Patent application title: NUCLEIC ACID PROBE-BASED DIAGNOSTIC ASSAYS TARGETING SSRA GENES OF PROKARYOTIC AND EUKARYOTIC ORGANISMS
Inventors:
Thomas Gerard Barry (County Galway, IE)
Terence James Smith (Galway, IE)
IPC8 Class: AC12Q168FI
USPC Class:
435 6
Class name: Chemistry: molecular biology and microbiology measuring or testing process involving enzymes or micro-organisms; composition or test strip therefore; processes of forming such composition or test strip involving nucleic acid
Publication date: 2011-05-12
Patent application number: 20110111398
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Patent application title: NUCLEIC ACID PROBE-BASED DIAGNOSTIC ASSAYS TARGETING SSRA GENES OF PROKARYOTIC AND EUKARYOTIC ORGANISMS
Inventors:
Terence James Smith
Thomas Gerard BARRY
Agents:
Assignees:
Origin: ,
IPC8 Class: AC12Q168FI
USPC Class:
Publication date: 05/12/2011
Patent application number: 20110111398
Abstract:
Use of the ssrA gene or tmRNA, an RNA transcript of the ssrA gene, or
fragments thereof as target regions in a nucleic acid probe assay for the
detection and identification of prokaryotic and/or eukaryotic organisms
is described. Nucleotide sequence alignment of tmRNA sequences from
various organisms can be used to identify regions of homology and
non-homology within the sequences which in turn can be used to design
both genus specific and species specific oligonucleotide probes. These
newly identified regions of homology and non-homology provide the basis
of identifying and detecting organisms at the molecular level.
Oligonucleotide probes identified in this way can be used to detect tmRNA
in samples thereby giving an indication of the viability of non-viral
organisms present in various sample types.Claims:
1-29. (canceled)
30. An isolated nucleic acid sequence selected from the group consisting of the tmRNA sequence for Neisseria gonorrhoeae set forth in SEQ ID NO:86, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence.
31. An isolated nucleic acid sequence according to claim 30, wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:85.
32. A method for diagnosing a bacterial infectious agent comprising determining the presence of a bacterial nucleic acid sequence selected from the group consisting of the tmRNA sequence for Neisseria gonorrhoeae set forth in SEQ ID NO:86, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence.
33. A method according to claim 32, wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:85.
34. The method of claim 32, wherein the determination is made by performing an amplification-based assay.
35. The isolated nucleic acid sequence of claim 30, wherein the nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Neisseria gonorrhoeae set forth in SEQ ID NO:86.
36. The method of claim 32, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Neisseria gonorrhoeae set forth in SEQ ID NO:86.
37. The method of claim 34, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Neisseria gonorrhoeae set forth in SEQ ID NO:86.
Description:
[0001] This application is a divisional application of co-pending
application Ser. No. 09/959,964, filed Jan. 13, 2002, and for which
priority is claimed under 35 U.S.C. §120; which is the national
phase under 35 U.S.C. §371 of PCT International Application No.
PCT/IE00/00066 which has an International filing date of May 15, 2000,
which designated the United States of America and was published in
English; which claims priority to PCT/IE99/00043, filed May 14, 1999,
under 35 U.S.C. §119; the entire contents of all are hereby
incorporated by reference.
TECHNICAL FIELD
[0002] This invention relates to the identification of target sequences for use in nucleic acid assays for the detection and identification of prokaryotic and/or eukaryotic organisms.
BACKGROUND ART
[0003] The ssrA gene, which encodes a small stable high copy number RNA transcript (tmRNA), is found in all bacteria and has recently been identified in chloroplasts and diatoms. It has a dual function both as a tRNA and as an mRNA molecule and is involved in rescuing truncated mRNAs which have lost stop codons, facilitating trans-translation of truncated peptides prior to protease degradation (Keiler, K. C. et al. (1996), Science, 271, 990-993). The unique function of tmRNAs has directed researchers to analyse the relationship of the secondary structure of these molecules with their function. These studies have focussed on the conservation of the secondary structure of tmRNAs from different microorganisms, and on the evolutionary significance and functional relevance of such structural conservation. Studies were carried out by Matveeva, O et al (1998), Vol. 16, No. 13, 1374-1375 to investigate oligonucleotide binding to RNA molecules using tmRNA as a model of RNA containing secondary structure. The studies did not have as their objective the identification of sites in tmRNA with the goal of designing antisense oligonucleotide for therapeutic purposes.
[0004] The number of nucleic acid targets/probes for bacterial diagnostics is currently limited. As such, the need to identify and characterise novel DNA and RNA targets for diagnostic purposes is now seen as a priority. Target nucleic acid sequences for the development of probes can be for example, plasmids, ribosomal RNA genes, intergenic regions, genes encoding virulence factors or random genomic DNA fragments. In addition, a number of RNA molecules have been described which are used as targets for RNA-based detection for example, ribosomal RNA and RNase P.
[0005] The basis of any nucleic acid-based probe assay is the requirement for well characterised nucleic acid sequences which are present in all prokaryotes and eukaryotes under study. For reliable detection of a prokaryotic or eukaryotic organism, the nucleic acid probes used should be highly specific (i.e. not cross-react with nucleic acids from other organisms) and highly sensitive (i.e. most or all strains of the organism to be detected should react with the probe). Therefore, preferred target sequences would be present in all strains of the organism concerned. Such sequences would have significant sequence variability to allow differentiation of the species concerned from other closely related species but, on the other hand, have sufficient sequence conservation to allow the detection of all strains of the species concerned. In general, the precise identification of a nucleic acid sequence, which could form the basis of a specific nucleic acid probe assay, is tedious, difficult and uncertain. To date there are few general approaches which would facilitate the development of nucleic acid probes for a wide variety of microorganisms. The nucleic acid sequences which have been identified as potentially useful targets for probe development are, for example, rRNA genes and RNA, and the rRNA 16S/23S intergenic region.
[0006] The majority of nucleic acid probe/target assays centre on the high copy number ribosomal RNAs (rRNA) and rRNA 16S/23S spacer regions (European Patent No. 0 395 292) of the bacterial cell for the purposes of detection and identification. A number of successful commercial bacterial diagnostic kits have been marketed based on these rRNA probes/targets for the detection of a variety of microorganisms. These include a range of commercial probe kits based on the 16S rRNA gene marketed by Gen-probe Inc. San Diego Calif., and DNA probes based on the 16S/23S spacer region marketed by Innogenetics N.V. Ghent, Belgium. However, many of these diagnostic kits have limitations, including lack of sensitivity due to low copy-number target sequences and lack of specificity due to sequence identity between closely related organisms in many cases.
[0007] Nucleic acid-based methods that could be applied directly to samples to give an indication of the viability of any microbes present therein would be of enormous significance for food, industrial, environmental and medical applications.
[0008] A disadvantage of DNA-based methods is that they do not distinguish between living and dead organisms. Some studies have focussed on using rRNA and mRNA as indicators of cell viability (Sheridan, G. E. C. et al. (1998) Applied and Environmental Microbiology, 64, 1313-1318). However, these sequences are not satisfactory targets as rRNA and mRNA can be present in bacterial cells up to 48 hours after cell death.
[0009] With the advent of nucleic acid based microarray-like formatting, incorporating simultaneous monitoring of multiple nucleic acid targets, there is now a clear requirement to identify and characterise novel nucleic acid sequences for use as probes and/or target regions to detect and identify viable prokaryotic and eukaryotic cells.
DISCLOSURE OF INVENTION
[0010] The invention provides use of the ssrA gene or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.
[0011] Thus, the invention has application in relation to all organisms other than viruses.
[0012] No other nucleic acid probe assay has been reported which uses regions of the ssrA gene as a target region to detect and identify species of prokaryotes and eukaryotes with the attendant advantages.
[0013] According to one embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 5' end of the DNA molecule can be used as a universal target region.
[0014] In an alternative embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 3' end of the DNA molecule can be used as a universal target region.
[0015] In a further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.
[0016] In a still further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.
[0017] As hereinafter described nucleotide sequence alignments of ssrA gene sequences from different organisms show that the 5' and 3' regions of these molecules demonstrate a high degree of homology and are therefore useful as universal target regions. The ssrA genes also demonstrate a more significant degree of nucleotide sequence variability between closely related organisms than any other bacterial high copy number RNA. These variable regions are ideal targets for nucleic acid assays to distinguish between species.
[0018] The invention also provides use of tmRNA, an RNA transcript of the ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.
[0019] According to one embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of high homology from the 5' end of the tmRNA molecule can be used as a universal target region.
[0020] Alternatively, a fragment of a tmRNA molecule corresponding to a region of high homology from the 3' end of the tmRNA molecule can be used as a universal target region.
[0021] According to a further embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.
[0022] According to a still further embodiment a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.
[0023] The nucleic acid probe (DNA or RNA) in accordance with the invention typically consists of at least 10 nucleotides of the ssrA gene and/or tmRNA transcript or their complementary sequence and is used in a nucleic acid probe hybridisation assay for a prokaryotic or eukaryotic organism. Probe hybridisation to its complementary sequence is typically revealed by labelling the nucleic acid probe with a radioactive or non-radioactive (e.g. colorimetric or fluorimetric) label.
[0024] In preferred embodiments said ssrA gene fragment or said tmRNA fragment can be used as the basis of a primer to be used in an amplification procedure.
[0025] Universal oligonucleotide primers directed to the 5' and 3' regions of either the ssrA gene or the tmRNA sequence can be used in accordance with the invention to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria, facilitating amplification of a wide range of organisms simultaneously, whilst also enabling specific nucleic acid probe hybridisation and detection.
[0026] Preferably, the product of the amplification procedure is used as a target region in a nucleic probe assay.
[0027] Further, preferably, a cDNA transcript of a tmRNA molecule is used as a probe in a nucleic acid hybridisation assay.
[0028] Such assays can be carried out in vitro or in situ.
[0029] The target region as defined herein can be used as the basis of an assay for distinguishing between living and dead prokaryotic or eukaryotic organisms.
[0030] In contrast to rRNA and mRNA which can be present in bacterial cells following cell death, tmRNA is rapidly degraded in dead organisms. Thus, tmRNA can be a useful target for distinguishing between living and dead prokaryotic or eukaryotic organisms either directly by nucleic acid probe hybridisation to isolated bacterial RNA, or by combined RNA amplification and nucleic acid probe hybridisation to the amplified product.
[0031] Preferably, the target region is used in a multiple probe format for broad scale detection and/or identification of prokaryotic or eukaryotic organisms.
[0032] An ssrA gene probe or a tmRNA transcript probe in accordance with the invention can be linked to a microarray gene chip system for the broad scale high throughput detection and identification of prokaryotic or eukaryotic organisms.
[0033] A target region in accordance with the invention can also be used as a probe in an assay to detect prokaryotic or eukaryotic organisms in a sample of matter.
[0034] Such a sample of matter can include biological samples such as samples of tissue from the respiratory tract, the uro-genital tract or the gastrointestinal tract, or body fluids such as blood and blood fractions, sputum or cerebrospinal fluid.
[0035] An assay in accordance with the invention can also be carried out on food samples, environmental samples including air, water, marine and soil samples, and plant and animal derived samples.
[0036] According to the invention a fragment of the ssrA gene or the tmRNA transcript can also be used in an assay to obtain a DNA profile of a prokaryotic or eukaryotic organism and, thereby, distinguish between strains of the same species.
[0037] Nucleic acid sequence alignments have shown that sequence variation occurs in the ssrA gene and the tmRNA transcript within individual species. This intra-species sequence variation can be used to distinguish between strains of the same species for epidemiology, tracing of infectious agents for example, in outbreaks, or for population studies.
[0038] Other applications of the invention include the use of the ssrA gene, the tmRNA transcript or a DNA sequence complementary thereto, or a fragment thereof, to design an agent directed against infectious prokaryotic or eukaryotic organisms for therapeutic purposes.
[0039] Such agents can include antisense mRNA or oligonucleotides, ribozymes, and antagonistic peptides and are suitable for use in any kind of medical condition.
[0040] Thus, the invention can be used for the detection of viable organisms only in biological samples using the tmRNA target. Thus, during and following any anti-infectious agent drug treatment, the tmRNA target can be used to monitor the efficacy of the therapy on those specific infectious agents (e.g. antimicrobial and/or anti-parasitic treatments).
[0041] In one embodiment, the target region is used to monitor the efficacy of drug therapies against infectious agents.
[0042] In another embodiment, the target region is used to monitor the viability and level of health-promoting organisms in the gastrointestinal tract.
[0043] This aspect of the invention relates, for example, to the introduction into the gut flora of health-promoting (probiotic) organisms contained in for example yoghurt or other food to improve health. There is an interest and need to continuously monitor the presence and levels of these organisms to ensure their continued function in promoting health. The tmRNA region can be used as a target to detect viable organisms, for example in faeces, so as to monitor the presence of the health promoting organisms.
[0044] In a further embodiment, the assay is used for the quantification of prokaryotic or eukaryotic organisms.
[0045] When using probe hybridisation and/or in vitro amplification to detect organisms in a sample it is possible to determine the number of organisms present, based on the signal intensity. Real-time methods of in vitro amplification can also be used to enable the quantification of organisms in a sample. Thus, the ability to quantify the number of organisms in a sample can be important in clinical situations for treatment purposes, for example for antibiotic or other treatments or for monitoring treatment efficacy.
[0046] A still further application of the invention is the use of a database of ssrA gene sequences to identify a prokaryotic or eukaryotic organism.
