60 caagtttccg tgaaggttta acagtacttg
agtacttcat ctcaacccac ggtgcga 117 1461 98 DNA Artificial Sequence
Calibration Polynucleotide 1461 tcaagcaaac gcacaatcag aagctaagaa
agcgcaagct tctggaaagc acaaatgcta 60 gttatggtac agaatttgca
actgaaacag acgtgcaa 98 1462 99 DNA Artificial Sequence Calibration
Polynucleotide 1462 tccacacgcc gttcttcaac aactaccgtg ttctacttcc
gtacgacgga cgtgacgggc 60 tcgatcgagc tgccgaagga caaggaaatg gtgatgcca
99 1463 111 DNA Artificial Sequence Calibration Sequence 1463
tcgtggcggc gtggttatcg aacccatgct gaccgatcaa tggtacgtgc acaccgcccc
60 ccaaagtcgc gattgaagcc gtagagaacg gcgacatcca gttcgtaccg a 111
1464 2100 DNA Artificial Sequence Combination Calibration
Polynucleotide 1464 gaagtagaga tatggaggaa caccagtggc gaaggcgact
ttctggtctg taactgacac 60 tgagaaagcg tggggagcaa acaggattag
ataccctggt agtccacgcc gtaaacgatg 120 agtgctaagt gttagaggcc
tttagtgctg aagttaacgc attaagcact ccgcctgggg 180 agtacggccg
caaggctgaa actcaaagga attgacgggg cacaagcggt ggagcatgtg 240
gtttaattcg aagcaacgcg aagaacctta ccaggtcttg acatcctctg acaaccctag
300 cttctccttc gggagcagag tgacaggtgg tgcatggttg tcgtcagctc
gtgtcgtgag 360 atgttgggtt aagtcccgca acgagcgcaa cccttgatct
tagttgttta gttgggcact 420 ctaaggtgac tgccggtgac aaaccggagg
aaggtgggga tgacgtcaaa tcatcatgcc 480 ccagtaccgt gagggaaagg
tgaaaagcac cccggaaggg gagtgaaaga gatcctgaaa 540 ccgtgtgcca
tagtcagagc ccgttaacgg gtgatggcgt gccttttgta gaatgaaccg 600
gcgagttata agatccgtag tcaaaaggga aacagcccag accgccagct aaggtcccaa
660 agtgtgtatt gaaaaggatg tggagttgct tagacaacta ggatgttggc
ttagaagcag 720 ccaccattta aagagtatag ggggtgacac ctgcccggtg
ctggaaggtt aaggagaggg 780 gttagcgtaa ctctgaactg aagccccagt
aaacggcggc cgtaactata acggtcctaa 840 ggtagcgaaa gaaatttgag
aggagctgtc cttagtacga gaggaccggg atggacgcac 900 cggtaccagt
tgttctgcca agggcatagc tgggtagcta tgtgcggaag ggataagtgc 960
tgaaagcatc taagcatgaa gcccccctca agatgagagc agtaaaacaa gcaaacgcac
1020 aatcagaagc taagaaagcg caagcttctg gaaagcacaa atgctagtta
tggtacagaa 1080 tttgcaactg aaacagacgt gcatgctgtg aaatttgcga
aagcttttgc atattatatc 1140 gagccacagc atcgtgatgt tttacagctt
tatgcaccgg aagcttttaa tggataaatt 1200 taacgaacaa gaaataaatc
tatccttgga agaacttaaa gatcaacgga tgctggcaag 1260 atatgaaaaa
taagataaaa cagcactatc aacactggag cgattcttta tctgaagaag 1320
gaagagcgat gaaaacaacg aagtacaata caagacaaaa gaaggtaaaa ttactgtttt
1380 aggggaaaaa ttcaagaaat atagaagtga tggctaaaaa tgtagaaggg
gtcttgaagc 1440 cgttaacagc tgttatggcg accgtggcgg cgtggttatc
gaacccatgc tgaccgatca 1500 atggtacgtg cacaccgccc cccaaagtcg
cgattgaagc cgtagagaac ggcgagatcc 1560 agttcgtccc taaacagtac
ggcaacttcg ttatcgctca ggcgaactcc aacctggatg 1620 atgaaggccg
ctttttagaa ggtgacttgt cgtagcaaag gcgaatcaag cctgtttagc 1680
cacaactatg cgtgctcgtg gtgcacaagt aacggatatt acaatcattg ttgttgcagc
1740 tgatgacggc gtaataaaca gttgaagcga ttaaccatgc gaaagcagca
ggagtaccaa 1800 ctttactcag cttgctggta tgcgtggtct gatggccaat
ccatctggtc gtatcatcga 1860 acttccaatc aagtttccgt gaaggtttaa
cagtacttga gtacttcatc tctacgcatg 1920 gtgcgcgtaa aggtcatggg
agtaagacct acagtaagag gttctgtaat gaaccctaat 1980 gaccatccac
acggtggtgg tgaaggtaga tctcctatcg gaaagtccac gtactccatg 2040
gggtaaacca gcacttggat acaaaacaag cgcagttcgg cggccagcgc ttcggtgaaa
2100
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