[0047] The invention provides a variety of probes for the 5' and 3' homologous regions and the variable regions of the ssrA gene and tmRNA sequences, the probes being derived from these sequences or sequences complementary thereto. Representative sequences are as follows:
TABLE-US-00001 Actinobacillus actinomycetemcomitans ssrA SEQ ID NO: 1 GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCGAAGT GCACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAA AATAGTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATA ACCTGCCTTTAGCCTTCGCTCCCCAGCTTCCGCTCGTAAGACG GGGATAAAGCGGAGTCAAACCAAAACGAGATCGTGTGGAAG CCACCGTTTGAGGATCGAAGCATTAAATTAAATCAAAGTAGC TTAATTGTCGCGTGTCCGTCAGCAGGATTAAGTGAATTTAAAG ACCGGACTAAACGTGTAGTGCTAACGGCAGAGGAATTTCGGA CGGGGGTTCAACTCCCCCCAGCTCCACCA Actinobacillus actinomycetemcomitans tmRNA SEQ ID NO: 2 GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCGAAG UGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAA AAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUA AUAACCUGCCUUUAGCCUUCGCUCCCCAGCUUCCGCUCGUA AGACGGGGAUAAAGCGGAGUCAAACCAAAACGAGAUCGUGU GGAAGCCACCGUUUGAGGAUCGAAGCAUUAAAUUAAAUCAA AGUAGCUUAAUUGUCGCGUGUCCGUCAGCAGGAUUAAGUGA AUUUAAAGACCGGACUAAACGUGUAGUGCUAACGGCAGAGG AAUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Aeromonas salmonicida ssrA, internal partial SEQ ID NO: 3 AAGATTCACGAAACCCAAGGTGCATGCCGAGGTGCGGTAGGC CTCGTTAACAAACCGCAAAAAAATAGTCGCAAACGACGAAAA CTACGCACTAGCAGCtTAATAACCTGCATAGAGCCCTTCTACC CTAGCTTGCCTGTGTCCTAGGGAATCGGAAGGTCATCCTTCAC AGGATCGTGTGGAAGTCCTGCTCGGGGCGGAAGCATTAAAAC CAATCGAGCTAGTCAATTCGTGGCGTGTCTCTCCGCAGCGGGT TGGCGAATGTAAAGAGTGACTAAGCATGTAGTACCGAGGATG TAGTAATTTTGGACGGGG Aeromonas salmonicida tmRNA, internal partial SEQ ID NO: 4 AAGAUUCACGAAACCCAAGGUGCAUGCCGAGGUGCGGUAGG CCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAA AACUACGCACUAGCAGCUUAAUAACCUGCAUAGAGCCCUUC UACCCUAGCUUGCCUGUGUCCUAGGGAAUCGGAAGGUCAUC CUUCACAGGAUCGUGUGGAAGUCCUGCUCGGGGCGGAAGCA UUAAAACCAAUCGAGCUAGUCAAUUCGUGGCGUGUCUCUCC GCAGCGGGUUGGCGAAUGUAAAGAGUGACUAAGCAUGUAGU ACCGAGGAUGUAGUAAUUUUGGACGGGG Alcaligenes eutrophus ssrA SEQ ID NO: 5 TGGGCCGACCTGGTTTCGACGTGGTTACAAAGCAGTGAGGCA TACCGAGGACCCGTCACCTCGTTAATCAATGGAATGCAATAA CTGCTAACGACGAACGTTACGCACTCGCTTAATTGCGGCCGTC CTCGCACTGGCTCGCTGACGGGCTAGGGTCGCAAGACCACGC GAGGTATTTACGTCAGATAAGCTCCGGAAGGGTCACGAAGCC GGGGACGAAAACCTAGTGACTCGCCGTCGTAGAGCGTGTTCG TCCGATGCGCCGGTTAAATCAAATGACAGAACTAAGTATGTA GAACTCTCTGTGGAGGGCTTACGGACGCGGGTTCGATTCCCGC CGGCTCCACCA Alcaligenes eutrophus tmRNA SEQ ID NO: 6 UGGGCCGACCUGGUUUCGACGUGGUUACAAAGCAGUGAGGC AUACCGAGGACCCGUCACCUCGUUAAUCAAUGGAAUGCAAU AACUGCUAACGACGAACGUUACGCACUCGCUUAAUUGCGGC CGUCCUCGCACUGGCUCGCUGACGGGCUAGGGUCGCAAGAC CACGCGAGGUAUUUACGUCAGAUAAGCUCCGGAAGGGUCAC GAAGCCGGGGACGAAAACCUAGUGACUCGCCGUCGUAGAGC GUGUUCGUCCGAUGCGCCGGUUAAAUCAAAUGACAGAACUA AGUAUGUAGAACUCUCUGUGGAGGGCUUACGGACGCGGGUU CGAUUCCCGCCGGCUCCACCA Aquifex aeolicus ssrA SEQ ID NO: 7 GGGGGCGGAAAGGATTCGACGGGGACAGGCGGTCCCCGAGG AGCAGGCCGGGTGGCTCCCGTAACAGCCGCTAAAACAGCTCC CGAAGCTGAACTCGCTCTCGCTGCCTAATTAAACGGCAGCGC GTCCCCGGTAGGTTTGCGGGTGGCCTACCGGAGGGCGTCAGA GACACCCGCTCGGGCTACTCGGTCGCACGGGGCTGAGTAGCT GACACCTAACCCGTGCTACCCTCGGGGAGCTTGCCCGTGGGC GACCCGAGGGGAAATCCTGAACACGGGCTAAGCCTGTAGAGC CTCGGATGTGGCCGCCGTCCTCGGACGCGGGTTCGATTCCCGC CGCCTCCACCA Aquifex aeolicus tmRNA SEQ ID NO: 8 GGGGGCGGAAAGGAUUCGACGGGGACAGGCGGUCCCCGAGG AGCAGGCCGGGUGGCUCCCGUAACAGCCGCUAAAACAGCUC CCGAAGCUGAACUCGCUCUCGCUGCCUAAUUAAACGGCAGC GCGUCCCCGGUAGGUUUGCGGGUGGCCUACCGGAGGGCGUC AGAGACACCCGCUCGGGCUACUCGGUCGCACGGGGCUGAGU AGCUGACACCUAACCCGUGCUACCCUCGGGGAGCUUGCCCG UGGGCGACCCGAGGGGAAAUCCUGAACACGGGCUAAGCCUG UAGAGCCUCGGAUGUGGCCGCCGUCCUCGGACGCGGGUUCG AUUCCCGCCGCCUCCACCA Bacillus megaterium ssrA, internal partial SEQ ID NO: 9 AGGGTAGTTCGAGCTTAGGTTGCGAGTCGAGGAGATGGCCTC GTTAAAACATCAACGCCAATAATAACTGGCAAATCTAACAAT AACTTCGCTTTAGCTGCATAATAGTAGCTTAGCGTTCCTCCCT CCATCGCCCATGTGGTAGGGTAAGGGACTCACTTTAAGTGGG CTACGCCGGAGTTCGCCGTCTGAGGACGAAGGAAGAGAATAA TCAGACTAGCGACTGGGACGCCTGTTGGTAGGCAGAACAGCT CGCGAATGATCAATATGCCAACTACACTCGTAGACGCTTAAGT GGCCATATTTCTGGACGTGG Bacillus megaterium tmRNA, internal partial SEQ ID NO: 10 AGGGUAGUUCGAGCUUAGGUUGCGAGUCGAGGAGAUGGCCU CGUUAAAACAUCAACGCCAAUAAUAACUGGCAAAUCUAACA AUAACUUCGCUUUAGCUGCAUAAUAGUAGCUUAGCGUUCCU CCCUCCAUCGCCCAUGUGGUAGGGUAAGGGACUCACUUUAA GUGGGCUACGCCGGAGUUCGCCGUCUGAGGACGAAGGAAGA GAAUAAUCAGACUAGCGACUGGGACGCCUGUUGGUAGGCAG AACAGCUCGCGAAUGAUCAAUAUGCCAACUACACUCGUAGA CGCUUAAGUGGCCAUAUUUCUGGACGUGG Bacillus subtilis ssrA SEQ ID NO: 11 GGGGACGTTACGGATTCGACAGGGATGGATCGAGCTTGAGCT GCGAGCCGAGAGGCGATCTCGTAAACACGCACTTAAATATAA CTGGCAAAACTAACAGTTTTAACCAAAACGTAGCATTAGCTG CCTAATAAGCGCAGCGAGCTCTTCCTGACATTGCCTATGTGTC TGTGAAGAGCACATCCAAGTAGGCTACGCTTGCGTTCCCGTCT GAGAACGTAAGAAGAGATGAACAGACTAGCTCTCGGAAGGCC CGCCCGCAGGCAAGAAGATGAGTGAAACCATAAATATGCAGG CTACGCTCGTAGACGCTTAAGTAATCGATGTTTCTGGACGTGG GTTCGACTCCCACCGTCTCCACCA Bacillus subtilis tmRNA SEQ ID NO: 12 GGGGACGUUACGGAUUCGACAGGGAUGGAUCGAGCUUGAGC UGCGAGCCGAGAGGCGAUCUCGUAAACACGCACUUAAAUAU AACUGGCAAAACUAACAGUUUUAACCAAAACGUAGCAUUAG CUGCCUAAUAAGCGCAGCGAGCUCUUCCUGACAUUGCCUAU GUGUCUGUGAAGAGCACAUCCAAGUAGGCUACGCUUGCGUU CCCGUCUGAGAACGUAAGAAGAGAUGAACAGACUAGCUCUC GGAAGGCCCGCCCGCAGGCAAGAAGAUGAGUGAAACCAUAA AUAUGCAGGCUACGCUCGUAGACGCUUAAGUAAUCGAUGUU UCUGGACGUGGGUUCGACUCCCACCGUCUCCACCA Bordetella pertussis ssrA SEQ ID NO: 13 GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAGG GCATGCCGAGCACCAGTAAGCTCGTTAATCCACTGGAACACT ACAAACGCCAACGACGAGCGTCTCGCTCTCGCCGCTTAAGCG GTGAGCCGCTGCACTGATCTGTCCTTGGGTCAGGCGGGGGAA GGCAACTTCACAGGGGGCAACCCCGAACCGCAGCAGCGACAT TCACAAGGAATCGGCCACCGCTGGGGTCACACGGCGTTGGTT TAAATTACGTGAATCGCCCTGGTCCGGCCCGTCGATCGGCTAA GTCCAGGGTTAAATCCAAATAGATCGACTAAGCATGTAGAAC
TGGTTGCGGAGGGCTTGCGGACGGGGGTTCAATTCCCCCCGG CTCCACCA Bordetella pertussis tmRNA SEQ ID NO: 14 GGGGCCGAUCCGGAUUCGACGUGGGUCAUGAAACAGCUCAG GGCAUGCCGAGCACCAGUAAGCUCGUUAAUCCACUGGAACA CUACAAACGCCAACGACGAGCGUCUCGCUCUCGCCGCUUAA GCGGUGAGCCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGG GGAAGGCAACUUCACAGGGGGCAACCCCGAACCGCAGCAGC GACAUUCACAAGGAAUCGGCCACCGCUGGGGUCACACGGCG UUGGUUUAAAUUACGUGAAUCGCCCUGGUCCGGCCCGUCGA UCGGCUAAGUCCAGGGUUAAAUCCAAAUAGAUCGACUAAGC AUGUAGAACUGGUUGCGGAGGGCUUGCGGACGGGGGUUCAA UUCCCCCCGGCUCCACCA Borrelia burgdorferi ssrA SEQ ID NO: 15 GGGGATGTTTTGGATTTGACTGAAAATGTTAATATTGTAAGTT GCAGGCAGAGGGAATCTCTTAAAACTTCTAAAATAAATGCAA AAAATAATAACTTTACAAGCTCAAATCTTGTAATGGCTGCTTA AGTTAGCAGAGGGTTTTGTTGAATTTGGCTTTGAGGTTCACTT ATACTCTTTTCGACATCAAAGCTTGCTTAAAAATGTTTTCAAG TTGATTTTTAGGGACTTTTATACTTGAGAGCAATTTGGTGGTTT GCTAGTATTTCCAAACCATATTGCTTAATAAAATACTAGATAA GCTTGTAGAAGCTTATAGTATTATTTTTAGGACGCGGGTTCAA TTCCCGCCATCTCCACCA Borrelia burgdorferi tmRNA SEQ ID NO: 16 GGGGAUGUUUUGGAUUUGACUGAAAAUGUUAAUAUUGUAA GUUGCAGGCAGAGGGAAUCUCUUAAAACUUCUAAAAUAAAU GCAAAAAAUAAUAACUUUACAAGCUCAAAUCUUGUAAUGGC UGCUUAAGUUAGCAGAGGGUUUUGUUGAAUUUGGCUUUGA GGUUCACUUAUACUCUUUUCGACAUCAAAGCUUGCUUAAAA AUGUUUUCAAGUUGAUUUUUAGGGACUUUUAUACUUGAGA GCAAUUUGGUGGUUUGCUAGUAUUUCCAAACCAUAUUGCUU AAUAAAAUACUAGAUAAGCUUGUAGAAGCUUAUAGUAUUA UUUUUAGGACGCGGGUUCAAUUCCCGCCAUCUCCACCA Campylobacter jejuni ssrA SEQ ID NO: 17 GGGAGCGACTTGGCTTCGACAGGAGTAAGTCTGCTTAGATGG CATGTCGCTTTGGGCAAAGCGTAAAAAGCCCAAATAAAATTA AACGCAAACAACGTTAAATTCGCTCCTGCTTACGCTAAAGCTG CGTAAGTTCAGTTGAGCCTGAAATTTAAGTCATACTATCTAGC TTAATTTTCGGTCATTTTTGATAGTGTAGCCTTGCGTTTGACAA GCGTTGAGGTGAAATAAAGTCTTAGCCTTGCTTTTGAGTTTTG GAAGATGAGCGAAGTAGGGTGAAGTAGTCATCTTTGCTAAGC ATGTAGAGGTCTTTGTGGGATTATTTTTGGACAGGGGTTCGAT TCCCCTCGCTTCCACCA Campylobacter jejuni tmRNA SEQ ID NO: 18 GGGAGCGACUUGGCUUCGACAGGAGUAAGUCUGCUUAGAUG GCAUGUCGCUUUGGGCAAAGCGUAAAAAGCCCAAAUAAAAU UAAACGCAAACAACGUUAAAUUCGCUCCUGCUUACGCUAAA GCUGCGUAAGUUCAGUUGAGCCUGAAAUUUAAGUCAUACUA UCUAGCUUAAUUUUCGGUCAUUUUUGAUAGUGUAGCCUUGC GUUUGACAAGCGUUGAGGUGAAAUAAAGUCUUAGCCUUGCU UUUGAGUUUUGGAAGAUGAGCGAAGUAGGGUGAAGUAGUC AUCUUUGCUAAGCAUGUAGAGGUCUUUGUGGGAUUAUUUU UGGACAGGGGUUCGAUUCCCCUCGCUUCCACCA Chlamydia trachomatis (D/UW-3/CX) ssrA SEQ ID NO: 19 GGGGGTGTAAAGGTTTCGACTTAGAAATGAAGCGTTAATTGC ATGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAAC AATAAATGCCGAACCTAAGGCTGAATGCGAAATTATCAGCTT CGCTGATCTCGAAGATCTAAGAGTAGCTGCTTAATTAGCAAA GTTGTTACCTAAATACGGGTGACCCGGTGTTCGCGAGCTCCAC CAGAGGTTTTCGAAACACCGTCATGTATCTGGTTAGAACTTAG GTCCTTTAATTCTCGAGGAAATGAGTTTGAAATTTAATGAGAG TCGTTAGTCTCTATAGGGGTTTCTAGCTGAGGAGACATAACGT ATAGTACCTAGGAACTAAGCATGTAGAGGTTAGCGGGGAGTT TACTAAGGACGAGAGTTCGACTCTCTCCACCTCCACCA Chlamydia trachomatis (D/UW-3/CX) tmRNA SEQ ID NO: 20 GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCA GCUUCGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUUAAUUA GCAAAGUUGUUACCUAAAUACGGGUGACCCGGUGUUCGCGA GCUCCACCAGAGGUUUUCGAAACACCGUCAUGUAUCUGGUU AGAACUUAGGUCCUUUAAUUCUCGAGGAAAUGAGUUUGAAA UUUAAUGAGAGUCGUUAGUCUCUAUAGGGGUUUCUAGCUGA GGAGACAUAACGUAUAGUACCUAGGAACUAAGCAUGUAGAG GUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGACUCUCUC CACCUCCACCA Chlamydia trachomatis (mouse pneumonitis) ssrA SEQ ID NO: 21 GGGGGTGTAAAGGTTTCGACTTAGAAATGAAGCGTTAATTGC ATGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAAC AATAAATGCCGAACCTAAGGCTGAATGCGAAATTATCAGCTT CGCTGATCTTAATGATCTAAGAGTTGCTGCTTAATTAGCAAAG TTGTTACCTAAGTACTGGTAACCCGGTGTTCGCGAGCTCCACC AGAGGTTTTCGAAACGCCGTCATTTATCTGGTTAGAATTAGGG CCTTTTAACTCTCAAGGGAACTAATTTGAATTTTAATGAGAGT CGTTGGTCTCTATAGAGGTTTCTAGCTGAGGAGATATAACGTA AAATATTCTAGAAACTAAGCATGTAGAGGTTAGCGGGGAGTT TACTAAGGACGAGAGTTCGAATCTCTCCACCTCCACCA Chlamydia trachomatis (mouse pneumonitis) tmRNA SEQ ID NO: 22 GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCA GCUUCGCUGAUCUUAAUGAUCUAAGAGUUGCUGCUUAAUUA GCAAAGUUGUUACCUAAGUACUGGUAACCCGGUGUUCGCGA GCUCCACCAGAGGUUUUCGAAACGCCGUCAUUUAUCUGGUU AGAAUUAGGGCCUUUUAACUCUCAAGGGAACUAAUUUGAAU UUUAAUGAGAGUCGUUGGUCUCUAUAGAGGUUUCUAGCUGA GGAGAUAUAACGUAAAAUAUUCUAGAAACUAAGCAUGUAG AGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGAAUCUC UCCACCUCCACCA Chlorobium tepidum ssrA SEQ ID NO: 23 GGGGATGACAGGCTATCGACAGGATAGGTGTGAGATGTCGTT GCACTCCGAGTTTCAGCATGGACGGACTCGTTAAACAAGTCTA TGTACCAATAGATGCAGACGATTATTCGTATGCAATGGCTGCC TGATTAGCACAAGTTAATTCAGAAGCCATCGTCCTGCGGTGAA TGCGCTTACTCTGAAGCCGCCGGATGGCATAACCCGCGCTTGA GCCTACGGGTTCGCGCAAGTAAGCTCCGTACATTCATGCCCGA GGGGGTGTGCGGGTAACCAATCGGGATAAGGGGACGAACGCT GCTGGCGGTGTAATCGGACCACGAAAAACCAACCACCAGAGA TGAGTGTGGTAACTGCATCGAGCAGTGTCCTGGACGCGGGTTC AAGTCCCGCCATCTCCACCA Chlorobium tepidum tmRNA SEQ ID NO: 24 GGGGAUGACAGGCUAUCGACAGGAUAGGUGUGAGAUGUCGU UGCACUCCGAGUUUCAGCAUGGACGGACUCGUUAAACAAGU CUAUGUACCAAUAGAUGCAGACGAUUAUUCGUAUGCAAUGG CUGCCUGAUUAGCACAAGUUAAUUCAGAAGCCAUCGUCCUG CGGUGAAUGCGCUUACUCUGAAGCCGCCGGAUGGCAUAACC CGCGCUUGAGCCUACGGGUUCGCGCAAGUAAGCUCCGUACA UUCAUGCCCGAGGGGGUGUGCGGGUAACCAAUCGGGAUAAG GGGACGAACGCUGCUGGCGGUGUAAUCGGACCACGAAAAAC CAACCACCAGAGAUGAGUGUGGUAACUGCAUCGAGCAGUGU CCUGGACGCGGGUUCAAGUCCCGCCAUCUCCACCA Cyanophora paradoxa (alga) cyanelle ssrA SEQ ID NO: 25 GGGGCTGTTTAGGTTTCGACGTTTTTTTCTAATTATGTTTGTTA AGCAAGTCGAGGATTTGTTCTATCTCGAAAATCAAGAACTCTC AAAATTTAAACGCAACTAATATTGTACGTTTTAACCGTAAAGC AGCTTTCGCTGTTTAATAATTACTTTTAATTTAAAAACCTAATT
TTTTTAGGAATTTATTTATTTATTGTTTATCCTGCTTAATGAAT TAAAAAAAGCTATACTTGTGAATAAACGCATAATTTAAAAAA ACGGACGTGGGTTCAAATCCCACCAGCTCCACCA Cyanophora paradoxa (alga) cyanelle tmRNA SEQ ID NO: 26 GGGGCUGUUUAGGUUUCGACGUUUUUUUCUAAUUAUGUUU GUUAAGCAAGUCGAGGAUUUGUUCUAUCUCGAAAAUCAAGA ACUCUCAAAAUUUAAACGCAACUAAUAUUGUACGUUUUAAC CGUAAAGCAGCUUUCGCUGUUUAAUAAUUACUUUUAAUUUA AAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGUUUA UCCUGCUUAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAA CGCAUAAUUUAAAAAAACGGACGUGGGUUCAAAUCCCACCA GCUCCACCA Clostridium acetobutylicum ssrA, 3' partial SEQ ID NO: 27 AATCTGGCGTCGAGAGCGGGGAAACGAGCCTTACAAAGCTTT GAGTAAGGAACGGAATTTATGAAGCTACTGAAGTGAAAAGCT TGTTTGTAGGCGTTTCATGGAGGGAATGTTAAAATACAAACTG CACTCGGAGATGCTTAATGAAACCATTTTCGGACAGGGGTTCG ATTCCCCTCGCCTCCACCA Clostridium acetobutylicum tmRNA, 3' partial SEQ ID NO: 28 AAUCUGGCGUCGAGAGCGGGGAAACGAGCCUUACAAAGCUU UGAGUAAGGAACGGAAUUUAUGAAGCUACUGAAGUGAAAA GCUUGUUUGUAGGCGUUUCAUGGAGGGAAUGUUAAAAUAC AAACUGCACUCGGAGAUGCUUAAUGAAACCAUUUUCGGACA GGGGUUCGAUUCCCCUCGCCUCCACCA Deinococcus radiodurans ssrA SEQ ID NO: 29 GGGGGTGACCCGGTTTCGACAGGGGAACTGAAGGTGATGTTG CGTGTCGAGGTGCCGTTGGCCTCGTAAACAAACGGCAAAGCC ATTTAACTGGCAACCAGAACTACGCTCTCGCTGCTTAAGTGAG ATGACGACCGTGCAGCCCGGCCTTTGGCGTCGCGGAAGTCAC TAAAAAAGAAGGCTAGCCCAGGCGATTCTCCATAGCCGACGG CGAAACTTTATGGAGCTACGGCCTGCGAGAACCTGCCCACTG GTGAGCGCCGGCCCGACAATCAAACAGTGGGATACACACGTA GACGCACGCTGGACGGACCTTTGGACGGCGGTTCGACTCCGC CCACCTCCACCA Deinococcus radiodurans tmRNA SEQ ID NO: 30 GGGGGUGACCCGGUUUCGACAGGGGAACUGAAGGUGAUGUU GCGUGUCGAGGUGCCGUUGGCCUCGUAAACAAACGGCAAAG CCAUUUAACUGGCAACCAGAACUACGCUCUCGCUGCUUAAG UGAGAUGACGACCGUGCAGCCCGGCCUUUGGCGUCGCGGAA GUCACUAAAAAAGAAGGCUAGCCCAGGCGAUUCUCCAUAGC CGACGGCGAAACUUUAUGGAGCUACGGCCUGCGAGAACCUG CCCACUGGUGAGCGCCGGCCCGACAAUCAAACAGUGGGAUA CACACGUAGACGCACGCUGGACGGACCUUUGGACGGCGGUU CGACUCCGCCCACCUCCACCA Desulfovibrio desulfuricans ssrA, internal partial SEQ ID NO: 31 GGGACTGGAACCGTAGCGGCAGGTCGAGGCGCCGCTGGCCTC GTAAAAAGCGGCACAAAAGTAATTGCCAACAACGATTACGAC TACGCTTACGCTGCCTAATAACAGCGAGGCAATGACCGTTTAA CGGTCGCGCCGATCAGGGCCATGCCTGATAACCCTGATTGGC GACACTTATCAGGCTGGCGAAAACCGGCTCTCGCCGGGGTTTT TCGCGAGGAGTTTACCGGCGGGATTGCTGCGTTGTGCCTGGTC AGGGGCCAACAGCGCGGTGAAATACATACTTGACCTAAACCT GTAATGCTTCGTGTGGAATGTTCTCGGACGGGG Desulfovibrio desulfuricans tmRNA, internal partial SEQ ID NO: 32 GGGACUGGAACCGUAGCGGCAGGUCGAGGCGCCGCUGGCCU CGUAAAAAGCGGCACAAAAGUAAUUGCCAACAACGAUUACG ACUACGCUUACGCUGCCUAAUAACAGCGAGGCAAUGACCGU UUAACGGUCGCGCCGAUCAGGGCCAUGCCUGAUAACCCUGA UUGGCGACACUUAUCAGGCUGGCGAAAACCGGCUCUCGCCG GGGUUUUUCGCGAGGAGUUUACCGGCGGGAUUGCUGCGUUG UGCCUGGUCAGGGGCCAACAGCGCGGUGAAAUACAUACUUG ACCUAAACCUGUAAUGCUUCGUGUGGAAUGUUCUCGGACGG GG Dichelobacter nodosus ssrA, 3' partial SEQ ID NO: 33 CTCGAGGTGCATGTCGAGAATGAGAGAATCTCGTTAAATACTT TCAAAACTTATAGTTGCAAACGACGACAACTACGCTTTAGCG GCTTAATTCCCGCTTTCGCTTACCTAGATTTGTCTGTGGGTTTA CCGTAAGCGACATTAACACAGAATCGCTGGTTAACGCGTCCG CTGTTAATCGGTTAAATTAAGCGGAATCGCTTGTAAAATGCCT GAGCGTTGGCTGTTTATGAGTTAAACCTAATTAACTGCTCTAA ACATGTAGTACCAAAAGTTAAGGATTCGCGGACGGGGGTTCA AATCCCCCCGCCTCCACCA Dichelobacter nodosus tmRNA, 3' partial SEQ ID NO: 34 CUCGAGGUGCAUGUCGAGAAUGAGAGAAUCUCGUUAAAUAC UUUCAAAACUUAUAGUUGCAAACGACGACAACUACGCUUUA GCGGCUUAAUUCCCGCUUUCGCUUACCUAGAUUUGUCUGUG GGUUUACCGUAAGCGACAUUAACACAGAAUCGCUGGUUAAC GCGUCCGCUGUUAAUCGGUUAAAUUAAGCGGAAUCGCUUGU AAAAUGCCUGAGCGUUGGCUGUUUAUGAGUUAAACCUAAUU AACUGCUCUAAACAUGUAGUACCAAAAGUUAAGGAUUCGCG GACGGGGGUUCAAAUCCCCCCGCCUCCACCA Enterococcus faecalis ssrA SEQ ID NO: 35 GGGGGCGTTACGGATTCGACAGGCATAGTTGAGCTTGAATTG CGTTTCGTAGGTTACGGCTACGTTAAAACGTTACAGTTAAATA TAACTGCTAAAAACGAAAACAATTCTTTCGCTTTAGCTGCCTA AAAACCAGCTAGCGAAGATCCTCCCGGCATCGCCCATGTGCT CGGGTCAGGGTCCTAATCGAAGTGGGATACGCTAAATTTTTCC GTCTGTAAAATTTAGAGGAGCTTACCAGACTAGCAATACAGA ATGCCTGTCACTCGGCACGCTGTAAAGCGAACCTTTAAATGAG TGTCTATGAACGTAGAGATTTAAGTGGCAATATGTTTGGACGC GGGTTCGACTCCCGCCGTCTCCACCA Enterococcus faecalis tmRNA SEQ ID NO: 36 GGGGGCGUUACGGAUUCGACAGGCAUAGUUGAGCUUGAAUU GCGUUUCGUAGGUUACGGCUACGUUAAAACGUUACAGUUAA AUAUAACUGCUAAAAACGAAAACAAUUCUUUCGCUUUAGCU GCCUAAAAACCAGCUAGCGAAGAUCCUCCCGGCAUCGCCCA UGUGCUCGGGUCAGGGUCCUAAUCGAAGUGGGAUACGCUAA AUUUUUCCGUCUGUAAAAUUUAGAGGAGCUUACCAGACUAG CAAUACAGAAUGCCUGUCACUCGGCACGCUGUAAAGCGAAC CUUUAAAUGAGUGUCUAUGAACGUAGAGAUUUAAGUGGCA AUAUGUUUGGACGCGGGUUCGACUCCCGCCGUCUCCACCA Escherichia coli ssrA SEQ ID NO: 37 GGGGCTGATTCTGGATTCGACGGGATTTGCGAAACCCAAGGT GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAA TAGTCGCAAACGACGAAAACTACGCTTTAGCAGCTTAATAAC CTGCTTAGAGCCCTCTCTCCCTAGCCTCCGCTCTTAGGACGGG GATCAAGAGAGGTCAAACCCAAAAGAGATCGCGTGGAAGCCC TGCCTGGGGTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTT AGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACT GACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCG GGTTCAACTCCCGCCAGCTCCACCA Escherichia coli tmRNA SEQ ID NO: 38 GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGG UGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAA AAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAU AACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGG ACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGG AAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCU AGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAU GUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAU UUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA Haemophilus influenzae ssrA SEQ ID NO: 39 GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCAAGGT GCACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAA
AATAGTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATA ACCTGCATTTAGCCTTCGCGCTCCAGCTTCCGCTCGTAAGACG GGGATAACGCGGAGTCAAACCAAAACGAGATCGTGTGGAAGC CACCGTTTGAGGATCGAAGCACTAAATTGAATCAAACTAGCTT AAGTTTAGCGTGTCTGTCCGCATGCTTAAGTGAAATTAAAGAC GAGACTAAACGTGTAGTACTGAAGGTAGAGTAATTTCGGACG GGGGTTCAACTCCCCCCAGCTCCACCA Haemophilus influenzae tmRNA SEQ ID NO: 40 GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCAAGG UGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAA AAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUA AUAACCUGCAUUUAGCCUUCGCGCUCCAGCUUCCGCUCGUA AGACGGGGAUAACGCGGAGUCAAACCAAAACGAGAUCGUGU GGAAGCCACCGUUUGAGGAUCGAAGCACUAAAUUGAAUCAA ACUAGCUUAAGUUUAGCGUGUCUGUCCGCAUGCUUAAGUGA AAUUAAAGACGAGACUAAACGUGUAGUACUGAAGGUAGAG UAAUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Helicobacter pylori (ATCC 43504) ssrA, internal partial SEQ ID NO: 41 AGATTTCTTGTCGCGCAGATAGCATGCCAAGCGCTGCTTGTAA AACAGCAACAAAAATAACTGTAAACAACACAGATTACGCTCC AGCTTACGCTAAAGCTGCGTGAGTTAATCTCCTTTTGGAGCTG GACTGATTAGAATTTCTAGCGTTTTAATCGCTCCATAACCTTA AGCTAGACGCTTTTAAAAGGTGGTTCGCCTTTTAAACTAAGAA ACAAGAACTCTTGAAACTATCTTAAGGTTTTAGAAAGTTGGAC CAGAGCTAGTTTTAAGGCTAAAAACTAACCAATTTTCTAAGCA TTGTAGAAGTTTGTGTTTAGGGCAAGATTTTTGGACTGGG Helicobacter pylori (ATCC 43504) tmRNA, internal partial SEQ ID NO: 42 AGAUUUCUUGUCGCGCAGAUAGCAUGCCAAGCGCUGCUUGU AAAACAGCAACAAAAAUAACUGUAAACAACACAGAUUACGC UCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGG AGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAU AACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUA AACUAAGAAACAAGAACUCUUGAAACUAUCUUAAGGUUUUA GAAAGUUGGACCAGAGCUAGUUUUAAGGCUAAAAACUAACC AAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGGCAAGA UUUUUGGACUGGG Helicobacter pylori (strain 26695) ssrA SEQ ID NO: 43 GGGGCTGACTTGGATTTCGACAGATTTCTTGTCGCACAGATAG CATGCCAAGCGCTGCTTGTAAAACAGCAACAAAAATAACTGT AAACAACACAGATTACGCTCCAGCTTACGCTAAAGCTGCGTG AGTTAATCTCCTTTTGGAGCTGGACTGATTAGAATTTCTAGCG TTTTAATCGCTCCATAACCTTAAGCTAGACGCTTTTAAAAGGT GGTTCGCCTTTTAAACTAAGAAACAAGAACTCTTGAAACTATC TCAAGGTTTTAGAAAGTTGGACCAGAGCTAGTTTTAAGGCTAA AAAACCAACCAATTTTCTAAGCATTGTAGAAGTTTGTGTTTAG GGCAAGATTTTTGGACTGGGGTTCGATTCCCCACAGCTCCACCA Helicobacter pylori (strain 26695) tmRNA SEQ ID NO: 44 GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAU AGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAAC UGUAAACAACACAGAUUACGCUCCAGCUUACGCUAAAGCUG CGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUU CUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUU UAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCU UGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAGCUAG UUUUAAGGCUAAAAAACCAACCAAUUUUCUAAGCAUUGUAG AAGUUUGUGUUUAGGGCAAGAUUUUUGGACUGGGGUUCGA UUCCCCACAGCUCCACCA Klebsiella aerogenes (NCTC 9528)ssrA, internal partial SEQ ID NO: 45 GGGATTCGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAAC TACGCTTTAGCAGCTTAATAACCTGCTAAGAGCCCTCTCTCCC TAGCTTCCGCTCCTAAGACGGGGAATAAAGAGAGGTCAAACC CAAAAGAGATCGCGTGGAAGCCCTGCCTGGGGTTGAAGCGTT AAAACTAATCAGGCTAGTTTGTCAGTGGCGTGTCCGTCCGCAG CTGGCCAGCGAATGTAAAGACTGGACTAAGCATGTAGTGCCG AGGATGTAGGAATTTC Klebsiella aerogenes (NCTC 9528) tmRNA, internal partial SEQ ID NO: 46 GGGAUUCGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGG CCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAA ACUACGCUUUAGCAGCUUAAUAACCUGCUAAGAGCCCUCUC UCCCUAGCUUCCGCUCCUAAGACGGGGAAUAAAGAGAGGUC AAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGA AGCGUUAAAACUAAUCAGGCUAGUUUGUCAGUGGCGUGUCC GUCCGCAGCUGGCCAGCGAAUGUAAAGACUGGACUAAGCAU GUAGUGCCGAGGAUGUAGGAAUUUC Lactobacillus lactis (NCTC 662)ssrA, internal partial SEQ ID NO: 47 AAGCACAGTTCGAGCTTGAATTGCGTTTCGTAGGTTACGTCTA CGTTAAAACGTTACAGTTAAATATAACTGCTAAAAACGAAAA CAACTCTTACGCTTTAGCTGCCTAAAAACAGTTAGCGTAGATC CTCTCGGCATCGCCCATGTGCTCGAGTAAGGGTCTCAAATTTA GTGGGATACGTTAAACTTTTCCGTCTGTAAAGTTTAAAAGAGA TCATCAGACTAGCGATACAGAATGCCTGTCACTCGGCAAGCT GTAAAGCGAAACCTCAAATGAGTTGACTATGAACGTAGATTT TTAAGTGTCGATGTGTTT Lactobacillus lactis (NCTC 662) tmRNA, internal partial SEQ ID NO: 48 AAGCACAGUUCGAGCUUGAAUUGCGUUUCGUAGGUUACGUC UACGUUAAAACGUUACAGUUAAAUAUAACUGCUAAAAACGA AAACAACUCUUACGCUUUAGCUGCCUAAAAACAGUUAGCGU AGAUCCUCUCGGCAUCGCCCAUGUGCUCGAGUAAGGGUCUC AAAUUUAGUGGGAUACGUUAAACUUUUCCGUCUGUAAAGUU UAAAAGAGAUCAUCAGACUAGCGAUACAGAAUGCCUGUCAC UCGGCAAGCUGUAAAGCGAAACCUCAAAUGAGUUGACUAUG AACGUAGAUUUUUAAGUGUCGAUGUGUUU Legionella pneumophila ssrA, internal partial SEQ ID NO: 49 GTGGGTTGCAAAACCGGAAGTGCATGCCGAGAAGGAGATCTC TCGTAAATAAGACTCAATTAAATATAAATGCAAACGATGAAA ACTTTGCTGGTGGGGAAGCTATCGCTGCCTAATAAGCACTTTA GTTAAACCATCACTGTGTACTGGCCAATAAACCCAGTATCCCG TTCGACCGAGCCCGCTTATCGGTATCGAATCAACGGTCATAAG AGATAAGCTAGCGTCCTAATCTATCCCGGGTTATGGCGCGAA ACTCAGGGAATCGCTGTGTATCATCCTGCCCGTCGGAGGAGCC ACAGTTAAATTCAAAAGACAAGGCTATGCATGTAGAGCTAAA GGCAGAGGACTTGCGGACGCGG Legionella pneumophila tmRNA, internal partial SEQ ID NO: 50 GUGGGUUGCAAAACCGGAAGUGCAUGCCGAGAAGGAGAUCU CUCGUAAAUAAGACUCAAUUAAAUAUAAAUGCAAACGAUGA AAACUUUGCUGGUGGGGAAGCUAUCGCUGCCUAAUAAGCAC UUUAGUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGU AUCCCGUUCGACCGAGCCCGCUUAUCGGUAUCGAAUCAACG GUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUA UGGCGCGAAACUCAGGGAAUCGCUGUGUAUCAUCCUGCCCG UCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGCUAUGCA UGUAGAGCUAAAGGCAGAGGACUUGCGGACGCGG Listeria grayi ssrA, internal partial SEQ ID NO: 51 ACAGGGATAGGTCGAGCTTGAGTTGCGAGCCGGGGGGATCGG CCCGTCATCAACGTCAAAGCCAATAATAACTGGCAAACAAAA CAACAATTTAGCTTTCGCTGCCTAATAGCAGTCTGAATAGCTG ATCCTCCGTGCATCACCCATGTGCTACGGTAAGGGTCTCACTT TTAAGTGGGTTACGCTGGCTTATCTCCGTCTGGGGCAAACGAG AAGAGCATAATCAGACTAGCTAGATAGAGCCCTGACGCCGGG CAGACATCTATGCGAAATCCAAATACGGCAACTACGCTCGTA GATGCTCAAGTGCCGATATTTCTGG Listeria grayi tmRNA, internal partial
SEQ ID NO: 52 ACAGGGAUAGGUCGAGCUUGAGUUGCGAGCCGGGGGGAUCG GCCCGUCAUCAACGUCAAAGCCAAUAAUAACUGGCAAACAA AACAACAAUUUAGCUUUCGCUGCCUAAUAGCAGUCUGAAUA GCUGAUCCUCCGUGCAUCACCCAUGUGCUACGGUAAGGGUC UCACUUUUAAGUGGGUUACGCUGGCUUAUCUCCGUCUGGGG CAAACGAGAAGAGCAUAAUCAGACUAGCUAGAUAGAGCCCU GACGCCGGGCAGACAUCUAUGCGAAAUCCAAAUACGGCAAC UACGCUCGUAGAUGCUCAAGUGCCGAUAUUUCUGG Listeria innocua ssrA, internal partial SEQ ID NO: 53 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTTAAATAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTCAAGTGCCGATATTTCTGG Listeria innocua tmRNA, internal partial SEQ ID NO: 54 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGG UUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUCAAGUGCCGAUAUUUCUGG Listeria monocytogenes (NCTC 7973)ssrA, internal partial SEQ ID NO: 55 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGGGGTTAAATAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria monocytogenes (NCTC 7973)tmRNA, internal partial SEQ ID NO: 56 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGGGG UUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Listeria monocytogenes (NCTC 11994) ssrA, internal partial SEQ ID NO: 57 CAAAGCCAATAATAACTGGCAAAGAAAAACAAAACCTAGCTT TCGCTGCCTAATAAGCAGTAGCATAGCTGATCCTCCGTGCATC GCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTGGGCTACAC TAGTTAATCTCCGTCTGGGGTTAAATAGAAGAGCTTAATCAGA CTAGCTGAATGGAAGCCTGTTACCGGGCCGATGTTTATGCGAA ATGCTAATACGGTGACTACGCTCGTAGATATTT Listeria monocytogenes (NCTC 11994) tmRNA, internal partial SEQ ID NO: 58 CAAAGCCAAUAAUAACUGGCAAAGAAAAACAAAACCUAGCU UUCGCUGCCUAAUAAGCAGUAGCAUAGCUGAUCCUCCGUGC AUCGCCCAUGUGCUACGGUAAGGGUCUCACUCUAAGUGGGC UACACUAGUUAAUCUCCGUCUGGGGUUAAAUAGAAGAGCUU AAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGGCCGAUGU UUAUGCGAAAUGCUAAUACGGUGACUACGCUCGUAGAUAUUU Listeria murrayi ssrA, internal partial SEQ ID NO: 59 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTTAAATAG AAGAGCTTAATGAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTCAAGTGCCGATATTTCTGG Listeria murrayi tmRNA, internal partial SEQ ID NO: 60 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGG UUAAAUAGAAGAGCUUAAUGAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUCAAGUGCCGAUAUUUCUGG Listeria welshimeri ssrA, internal partial SEQ ID NO: 61 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTGGCTAATCTCCGTCTGAGGTTAGTTGG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria welshimeri tmRNA, internal partial SEQ ID NO: 62 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUGGCUAAUCUCCGUCUGAGG UUAGUUGGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Marinobacter hydrocarbonoclasticus ssrA, internal partial SEQ ID NO: 63 GCCGGTGACGAACCCTTGGGTGCATGCCGAGATGGCAGCGAA TCTCGTAAATCCAAAGCTGCAACGTAATAGTCGCAAACGACG AAAACTACGCACTGGCGGCGTAAGCCGTTCCAGTCGTCCTGG CTGAGGCGCCTATAACTCAGTAGCAACATCCCAGGACGTCAT CGCTTATAGGCTGCTCCGTTCACCAGAGCTCACTGGTGTTCGG CTAAGATTAAAGAGCTCGCCTCTTGCACCCTGACCTTCGGGTC GCTTGAGGTTAAATCAATAGAAGGACACTAAGCATGTAGACC TCAAGGCCTAGTGCTGGCGGACGCGG Marinobacter hydrocarbonoclasticus tmRNA, internal partial SEQ ID NO: 64 GCCGGUGACGAACCCUUGGGUGCAUGCCGAGAUGGCAGCGA AUCUCGUAAAUCCAAAGCUGCAACGUAAUAGUCGCAAACGA CGAAAACUACGCACUGGCGGCGUAAGCCGUUCCAGUCGUCC UGGCUGAGGCGCCUAUAACUCAGUAGCAACAUCCCAGGACG UCAUCGCUUAUAGGCUGCUCCGUUCACCAGAGCUCACUGGU GUUCGGCUAAGAUUAAAGAGCUCGCCUCUUGCACCCUGACC UUCGGGUCGCUUGAGGUUAAAUCAAUAGAAGGACACUAAGC AUGUAGACCUCAAGGCCUAGUGCUGGCGGACGCGG Mycobacterium avium ssrA, internal partial SEQ ID NO: 65 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACT GACCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCA CATCAGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTC CGTCAGCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGC TAGAGGGATCCACCGATGAGTTCGGTCGCGGGACTCATCGGG ACACCAACAGCGACTGGGATCGTCATCCTGGCTTGTTCGCGTG ACCAGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGAACCCGGGTTCGATTCCCAA Mycobacterium avium tmRNA, internal partial SEQ ID NO: 66
UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAC UGACCACCGUAAGCGUCGUUGCAAAUAGAUAAGCGCCGAUU CACAUCAGCGCGACUUACCUCUCGCUGCCUAAGCGACAGCU AGUCCGUCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCG UCAGCUAGAGGGAUCCACCGAUGAGUUCGGUCGCGGGACUC AUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUUG UUCGCGUGACCAGGAGAUCCGAGUAGAGGCAUAGCGAACUG CGCACGGAGAAGCCUUGAGGGAAUGCCGUAGAACCCGGGUU CGAUUCCCAA Mycobacterium bovis ssrA, internal partial SEQ ID NO: 67 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA GACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATTCA CATCAGCGCGACTACGTCTCGCTGCCTAAGCGACGGCTAGTCT GTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATCAGCT AGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTCGGGA CAACCACAGCGACTGGGATCGTCATCTCGGCTAGTTCGCGTGA CCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGG Mycobacterium bovis tmRNA, internal partial SEQ ID NO: 68 UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG AGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUU CACAUCAGCGCGACUACGUCUCGCUGCCUAAGCGACGGCUA GUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAU CAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCC UCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCUAGU UCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAACUGC GCACGGAGAAGCCUUGAGGGAAUGCCGUAGG Mycobacterium leprae ssrA SEQ ID NO: 69 GGGGCTGAAAGGTTTCGACTTCGCGCATCGAATCAAGGGAAG CGTGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCAG CAATATAAGCGCCGATTCATATCAGCGCGACTATGCTCTCGCT GCCTAAGCGATGGCTAGTCTGTCAGACCGGGAACGCCCTCGT CCCGGAGCCTGGCATCAGCTAGAGGGATCTACCGATGGGTTC GGTCGCGGGACTCGTCGGGACACCAACCGCGACTGGGATCGT CATCCTGGCTAGTTCGCGTGATCAGGAGATCCGAGTAGAGGC ATAGCGAACTACGCACGGAGAAGCCTTGAGGGAAATGCCGTA GGACCCGGGTTCGATTCCCGGCAGCTCCACCA Mycobacterium leprae tmRNA SEQ ID NO: 70 GGGGCUGAAAGGUUUCGACUUCGCGCAUCGAAUCAAGGGAA GCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGC AGCAAUAUAAGCGCCGAUUCAUAUCAGCGCGACUAUGCUCU CGCUGCCUAAGCGAUGGCUAGUCUGUCAGACCGGGAACGCC CUCGUCCCGGAGCCUGGCAUCAGCUAGAGGGAUCUACCGAU GGGUUCGGUCGCGGGACUCGUCGGGACACCAACCGCGACUG GGAUCGUCAUCCUGGCUAGUUCGCGUGAUCAGGAGAUCCGA GUAGAGGCAUAGCGAACUACGCACGGAGAAGCCUUGAGGGA AAUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCA Mycobacterium paratuberculosis ssrA, internal partial SEQ ID NO: 71 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACT GACCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCA CATCAGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTC CGTCAGCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGC TAGAGGGATCCACCGATGAGTTCGGTCGCGGGACTCATCGGG ACACCAACAGCGACTGGGATCGTCATCCTGGCTTGTTCGCGTG ACCAGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGAACCCGGGTTCGATTCCCAA Mycobacterium paratuberculosis tmRNA, internal partial SEQ ID NO: 72 UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAC UGACCACCGUAAGCGUCGUUGCAAAUAGAUAAGCGCCGAUU CACAUCAGCGCGACUUACCUCUCGCUGCCUAAGCGACAGCU AGUCCGUCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCG UCAGCUAGAGGGAUCCACCGAUGAGUUCGGUCGCGGGACUC AUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUUG UUCGCGUGACCAGGAGAUCCGAGUAGAGGCAUAGCGAACUG CGCACGGAGAAGCCUUGAGGGAAUGCCGUAGAACCCGGGUU CGAUUCCCAA Mycobacterium tuberculosis ssrA SEQ ID NO: 73 GGGGCTGAACGGTTTCGACTTCGCGCATCGAATCAAGGGAAG CGTGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCGA CCAAATAAGCGCCGATTCACATCAGCGCGACTACGCTCTCGCT GCCTAAGCGACGGCTAGTCTGTCAGACCGGGAACGCCCTCGG CCCGGACCCTGGCATCAGCTAGAGGGATCCACCGATGAGTCC GGTCGCGGGACTCCTCGGGACAACCACAGCGACTGGGATCGT CATCTCGGCTAGTTCGCGTGACCGGGAGATCCGAGCAGAGGC ATAGCGAACTGCGCACGGAGAAGCCTTGAGGGAATGCCGTAG GACCCGGGTTCGATTCCCGGCAGCTCCACCA Mycobacterium tuberculosis tmRNA SEQ ID NO: 74 GGGGCUGAACGGUUUCGACUUCGCGCAUCGAAUCAAGGGAA GCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGC GACCAAAUAAGCGCCGAUUCACAUCAGCGCGACUACGCUCU CGCUGCCUAAGCGACGGCUAGUCUGUCAGACCGGGAACGCC CUCGGCCCGGACCCUGGCAUCAGCUAGAGGGAUCCACCGAU GAGUCCGGUCGCGGGACUCCUCGGGACAACCACAGCGACUG GGAUCGUCAUCUCGGCUAGUUCGCGUGACCGGGAGAUCCGA GCAGAGGCAUAGCGAACUGCGCACGGAGAAGCCUUGAGGGA AUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCA Mycoplasma capricolum ssrA SEQ ID NO: 75 GGGGATGTCATGGATTTGACAGGATATCTTTAGTACATATAAG CAGTAGTGTTGTAGACTATAAATACTACTAGGTTTAAAAAAAC GCAAATAAAAACGAAGAAACTTTTGAAATGCCAGCATTTATG ATGAATAATGCATCAGCTGGAGCAAACTTTATGTTTGCTTAAT AACTACTAGTTTAGTTATAGTATTTCACGAATTATAGATATTTT AAGCTTTATTTATAACCGTATTACCCAAGCTTAATAGAATATA TGATTGCAATAAATATATTTGAAATCTAATTGCAAATGATATT TAACCTTTAGTTAATTTTAGTTAAATATTTTAATTAGAAAATTA ACTAAACTGTAGAAAGTATGTATTAATATATCTTGGACGCGAG TTCGATTCTCGCCATCTCCACCA Mycoplasma capricolum tmRNA SEQ ID NO: 76 GGGGAUGUCAUGGAUUUGACAGGAUAUCUUUAGUACAUAU AAGCAGUAGUGUUGUAGACUAUAAAUACUACUAGGUUUAA AAAAACGCAAAUAAAAACGAAGAAACUUUUGAAAUGCCAGC AUUUAUGAUGAAUAAUGCAUCAGCUGGAGCAAACUUUAUGU UUGCUUAAUAACUACUAGUUUAGUUAUAGUAUUUCACGAAU UAUAGAUAUUUUAAGCUUUAUUUAUAACCGUAUUACCCAAG CUUAAUAGAAUAUAUGAUUGCAAUAAAUAUAUUUGAAAUC UAAUUGCAAAUGAUAUUUAACCUUUAGUUAAUUUUAGUUA AAUAUUUUAAUUAGAAAAUUAACUAAACUGUAGAAAGUAU GUAUUAAUAUAUCUUGGACGCGAGUUCGAUUCUCGCCAUCU CCACCA Mycoplasma genitalium (ATTC 33530, #1) ssrA SEQ ID NO: 77 GGGGATGTTTTGGGTTTGACATAATGCTGATAGACAAACAGT AGCATTGGGGTATGCCCCTTACAGCGCTAGGTTCAATAACCGA CAAAGAAAATAACGAAGTGTTGGTAGAACCAAATTTGATCAT TAACCAACAAGCAAGTGTTAACTTTGCTTTTGCATAAGTAGAT ACTAAAGCTACAGCTGGTGAATAGTCATAGTTTGCTAGCTGTC ATAGTTTATGACTCGAGGTTAAATCGTTCAATTTAACCTTTAA AAATAGAACTTGTTGTTTCCATGATTGTTTTGTGATCAATTGG AAACAAGACAAAAATCCACAAAACTAAAATGTAGAAGCTGTT TGTTGTGTCCTTTATGGAAACGGGTTCGATTCCCGTCATCTCC ACCA Mycoplasma genitalium (ATTC 33530, #1) tmRNA SEQ ID NO: 78 GGGGAUGUUUUGGGUUUGACAUAAUGCUGAUAGACAAACA GUAGCAUUGGGGUAUGCCCCUUACAGCGCUAGGUUCAAUAA CCGACAAAGAAAAUAACGAAGUGUUGGUAGAACCAAAUUUG AUCAUUAACCAACAAGCAAGUGUUAACUUUGCUUUUGCAUA
AGUAGAUACUAAAGCUACAGCUGGUGAAUAGUCAUAGUUUG CUAGCUGUCAUAGUUUAUGACUCGAGGUUAAAUCGUUCAAU UUAACCUUUAAAAAUAGAACUUGUUGUUUCCAUGAUUGUUU UGUGAUCAAUUGGAAACAAGACAAAAAUCCACAAAACUAAA AUGUAGAAGCUGUUUGUUGUGUCCUUUAUGGAAACGGGUUC GAUUCCCGUCAUCUCCACCA Mycoplasma genitalium (ATTC 33530, #2) tmRNA, internal partial SEQ ID NO: 79 ACATAATGCTGATAGACAAACAGTAGCATTGGGGTATGCCCC TTACAGCGCTAGGTTCAATAACCGACAAAGAAAATAACGAAG TGTTGGTAGATCCAAATTTGATCATTAACCAACAAGCAAGTGT TAACTTTGCTTTTGCATAAGTAGATACTAAAGCTACAGCTGGT GAATAGTCATAGTTTGCTAGCTGTCATAGTTTATGACTCGAGG TTAAATCGTTCAATTTAACCTTTAAAAATAGAACTTGTTGTTTC CATGATTGTTTTGTGATCAATTGGAAACAAGACAAAAATCCAC AAAACTAAAATGTAGAAGCTGTTTGTTGTGTCCTTTATGGAAA CGGGTTC Mycoplasma genitalium (ATTC 33530, #2) tmRNA, internal partial SEQ ID NO: 80 ACAUAAUGCUGAUAGACAAACAGUAGCAUUGGGGUAUGCCC CUUACAGCGCUAGGUUCAAUAACCGACAAAGAAAAUAACGA AGUGUUGGUAGAUCCAAAUUUGAUCAUUAACCAACAAGCAA GUGUUAACUUUGCUUUUGCAUAAGUAGAUACUAAAGCUACA GCUGGUGAAUAGUCAUAGUUUGCUAGCUGUCAUAGUUUAUG ACUCGAGGUUAAAUCGUUCAAUUUAACCUUUAAAAAUAGAA CUUGUUGUUUCCAUGAUUGUUUUGUGAUCAAUUGGAAACAA GACAAAAAUCCACAAAACUAAAAUGUAGAAGCUGUUUGUUG UGUCCUUUAUGGAAACGGGUUC Mycoplasma pneumophila ssrA SEQ ID NO: 81 GGGGATGTAGAGGTTTTGACATAATGTTGAAAGGAAAACAGT TGCAGTGGGGTATGCCCCTTACAGCTCTAGGTATAATAACCGA CAAAAATAACGACGAAGTTTTGGTAGATCCAATGTTGATCGCT AACCAACAAGCAAGTATCAACTACGCTTTCGCTTAGAACATA CTAAAGCTACACGAATTGAATCGCCATAGTTTGGTTCGTGTCA CAGTTTATGGCTCGGGGTTAACTGGTTCAACTTAATCCTTAAA TTATGAACTTATCGTTTACTTGTTTGTCTTATGATCTAAAGTAA GCGAGACATTAAAACATAAGACTAAACTGTAGAAGCTGTTTT ACCAATCCTTTATGGAAACGGGTTCGATTCCCGTCATCTCCAC CA Mycoplasma pneumophila tmRNA SEQ ID NO: 82 GGGGAUGUAGAGGUUUUGACAUAAUGUUGAAAGGAAAACA GUUGCAGUGGGGUAUGCCCCUUACAGCUCUAGGUAUAAUAA CCGACAAAAAUAACGACGAAGUUUUGGUAGAUCCAAUGUUG AUCGCUAACCAACAAGCAAGUAUCAACUACGCUUUCGCUUA GAACAUACUAAAGCUACACGAAUUGAAUCGCCAUAGUUUGG UUCGUGUCACAGUUUAUGGCUCGGGGUUAACUGGUUCAACU UAAUCCUUAAAUUAUGAACUUAUCGUUUACUUGUUUGUCUU AUGAUCUAAAGUAAGCGAGACAUUAAAACAUAAGACUAAAC UGUAGAAGCUGUUUUACCAAUCCUUUAUGGAAACGGGUUCG AUUCCCGUCAUCUCCACCA Neisseria gonorrhoeae (ATCC 19424) ssrA, internal partial SEQ ID NO: 83 GGGGGTTGCGAAGCAGATGCGGGCATACCGGGGTCTCAGATT CCCGTAAAACACTGAATTCAAATAGTCGCAAACGACGAAACT TACGCTTTAGCCGCTTAAGGCTAGCCGTTGCAGCAGTCGGTCA ATGGGCTGTGTGGCGAAAGCCACCGCAACGTCATCTTACATTG ACTGGTTTCCAGCCGGGTTACTTGGCAGGAAATAAGACTTAA GGTAACTGGTTTCCAAAAGGCCTGTTGGTCGGCATGATGGAA ATAAGATTTTCAAATAGACACAACTAAGTATGTAGAACGCTTT GTAGAGGACTTTCGGACGGG Neisseria gonorrhoeae (ATCC 19424) tmRNA, internal partial SEQ ID NO: 84 GGGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGUCUCAGAU UCCCGUAAAACACUGAAUUCAAAUAGUCGCAAACGACGAAA CUUACGCUUUAGCCGCUUAAGGCUAGCCGUUGCAGCAGUCG GUCAAUGGGCUGUGUGGCGAAAGCCACCGCAACGUCAUCUU ACAUUGACUGGUUUCCAGCCGGGUUACUUGGCAGGAAAUAA GACUUAAGGUAACUGGUUUCCAAAAGGCCUGUUGGUCGGCA UGAUGGAAAUAAGAUUUUCAAAUAGACACAACUAAGUAUG UAGAACGCUUUGUAGAGGACUUUCGGACGGGG Neisseria gonorrhoeae (FA 1090) ssrA SEQ ID NO: 85 GGGGGCGACCTTGGTTTCGACGGGGGTTGCGAAGCAGATGCG GGCATACCGGGGTCTCAGATTCCCGTAAAACACTGAATTCAA ATAGTCGCAAACGACGAAACTTACGCTTTAGCCGCTTAAGGCT AGCCGTTGCAGCAGTCGGTCAATGGGCTGTGTGGTGAAAGCC ACCGCAACGTCATCTTACATTGACTGGTTTCCAGCCGGGTTAC TTGGCAGGAAATAAGACTTAAGGTAACTGGTTTCCAAAAGGC CTGTTGGTCGGCATGATGGAAATAAGATTTTCAAATAGACAC AACTAAGTATGTAGAACGCTTTGTAGAGGACTTTCGGACGGG GGTTCGATTCCCCCCGCCTCCACCA Neisseria gonorrhoeae (FA 1090) tmRNA SEQ ID NO: 86 GGGGGCGACCUUGGUUUCGACGGGGGUUGCGAAGCAGAUGC GGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUC AAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAA GGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGUGA AAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCAGCC GGGUUACUUGGCAGGAAAUAAGACUUAAGGUAACUGGUUUC CAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUCA AAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGACU UUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA Neisseria meningitidis ssrA SEQ ID NO: 87 GGGGGCGACCTTGGTTTCGACGGGGGTTGCGAAGCAGATGCG GGCATACCGGGGTCTCAGATTCCCGTAAAACACTGAATTCAA ATAGTCGCAAACGACGAAACTTACGCTTTAGCCGCTTAAGGCT AGCCGTTGCAGCAGTCGGTCAATGGGCTGTGTGGCGAAAGCC ACCGCAACGTCATCTTACATTGACTGGTTTCCTGCCGGGTTAT TTGGCAGGAAATGAGATTTAAGGTAACTGGTTTCCAAAAGGC CTGTTGGTCGGCATGATGGAAATAAGATTTTCAAATAGACAC AACTAAGTATGTAGAACGCTTTGTAGAGGACTTTCGGACGGG GGTTCGATTCCCCCCGCCTCCACCA Neisseria meningitidis tmRNA SEQ ID NO: 88 GGGGGCGACCUUGGUUUCGACGGGGGUUGCGAAGCAGAUGC GGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUC AAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAA GGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGCGA AAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCUGCC GGGUUAUUUGGCAGGAAAUGAGAUUUAAGGUAACUGGUUU CCAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUC AAAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGAC UUUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA Nostoc muscorum PCC7120 ssrA SEQ ID NO: 89 GGGTCCGTCGGTTTCGACAGGTTGGCGAACGCTACTCTGTGAT TCAGGTCGAGAGTGAGTCTCCTCTGCAAATCAAGGCTCAAAA CAAAAGTAAATGCGAATAACATCGTTAAATTTGCTCGTAAGG ACGCTCTAGTAGCTGCCTAAATAGCCTCTTTCAGGTTCGAGCG TCTTCGGTTTGACTCCGTTAAGGACTGAAGACCAACCCCCAAC GGATGCTCTAGCAATGTTCTCTGGTTGGCTTGCTAGCTAAGAT TTAATCAGAGCATCCTACGTTCGGGATAATGAACGATTCCCGC CTTGAGGGTCAGAAAGGCTAAACCTGTGAATGAGCGGGGGGT CAATACCCAATTTGGACAGCAGTTCGACTCTGCTCGATCCACCA Nostoc muscorum PCC7120 tmRNA SEQ ID NO: 90 GGGUCCGUCGGUUUCGACAGGUUGGCGAACGCUACUCUGUG AUUCAGGUCGAGAGUGAGUCUCCUCUGCAAAUCAAGGCUCA AAACAAAAGUAAAUGCGAAUAACAUCGUUAAAUUUGCUCGU AAGGACGCUCUAGUAGCUGCCUAAAUAGCCUCUUUCAGGUU CGAGCGUCUUCGGUUUGACUCCGUUAAGGACUGAAGACCAA CCCCCAACGGAUGCUCUAGCAAUGUUCUCUGGUUGGCUUGC
UAGCUAAGAUUUAAUCAGAGCAUCCUACGUUCGGGAUAAUG AACGAUUCCCGCCUUGAGGGUCAGAAAGGCUAAACCUGUGA AUGAGCGGGGGGUCAAUACCCAAUUUGGACAGCAGUUCGAC UCUGCUCGAUCCACCA Odontella sinensis (diatom) chloroplast ssrA SEQ ID NO: 91 GGGGCTGACTTGGTTTCGACATTTAAAAATTGTTACAGTATGA TGCAGGTCGAAGTTTCTAATCTTCGTAAAAAAAGAGAAATTTA TAATAAATGCTAATAATTTAATTTCTTCTGTGTTTAAAAGTTTA TCAACTAAGCAAAATAGTTTAAATTTAAGTTTTGCTGTTTAAG TTTTATGCACATTTAATGATCTAGTAAATAACTTTGTTCGCTAT AATTTATATTTATAACTAGACTTTTGTCTTTTTTATAGTTTAGA ATAACTTTATCATTTCAAACCTCGTTCCATCTAGTTGAACTAA ACCTGTGAACGAATACTATAATAAAATTTTTAGATGGACGTGG GTTCGACTCCCATCAGCTCCACCA Odontella sinensis (diatom) chloroplast tmRNA SEQ ID NO: 92 GGGGCUGACUUGGUUUCGACAUUUAAAAAUUGUUACAGUAU GAUGCAGGUCGAAGUUUCUAAUCUUCGUAAAAAAAGAGAAA UUUAUAAUAAAUGCUAAUAAUUUAAUUUCUUCUGUGUUUA AAAGUUUAUCAACUAAGCAAAAUAGUUUAAAUUUAAGUUU UGCUGUUUAAGUUUUAUGCACAUUUAAUGAUCUAGUAAAU AACUUUGUUCGCUAUAAUUUAUAUUUAUAACUAGACUUUUG UCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUUCAAACCUC GUUCCAUCUAGUUGAACUAAACCUGUGAACGAAUACUAUAA UAAAAUUUUUAGAUGGACGUGGGUUCGACUCCCAUCAGCUC CACCA Porphyra purpureum (red alga) chloroplast ssrA SEQ ID NO: 93 GGGGCTGCAAGGTTTCTACATTGTGAAAAAACAAATATATGA AAGTAAAACGAGCTCATTATTAGAGCTTTTAGTTAAATAAATG CAGAAAATAATATTATTGCTTTTTCTCGAAAATTAGCTGTTGC ATAAATAGTCTCAATTTTTGTAATTCGAAGTGATAGACTCTTA TACACTACGAATATTCTGTTAGAGTTGCTCTTAATAAAAGAAA AGTAAAAAAATACAAATTCTTATGTTTTTTACCTGAATTGATT CAATTTAAGGTTAGTATTTTTTGATTTTTACAATGGACGTGGG TTCAAGTCCCACCAGCTCCACCA Porphyra purpureum (red alga) chloroplast tmRNA SEQ ID NO: 94 GGGGCUGCAAGGUUUCUACAUUGUGAAAAAACAAAUAUAUG AAAGUAAAACGAGCUCAUUAUUAGAGCUUUUAGUUAAAUA AAUGCAGAAAAUAAUAUUAUUGCUUUUUCUCGAAAAUUAGC UGUUGCAUAAAUAGUCUCAAUUUUUGUAAUUCGAAGUGAU AGACUCUUAUACACUACGAAUAUUCUGUUAGAGUUGCUCUU AAUAAAAGAAAAGUAAAAAAAUACAAAUUCUUAUGUUUUU UACCUGAAUUGAUUCAAUUUAAGGUUAGUAUUUUUUGAUU UUUACAAUGGACGUGGGUUCAAGUCCCACCAGCUCCACCA Porphyromonas gingivalis ssrA SEQ ID NO: 95 GGGGCTGACCGGCTTTGACAGCGTGATGAAGCGGTATGTAAG CATGTAGTGCGTGGGTGGCTTGCACTATAATCTCAGACATCAA AAGTTTAATTGGCGAAAATAACTACGCTCTCGCTGCGTAATCG AAGAATAGTAGATTAGACGCTTCATCGCCGCCAAAGTGGCAG CGACGAGACATCGCCCGAGCAGCTTTTTCCCGAAGTAGCTCG ATGGTGCGGTGCTGACAAATCGGGAACCGCTACAGGATGCTT CCTGCCTGTGGTCAGATCGAACGGAAGATAAGGATCGTGCAT TGGGTCGTTTCAGCCTCCGCTCGCTCACGAAAATTCCAACTGA AACTAAACATGTAGAAAGCATATTGATTCCATGTTTGGACGA GGGTTCAATTCCCTCCAGCTCCACCA Porphyromonas gingivalis tmRNA SEQ ID NO: 96 GGGGCUGACCGGCUUUGACAGCGUGAUGAAGCGGUAUGUAA GCAUGUAGUGCGUGGGUGGCUUGCACUAUAAUCUCAGACAU CAAAAGUUUAAUUGGCGAAAAUAACUACGCUCUCGCUGCGU AAUCGAAGAAUAGUAGAUUAGACGCUUCAUCGCCGCCAAAG UGGCAGCGACGAGACAUCGCCCGAGCAGCUUUUUCCCGAAG UAGCUCGAUGGUGCGGUGCUGACAAAUCGGGAACCGCUACA GGAUGCUUCCUGCCUGUGGUCAGAUCGAACGGAAGAUAAGG AUCGUGCAUUGGGUCGUUUCAGCCUCCGCUCGCUCACGAAA AUUCCAACUGAAACUAAACAUGUAGAAAGCAUAUUGAUUCC AUGUUUGGACGAGGGUUCAAUUCCCUCCAGCUCCACCA Proteus rettgeri ssrA (NCTC 10975), internal partial SEQ ID NO: 97 GGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAAC TACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTCCC TAGCCTCCGCTCTTGGACGGGGATCAAGAGAGGTCAAACCCA AAAGAGATCGCGTGGATGCCTTGCCTGGGGTTGAAGCGTTAA ACTTAATCAGGATAGTTTGTTGGTGGCGTGTCTGTCCGCAGCT GGCAAATGAATTCAAAGACTAGACTAAGCATGTAGTACCGAG GATGTAGAAATTTC Proteus rettgeri tmRNA (NCTC 10975), internal partial SEQ ID NO: 98 GGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGG CCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAA ACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUC UCCCUAGCCUCCGCUCUUGGACGGGGAUCAAGAGAGGUCAA ACCCAAAAGAGAUCGCGUGGAUGCCUUGCCUGGGGUUGAAG CGUUAAACUUAAUCAGGAUAGUUUGUUGGUGGCGUGUCUGU CCGCAGCUGGCAAAUGAAUUCAAAGACUAGACUAAGCAUGU AGUACCGAGGAUGUAGAAAUUUC Pseudoalteromonas haloplanktoni ssrA, internal partial SEQ ID NO: 99 GGAATTCAAGAAGCCCGAGGTGCATGTCGAGGTGCGGTTTGC CTCGTAAAAAAGCCGCAATTTAAAGTAATCGCAAACGACGAT AACTACTCTCTAGCAGCTTAGGCTGGCTAGCGCTCCTTCCATG TATTCTTGTGGACTGGATTTTGGAGTGTCACCCTAACACCTGA TCGCGACGGAAACCCTGGCCGGGGTTGAAGCGTTAAAACTAA GCGGCCTCGCCTTTATCTACCGTGTTTGTCCGGGATTTAAAGG TTAATTAAATGACAATACTAAACATGTAGTACCGACGGTCGA GGCTTTTCGGACGGGG Pseudoalteromonas haloplanktoni tmRNA, internal partial SEQ ID NO: 100 GGAAUUCAAGAAGCCCGAGGUGCAUGUCGAGGUGCGGUUUG CCUCGUAAAAAAGCCGCAAUUUAAAGUAAUCGCAAACGACG AUAACUACUCUCUAGCAGCUUAGGCUGGCUAGCGCUCCUUC CAUGUAUUCUUGUGGACUGGAUUUUGGAGUGUCACCCUAAC ACCUGAUCGCGACGGAAACCCUGGCCGGGGUUGAAGCGUUA AAACUAAGCGGCCUCGCCUUUAUCUACCGUGUUUGUCCGGG AUUUAAAGGUUAAUUAAAUGACAAUACUAAACAUGUAGUA CCGACGGUCGAGGCUUUUCGGACGGGG Pseudomonas aeruginosa ssrA SEQ ID NO: 101 GGGGCCGATTAGGATTCGACGCCGGTAACAAAAGTTGAGGGG CATGCCGAGTTGGTAGCAGAACTCGTAAATTCGCTGCTGCAA ACTTATAGTTGCCAACGACGACAACTACGCTCTAGCTGCTTAA TGCGGCTAGCAGTCGCTAGGGGATGCCTGTAAACCCGAAACG ACTGTCAGATAGAACAGGATCGCCGCCAAGTTCGCTGTAGAC GTAACGGCTAAAACTCATACAGCTCGCTCCAAGCACCCTGCC ACTCGGGCGGCGCGGAGTTAACTCAGTAGAGCTGGCTAAGCA TGTAAAACCGATAGCGGAAAGCTGGCGGACGGGGGTTCAAAT CCCCCCGGTTCCACCA Pseudomonas aeruginosa tmRNA SEQ ID NO: 102 GGGGCCGAUUAGGAUUCGACGCCGGUAACAAAAGUUGAGGG GCAUGCCGAGUUGGUAGCAGAACUCGUAAAUUCGCUGCUGC AAACUUAUAGUUGCCAACGACGACAACUACGCUCUAGCUGC UUAAUGCGGCUAGCAGUCGCUAGGGGAUGCCUGUAAACCCG AAACGACUGUCAGAUAGAACAGGAUCGCCGCCAAGUUCGCU GUAGACGUAACGGCUAAAACUCAUACAGCUCGCUCCAAGCA CCCUGCCACUCGGGCGGCGCGGAGUUAACUCAGUAGAGCUG GCUAAGCAUGUAAAACCGAUAGCGGAAAGCUGGCGGACGGG GGUUCAAAUCCCCCCGGUUCCACCA Salmonella typhimurium ssrA SEQ ID NO: 103 GGGGCTGATTCTGGATTCGACGGGATTTGCGAAACCCAAGGT GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAA
ATAGTCGCAAACGACGAAACCTACGCTTTAGCAGCTTAATAA CCTGCTTAGAGCCCTCTCTCCCTAGCCTCCGCTCTTAGGACGG GGATCAAGAGAGGTCAAACCCAAAAGAGATCGCGCGGATGCC CTGCCTGGGGTTGAAGCGTTAAAACGAATCAGGCTAGTCTGG TAGTGGCGTGTCCGTCCGCAGGTGCCAGGCGAATGTAAAGAC TGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGC GGGTTCAACTCCCGCCAGCTCCACCA Salmonella typhimurium tmRNA SEQ ID NO: 104 GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGG UGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAA AAAUAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUUAA UAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAG GACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCG GAUGCCCUGCCUGGGGUUGAAGCGUUAAAACGAAUCAGGCU AGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGCGAAU GUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAU UUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA Shewanella putrefaciens ssrA SEQ ID NO: 105 GGGGGCGATTCTGGATTCGACAGGATTCACGAAACCCTGGGA GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAGTT ATAGTTGCAAACGACGATAACTACGCTCTAGCCGCTTAATGCC GCTAGCCATCTACCACACGCTTTGCACATGGGCAGTGGATTTG ATGGTCATCTCACATCGTGCTAGCGAGGGAACCCTGTCTGGGG GTGAACCGCGAAACAGTACCGGACTCACCGTGTGGGATCCTG TCTTTCGGAGTTCAAACGGTTAAACAATAGAAAGACTAAGCA TGTAGCGCCTTGGATGTAGGTTTTCTGGACGCGGGTTCAAGTC CCGCCGCCTCCACCA Shewanella putrefaciens tmRNA SEQ ID NO: 106 GGGGGCGAUUCUGGAUUCGACAGGAUUCACGAAACCCUGGG AGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAG UUAUAGUUGCAAACGACGAUAACUACGCUCUAGCCGCUUAA UGCCGCUAGCCAUCUACCACACGCUUUGCACAUGGGCAGUG GAUUUGAUGGUCAUCUCACAUCGUGCUAGCGAGGGAACCCU GUCUGGGGGUGAACCGCGAAACAGUACCGGACUCACCGUGU GGGAUCCUGUCUUUCGGAGUUCAAACGGUUAAACAAUAGAA AGACUAAGCAUGUAGCGCCUUGGAUGUAGGUUUUCUGGACG CGGGUUCAAGUCCCGCCGCCUCCACCA Staphylococcus aureus ssrA SEQ ID NO: 107 GGGGACGTTCATGGATTCGACAGGGGTCCCCCGAGCTCATTA AGCGTGTCGGAGGGTTGTCTTCGTCATCAACACACACAGTTTA TAATAACTGGCAAATCAAACAATAATTTCGCAGTAGCTGCCTA ATCGCACTCTGCATCGCCTAACAGCATTTCCTATGTGCTGTTA ACGCGATTCAACCTTAATAGGATATGCTAAACACTGCCGTTTG AAGTCTGTTTAGAAGAAACTTAATCAAACTAGCATCATGTTGG TTGTTTATCACTTTTCATGATGCGAAACCTATCGATAAACTAC ACACGTAGAAAGATGTGTATCAGGACCTTTGGACGCGGGTTC AAATCCCGCCGTCTCCACCA Staphylococcus aureus tmRNA SEQ ID NO: 108 GGGGACGUUCAUGGAUUCGACAGGGGUCCCCCGAGCUCAUU AAGCGUGUCGGAGGGUUGUCUUCGUCAUCAACACACACAGU UUAUAAUAACUGGCAAAUCAAACAAUAAUUUCGCAGUAGCU GCCUAAUCGCACUCUGCAUCGCCUAACAGCAUUUCCUAUGU GCUGUUAACGCGAUUCAACCUUAAUAGGAUAUGCUAAACAC UGCCGUUUGAAGUCUGUUUAGAAGAAACUUAAUCAAACUAG CAUCAUGUUGGUUGUUUAUCACUUUUCAUGAUGCGAAACCU AUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCU UUGGACGCGGGUUCAAAUCCCGCCGUCUCCACCA Streptococcus gordonii ssrA SEQ ID NO: 109 GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATTTTGC GACTCATCTAGCGGATGTAAAACGCCAGTTAAATATAACTGC AAAAAATAATACTTCTTACGCTTTAGCTGCCTAAAAACCAGCG GGCGTGACCCGATTCGGATTGCTTGTGTCTGATGACAGGTCTT ATTATTAGCAAGCTACGGTAGAATCTTGTCTAGTGATTTTACA AGAGATTGATAGACTCGCTTGATTTGGGCTTGAGTTATGTGTC AAAATCAAGTTAAAACAATACATAGCCTATGGTTGTAGACAA ATGTGTTGGCAGATGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus gordonii tmRNA SEQ ID NO: 110 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUU GCGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAAC UGCAAAAAAUAAUACUUCUUACGCUUUAGCUGCCUAAAAAC CAGCGGGCGUGACCCGAUUCGGAUUGCUUGUGUCUGAUGAC AGGUCUUAUUAUUAGCAAGCUACGGUAGAAUCUUGUCUAGU GAUUUUACAAGAGAUUGAUAGACUCGCUUGAUUUGGGCUUG AGUUAUGUGUCAAAAUCAAGUUAAAACAAUACAUAGCCUAU GGUUGUAGACAAAUGUGUUGGCAGAUGUUUGGACGUGGGU UCGACUCCCACCGGCUCCACCA Streptococcus mutans ssrA SEQ ID NO: 111 GGGGTCGTTACGGATTCGACAGGCATTATGAGACCTATTTTGC GACTCATCTAGCGGATGTAAAACGCCAGTTAAATATAACTGC AAAAAATACAAATTCTTACGCAGTAGCTGCCTAAAAACCAGC CTGTGTGATCAATAACAAATTGCTTGTGTTTGTTGATTGGTCTT ATTGTTAACAAGCTACGTTAGAACTGAGTCAGGCTGTTCTAAA AGAGTTCTACTGACTCGCATCGTTAGAGTTTGAGTTATGTATT GTAACGGTGTTAAATAAACACATAACCTATAGTTGTAGACAA ATGGGTTAGCAGATGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus mutans tmRNA SEQ ID NO: 112 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGACCUAUUUU GCGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAAC UGCAAAAAAUACAAAUUCUUACGCAGUAGCUGCCUAAAAAC CAGCCUGUGUGAUCAAUAACAAAUUGCUUGUGUUUGUUGAU UGGUCUUAUUGUUAACAAGCUACGUUAGAACUGAGUCAGGC UGUUCUAAAAGAGUUCUACUGACUCGCAUCGUUAGAGUUUG AGUUAUGUAUUGUAACGGUGUUAAAUAAACACAUAACCUAU AGUUGUAGACAAAUGGGUUAGCAGAUGUUUGGACGUGGGU UCGACUCCCACCGGCUCCACCA Streptococcus pneumoniae ssrA SEQ ID NO: 113 GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATTTTGC GACTCGTGTGGCGACGTAAACGCTCAGTTAAATATAACTGCA AAAAATAACACTTCTTACGCTCTAGCTGCCTAAAAACCAGCA GGCGTGACCCGATTTGGATTGCTCGTGTTCAATGACAGGTCTT ATTATTAGCGAGATACGATTAAGCCTTGTCTAGCGGTTTGATA AGAGATTGATAGACTCGCAGTTTCTAGACTTGAGTTATGTGTC GAGGGGCTGTTAAAATAATACATAACCTATGGTTGTAGACAA ATATGTTGGCAGGTGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus pneumoniae tmRNA SEQ ID NO: 114 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUU GCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACU GCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACC AGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACA GGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCG GUUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGA GUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUG GUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUU CGACUCCCACCGGCUCCACCA Streptococcus pyogenes ssrA SEQ ID NO: 115 GGGGTTGTTACGGATTCGACAGGCATTATGAGGCATGTTTTGC GTCCCATCGGCAGATGTAAATTGCCAGTTAAATATAACTGCAA AAAATACAAACTCTTACGCTTTAGCTGCCTAAAAACCAGCTAG CGTGACTTCTACAAGATTGCTTGTGTCCTGTTAGAAGTCTCAA AATAGCAAGCTACGGTTACGAAATTGTCTAGTTTCGTGACAAG AGATTGATAGACTCGCAAACTAATGGCTTGAGTTATGTGTCTT TAGTTTGTTAAATGAAGACATAACCTATGGACGTAGACAAAT
ATGTTGGCAGGTGTTTGGACGTGGGTTCGACTCCCACCAGCTC CACCA Streptococcus pyogenes tmRNA SEQ ID NO: 116 GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUU GCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACU GCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACC AGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGA AGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUU UCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGA GUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAU GGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGU UCGACUCCCACCAGCUCCACCA Synechococcus sp. PCC6301 ssrA SEQ ID NO: 117 GGGGCTGTAATGGTTTCGACGTGTTGGTGAATCCTTCACCGTG ATTCAGGCCGAGAGGGAGTCCACTCTCGTAAATCCAGGCTCA ACCAAAAGTAACTGCGAACAACATCGTTCCTTTCGCTCGTAAG GCTGCTCCTGTAGCTGCTTAAACGCCACAAACTTTCTGGCTCGAGCG TCTAGTCGTAGACTCCGTTAATACGCCTAGACTTAAACCCCCA ACGGATGCTCGAGTGGCGGCCTCAGGTCCGTCCTCTCGCTAAG CAAAAACCTGAGCATCCCGCCAACGGGGATAATCGTTGGCTC CCGCACAGTGGGTCAACCGTGCTAAGCCTGTGAACGAGCGGA AAGTTACTAGTCAATGCGGACAGCGGTTCGATTCCGCTCAGCT CCACCA Synechococcus sp. PCC6301 tmRNA SEQ ID NO: 118 GGGGCUGUAAUGGUUUCGACGUGUUGGUGAAUCCUUCACCG UGAUUCAGGCCGAGAGGGAGUCCACUCUCGUAAAUCCAGGC UCAACCAAAAGUAACUGCGAACAACAUCGUUCCUUUCGCUC GUAAGGCUGCUCCUGUAGCUGCUUAAACGCCACAAACUUUC UGGCUCGAGCGUCUAGUCGUAGACUCCGUUAAUACGCCUAG ACUUAAACCCCCAACGGAUGCUCGAGUGGCGGCCUCAGGUC CGUCCUCUCGCUAAGCAAAAACCUGAGCAUCCCGCCAACGG GGAUAAUCGUUGGCUCCCGCACAGUGGGUCAACCGUGCUAA GCCUGUGAACGAGCGGAAAGUUACUAGUCAAUGCGGACAGC GGUUCGAUUCCGCUCAGCUCCACCA Synechocystis sp. PCC6803 ssrA SEQ ID NO: 119 GGGGCCGCAATGGTTTCGACAGGTTGGCGAAAGCTTGCCCGT GATACAGGTCGAGAGTGAGTCTCCTCTCGCAAATCAAAGGCT CAAAAAAAAGTAACTGCGAATAACATCGTCAGCTTCAAACGG GTAGCCATAGCAGCCTAGTCTGTAAAAGCTACATTTTCTTGTC AAAGACCGTTTACTTCTTTTCTGACTCCGTTAAGGATTAGAGG TTAACCCCAACGGATGCTTTGTTTGGCTCTTCTCTAGTTAGCTA AACAATCAAGACTCAGACTAGAGCATCCCACCATCAGGGATA ATCGATGGTCCCCGTCCTAGGGCTAGAAGGACTAAACCTGTG AATGAGCGGAAAGTTAATACCCAGTTTGGACAGCAGTTCAAT TCTGCTCGGCTCCACCA Synechocystis sp. PCC6803 tmRNA SEQ ID NO: 120 GGGGCCGCAAUGGUUUCGACAGGUUGGCGAAAGCUUGCCCG UGAUACAGGUCGAGAGUGAGUCUCCUCUCGCAAAUCAAAGG CUCAAAAAAAAGUAACUGCGAAUAACAUCGUCAGCUUCAAA CGGGUAGCCAUAGCAGCCUAGUCUGUAAAAGCUACAUUUUC UUGUCAAAGACCGUUUACUUCUUUUCUGACUCCGUUAAGGA UUAGAGGUUAACCCCAACGGAUGCUUUGUUUGGCUCUUCUC UAGUUAGCUAAACAAUCAAGACUCAGACUAGAGCAUCCCAC CAUCAGGGAUAAUCGAUGGUCCCCGUCCUAGGGCUAGAAGG ACUAAACCUGUGAAUGAGCGGAAAGUUAAUACCCAGUUUGG ACAGCAGUUCAAUUCUGCUCGGCUCCACCA Thermotoga maritima ssrA SEQ ID NO: 121 GGGGGCGAACGGGTTCGACGGGGATGGAGTCCCCTGGGAAGC GAGCCGAGGTCCCCACCTCCTCGTAAAAAAGGTGGGACAAAG AATAAGTGCCAACGAACCTGTTGCTGTTGCCGCTTAATAGATA AGCGGCCGTCCTCTCCGAAGTTGGCTGGGCTTCGGAAGAGGG CGTGAGAGATCCAGCCTACCGATTCAGCTTCGCCTTCCGGCCT GAATCGGGAAAACTCAGGAAGGCTGTGGGAGAGGACACCCTG CCCGTGGGAGGTCCCTCCCGAGAGCGAAAACACGGGCTGCGC TCGGAGAAGCCCAGGGGCCTCCATCTTCGGACGGGGGTTCGA ATCCCCCCGCCTCCACCA Thermotoga maritima tmRNA SEQ ID NO: 122 GGGGGCGAACGGGUUCGACGGGGAUGGAGUCCCCUGGGAAG CGAGCCGAGGUCCCCACCUCCUCGUAAAAAAGGUGGGACAA AGAAUAAGUGCCAACGAACCUGUUGCUGUUGCCGCUUAAUA GAUAAGCGGCCGUCCUCUCCGAAGUUGGCUGGGCUUCGGAA GAGGGCGUGAGAGAUCCAGCCUACCGAUUCAGCUUCGCCUU CCGGCCUGAAUCGGGAAAACUCAGGAAGGCUGUGGGAGAGG ACACCCUGCCCGUGGGAGGUCCCUCCCGAGAGCGAAAACAC GGGCUGCGCUCGGAGAAGCCCAGGGGCCUCCAUCUUCGGAC GGGGGUUCGAAUCCCCCCGCCUCCACCA Thermus thermophilus ssrA SEQ ID NO: 123 GGGGGTGAAACGGTCTCGACGGGGGTCGCCGAGGGCGTGGCT GCGCGCCGAGGTGCGGGTGGCCTCGTAAAAACCCGCAACGGC ATAACTGCCAACACCAACTACGCTCTCGCGGCTTAATGACCGC GACCTCGCCCGGTAGCCCTGCCGGGGGCTCACCGGAAGCGGG GACACAAACCCGGCTAGCCCGGGGCCACGCCCTCTAACCCCG GGCGAAGCTTGAAGGGGGCTCGCTCCTGGCCGCCCGTCCGCG GGCCAAGCCAGGAGGACACGCGAAACGCGGACTACGCGCGT AGAGGCCCGCCGTAGAGACCTTCGGACGGGGGTTCGACTCCC CCCACCTCCACCA Thermus thermophilus tmRNA SEQ ID NO: 124 GGGGGUGAAACGGUCUCGACGGGGGUCGCCGAGGGCGUGGC UGCGCGCCGAGGUGCGGGUGGCCUCGUAAAAACCCGCAACG GCAUAACUGCCAACACCAACUACGCUCUCGCGGCUUAAUGA CCGCGACCUCGCCCGGUAGCCCUGCCGGGGGCUCACCGGAAG CGGGGACACAAACCCGGCUAGCCCGGGGCCACGCCCUCUAAC CCCGGGCGAAGCUUGAAGGGGGCUCGCUCCUGGCCGCCCGU CCGCGGGCCAAGCCAGGAGGACACGCGAAACGCGGACUACG CGCGUAGAGGCCCGCCGUAGAGACCUUCGGACGGGGGUUCG ACUCCCCCCACCUCCACCA Treponema pallidum ssrA SEQ ID NO: 125 GGGGATGACTAGGTTTCGACTAGGGATGTGGGGTGTTGCGCT GCAGGTGGAGTGTCGATCTCCTGATTCGGCGCCTTTATAACTG CCAATTCTGACAGTTTCGACTACGCGCTCGCCGCGTAATCGCG GGCCTGTGTTTGCGCTGCTCTGAGCGAACATATCGGCCCGACG CCAAACGGAGCTTGCTCTTACGTTGTGCACGGCGGACGTAGG GGGACTTTTGTCTGTGCTAAGACTCTGGCGCGTGCGGTGCAGG CCTAGCAGAGTCCGACAAACGCAGTACGCACCGCTAAACCTG TAGGCGCGCAGCACTCGCTCTTTAGGACGGGGGTTCGATTCCC CCCATCTCCACCA Treponema pallidum tmRNA SEQ ID NO: 126 GGGGAUGACUAGGUUUCGACUAGGGAUGUGGGGUGUUGCGC UGCAGGUGGAGUGUCGAUCUCCUGAUUCGGCGCCUUUAUAA CUGCCAAUUCUGACAGUUUCGACUACGCGCUCGCCGCGUAA UCGCGGGCCUGUGUUUGCGCUGCUCUGAGCGAACAUAUCGG CCCGACGCCAAACGGAGCUUGCUCUUACGUUGUGCACGGCG GACGUAGGGGGACUUUUGUCUGUGCUAAGACUCUGGCGCGU GCGGUGCAGGCCUAGCAGAGUCCGACAAACGCAGUACGCAC CGCUAAACCUGUAGGCGCGCAGCACUCGCUCUUUAGGACGG GGGUUCGAUUCCCCCCAUCUCCACCA Vibrio cholerae ssrA SEQ ID NO: 127 GGGGCTGATTCAGGATTCGACGGGAATTTTGCAGTCTGAGGT GCATGCCGAGGTGCGGTAGGCCTCGTTAACAAACCGCAAAAA AATAGTCGCAAACGACGAAAACTACGCACTAGCAGCTTAATA CCCTGCTCAGAGCCCTTCCTCCCTAGCTTCCGCTTGTAAGACG GGGAAATCAGGAAGGTCAAACCAAATCAAGCTGGCGTGGATT CCCCCACCTGAGGGATGAAGCGCGAGATCTAATTCAGGTTAG CCATTCGTTAGCGTGTCGGTTCGCAGGCGGTGGTGAAATTAAA GATCGACTAAGCATGTAGTACCAAAGATGAATGGTTTTCGGA CGGGGGTTCAACTCCCCCCAGCTCCACCA
Vibrio cholerae tmRNA SEQ ID NO: 128 GGGGCUGAUUCAGGAUUCGACGGGAAUUUUGCAGUCUGAGG UGCAUGCCGAGGUGCGGUAGGCCUCGUUAACAAACCGCAAA AAAAUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUA AUACCCUGCUCAGAGCCCUUCCUCCCUAGCUUCCGCUUGUA AGACGGGGAAAUCAGGAAGGUCAAACCAAAUCAAGCUGGCG UGGAUUCCCCCACCUGAGGGAUGAAGCGCGAGAUCUAAUUC AGGUUAGCCAUUCGUUAGCGUGUCGGUUCGCAGGCGGUGGU GAAAUUAAAGAUCGACUAAGCAUGUAGUACCAAAGAUGAAU GGUUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Yersinia pestis ssrA SEQ ID NO: 129 GGGGCTGATTCTGGATTCGACGGGATTCGCGAAACCCAAGGT GCATGCCGAGGTGCGGTGGCCTCGTAAAAAACCGCAAAAAAA ATAGTTGCAAACGACGAAAACTACGCACTAGCAGCTTAATAA CCTGCTTAGAGCCCTCTCTGCCTAGCCTCCGCTCTTAGGACGG GGATCAAGAGAGGTCAAACCTAAAAGAGCTCGTGTGGAAACC TTGCCTGGGGTGGAAGCATTAAAACTAATCAGGATAGTTTGTC AGTAGCGTGTCCATCCGCAGCTGGCCGGCGAATGTAATGATT GGACTAAGCATGTAGTGCCGACGGTGTAGTAATTTCGGACGG GGGTTCAAATCCCCCCAGCTCCACCA Yersinia pestis tmRNA SEQ ID NO: 130 GGGGCUGAUUCUGGAUUCGACGGGAUUCGCGAAACCCAAGG UGCAUGCCGAGGUGCGGUGGCCUCGUAAAAAACCGCAAAAA AAAUAGUUGCAAACGACGAAAACUACGCACUAGCAGCUUAA UAACCUGCUUAGAGCCCUCUCUGCCUAGCCUCCGCUCUUAG GACGGGGAUCAAGAGAGGUCAAACCUAAAAGAGCUCGUGUG GAAACCUUGCCUGGGGUGGAAGCAUUAAAACUAAUCAGGAU AGUUUGUCAGUAGCGUGUCCAUCCGCAGCUGGCCGGCGAAU GUAAUGAUUGGACUAAGCAUGUAGUGCCGACGGUGUAGUAA UUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA Campylobacter fetus ssrA, internal partial SEQ ID NO: 131 AGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGGCAAAGC GTAAAAAGCCCAAATAAAATTAAACGCAAACAACGTTAAATT CGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCTG AAATTTAAGTCATACTATCTAGCTTAATTTTCGGTCATCTTTGA TAGTGTAGCCTTGCGTTTGACAAGCGTTGAGGTGAAATAAAGT CTTAGCCTTGCTTTTGAGTTTTGGAAGATGAGCGAAGTAGGGT GAAGTAGTCATCTTTGCTAAGCATGTAGAGGTCTTTGTGGGAT TATTTTTGG Campylobacter fetus tmRNA, internal partial SEQ ID NO: 132 AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGGCAAAG CGUAAAAAGCCCAAAUAAAAUUAAACGCAAACAACGUUAAA UUCGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGAG CCUGAAAUUUAAGUCAUACUAUCUAGCUUAAUUUUCGGUCA UCUUUGAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGGUG AAAUAAAGUCUUAGCCUUGCUUUUGAGUUUUGGAAGAUGA GCGAAGUAGGGUGAAGUAGUCAUCUUUGCUAAGCAUGUAGA GGUCUUUGUGGGAUUAUUUUUGG Campylobacter coli (BM2509) ssrA, internal partial SEQ ID NO: 133 AGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGACAAAGC GTAAAAAGTCCAAATTAAAATTAAACGCAAATAACGTTAAAT TTGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCC GAAACTCAAGTGATGCTATCTAGCTTGAATTTTGGTCATCTTT GATAGTGTAGATTGAAAATTGACAACTTTTAATCGAAGTTAAA GTCTTAGTCTAGCTTGAAATTTTGGAAGGTGAGTTTAGCCAGA TGAAGTTTTCACCTTTGCTAAACATGTAGAAGTCTTTGTGGGG TTATTTTTGG Campylobacter coli (BM2509) tmRNA, internal partial SEQ ID NO: 134 AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGACAAAG CGUAAAAAGUCCAAAUUAAAAUUAAACGCAAAUAACGUUAA AUUUGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGA GCCCGAAACUCAAGUGAUGCUAUCUAGCUUGAAUUUUGGUC AUCUUUGAUAGUGUAGAUUGAAAAUUGACAACUUUUAAUC GAAGUUAAAGUCUUAGUCUAGCUUGAAAUUUUGGAAGGUG AGUUUAGCCAGAUGAAGUUUUCACCUUUGCUAAACAUGUAG AAGUCUUUGUGGGGUUAUUUUUGG Camplyobacter chicken isolate ssrA, internal partial SEQ ID NO: 135 ACAGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGGCAAA GCGTAAAAAGCCCAAATAAAATTAAACGCAAACAACGTTAAA TTCGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCC TGAAATTTAAGTCATACTATCTAGCTTAATTTTCGGTCATTTTT GATAGTGTAGCCTTGCGTTTGACAAGCGTTGAGGTGAAATAA GGTCTTAGCCTTGCTTTTGAGTTTTGGAAGATGAGCGAAGTAG GGTGAAGTAGTCATCTTTGCTAAGCATGTAGAGGTCTTTGTGG GATTATTTTTGG Camplyobacter chicken isolate tmRNA, internal partial SEQ ID NO: 136 ACAGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGGCAA AGCGUAAAAAGCCCAAAUAAAAUUAAACGCAAACAACGUUA AAUUCGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUG AGCCUGAAAUUUAAGUCAUACUAUCUAGCUUAAUUUUCGGU CAUUUUUGAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGG UGAAAUAAGGUCUUAGCCUUGCUUUUGAGUUUUGGAAGAU GAGCGAAGUAGGGUGAAGUAGUCAUCUUUGCUAAGCAUGUA GAGGUCUUUGUGGGAUUAUUUUUGG Clostridium perfringens ssrA, internal partial SEQ ID NO: 137 ACGGGGGTAGGATGGGTTTGATAAGCGAGTCGAGGGAAGCAT GGTGCCTCGATAATAAAGTATGCATTAAAGATAAACGCACGA GATAATTTTGCATTAGCAGCTTAAGTTAGCGCTGCTCATCCTT CCTCAATTGCCCACGGTTGAGAGTAAGGGTGTCATTTAAAAGT GGGGAACCGAGCCTAGCAAAGCTTTGAGCTAGGAACGGAATT TATGAAGCTTACCAAAGAGGAAGTTTGTCTGTGGACGTTCTCT GAGGGAATTTTAAAACACAAGACTACACTCGTAGAAAGTCTT ACTGGTCTGCTTTCGG Clostridium perfringens tmRNA, internal partial SEQ ID NO: 138 ACGGGGGUAGGAUGGGUUUGAUAAGCGAGUCGAGGGAAGC AUGGUGCCUCGAUAAUAAAGUAUGCAUUAAAGAUAAACGCA CGAGAUAAUUUUGCAUUAGCAGCUUAAGUUAGCGCUGCUCA UCCUUCCUCAAUUGCCCACGGUUGAGAGUAAGGGUGUCAUU UAAAAGUGGGGAACCGAGCCUAGCAAAGCUUUGAGCUAGGA ACGGAAUUUAUGAAGCUUACCAAAGAGGAAGUUUGUCUGUG GACGUUCUCUGAGGGAAUUUUAAAACACAAGACUACACUCG UAGAAAGUCUUACUGGUCUGCUUUCGG Haemophilus ducreyi (NCTC 10945) ssrA, internal partial SEQ ID NO: 139 ACGGGATTAGCGAAGTCCAAGGTGCACGTCGAGGTGCGGTAG GCCTCGTAACAAACCGCAAAAAAATAGTCGCAAACGACGAAC AATACGCTTTAGCAGCTTAATAACCTGCATTTAGCCTTCGCGC CCTAGCTTTCGCTCGTAAGACGGGGAGCACGCGGAGTCAAAC CAAAACGAGATCGTGTGGACGCTTCCGCTTGTAGATGAAACA CTAAATTGAATCAAGCTAGTTTATTTCTTGCGTGTCTGTCCGCT GGAGATAAGCGAAATTAAAGACCAGACTAAACGTGTAGTACT GAAGATAGAGTAATTTCGGACCCGGGTTCGACTC Haemophilus ducreyi (NCTC 10945) tmRNA, internal partial SEQ ID NO: 140 ACGGGAUUAGCGAAGUCCAAGGUGCACGUCGAGGUGCGGUA GGCCUCGUAACAAACCGCAAAAAAAUAGUCGCAAACGACGA ACAAUACGCUUUAGCAGCUUAAUAACCUGCAUUUAGCCUUC GCGCCCUAGCUUUCGCUCGUAAGACGGGGAGCACGCGGAGU CAAACCAAAACGAGAUCGUGUGGACGCUUCCGCUUGUAGAU GAAACACUAAAUUGAAUCAAGCUAGUUUAUUUCUUGCGUGU CUGUCCGCUGGAGAUAAGCGAAAUUAAAGACCAGACUAAAC GUGUAGUACUGAAGAUAGAGUAAUUUCGGACCCGGGUUCGA CUC
Listeria innocua (food isolate #1) ssrA, internal partial SEQ ID NO: 141 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAACCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACCGGGCTGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTCAA Listeria innocua (food isolate #1) tmRNA, internal partial SEQ ID NO: 142 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAACC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUCAA Listeria innocua (food isolate #2) ssrA, internal partial SEQ ID NO: 143 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACCGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (food isolate #2) tmRNA, internal partial SEQ ID NO: 144 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria innocua (food isolate #3) ssrA, internal partial SEQ ID NO: 145 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGAATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCGGACTAGCTGAATGGAAGC CTGTTACCGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (food isolate #3) tmRNA, internal partial SEQ ID NO: 146 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGAAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCGGACUAGCUGAAU GGAAGCCUGUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria innocua (ATCC 12210) ssrA, internal partial SEQ ID NO: 147 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG GGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACTGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (ATCC 12210) tmRNA, internal partial SEQ ID NO: 148 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGGGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACUGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria ivanovii (NCTC 11846) ssrA, internal partial SEQ ID NO: 149 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATTAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria ivanovii (NCTC 11846) tmRNA, internal partial SEQ ID NO: 150 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUUAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UCGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Listeria seeligeri (NCTC 11856) ssrA, internal partial SEQ ID NO: 151 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATACTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCCATATTTCTGG Listeria seeligeri (NCTC 11856) tmRNA, internal partial SEQ ID NO: 152 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUACUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCCAUAUUUCUGG Salmonella enteritidis ssrA, internal partial SEQ ID NO: 153 ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTG GCCTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAA CCTACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTC CCTAGCCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAAC CCAAAAGAGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGT TAAAACGAATCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGC AGGTGCCAGGCGAATGTAAAGACTGACTAAGCATGTAGTACC GAGGATGTAGGAATTTCGG Salmonella enteritidis tmRNA, internal partial SEQ ID NO: 154 ACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUU GGCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGA AACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUC UCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGU CAAACCCAAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUG AAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUC CGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAU GUAGUACCGAGGAUGUAGGAAUUUCGG Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial SEQ ID NO: 155 ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGC TCCGTCATCAACACATTTCGGTTAAATATAACTGACAAATCAA ACAATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCT AACAGCATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTA GGATATGCTAAACACTGCCGCTTGAAGTCTGTTTAGATGAAAT ATAATCAAGCTAGTATCATGTTGGTTGTTTATTGCTTAGCATG ATGCGAAAATTATCAATAAACTACACACGTAGAAAGATTTGT ATCAGGACCTCTGG
Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial SEQ ID NO: 156 ACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGG CUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAU CAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAU CGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAAC CCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUU AGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUA UUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACG UAGAAAGAUUUGUAUCAGGACCUCUGG Streptococcus agalactiae (NCTC 8181) ssrA, internal partial SEQ ID NO: 157 ACAGGCATTATGAGGTATATTTTGCGACTCATCGGCAGATGTA AAATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTAC GCATTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGAT TGTTTGCGTTTTGCTAGAAGGTCTTATTTATCAGCAAACTACG TTTGGCTACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCG CTATGTGAGGGCTTGAGTTATGTGTCATCACCTAGTTAAATCA ATACATAACCTATAGTTGTAGACAAATATATTAGCAGATGTTT GG Streptococcus agalactiae (NCTC 8181) tmRNA, internal partial SEQ ID NO: 158 ACAGGCAUUAUGAGGUAUAUUUUGCGACUCAUCGGCAGAUG UAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCU UACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCAC AAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCA AACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUU AUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACC UAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUA UUAGCAGAUGUUUGG Bordetella bronchiseptica ssrA SEQ ID NO: 159 GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAAG GCATGCCGAGCACCAGTAAGCTCGTTAATCCACTGGAACACT ACAAACGCCAACGACGAGCGTTTCGCTCTCGCCGCTTAAGCG GTGAGCCGCTGCACTGATCTGTCCTTGGGTCACGCGGGGGAA Bordetella bronchiseptica tmRNA SEQ ID NO: 160 GGGGCCGAUCCGGAUUCGACGUGGGUCAUGAAACAGCUCAAG GCAUGCCGAGCACCAGUAAGCUCGUUAAUCCACUGGAACACU ACAAACGCCAACGACGAGCGUUUCGCUCUCGCCGCUUAAGCG GUGAGCCGCUGCACUGAUCUGUCCUUGGGUCACGCGGGGGAA Chlamydia pneumoniae (CWL029), ssrA SEQ ID NO: 161 GGGGGTGTATAGGTTTCGACTTGAAAATGAAGTGTTAATTGCA TGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCAACAAAACA ATAAATGCCGAACCTAAGGCTGAATGCGAAATTATTAGCTTGT TTGACTCAGTAGAGGAAAGACTAGCTGCTTAATTAGCAAAAG TTGTTAGCTAGATAATCTCTAGGTAACCCGGTATCTGCGAGCT CCACCAGAGGCTTGCAAAATACCGTCATTTATCTGGTTGGAAC TTACTTTCTCTAATTCTCAAGGAAGTTCGTTCGAGATTTTTGAG AGTCATTGGCTGCTATAGAGGCTTCTAGCTAAGGGAGTCCAAT GTAAACAATTCTAGAAGATAAGCATGTAGAGGTTAGCAGGGA GTTTGTCAAGGACGAGAGTTCGAGTCTCTCCACCTCCACCA Chlamydia pneumoniae (CWL029) tmRNA SEQ ID NO: 162 GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUA GCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUA GCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAU CUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAU CUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGU UCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUA GCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAU GUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGA GUCUCUCCACCUCCACCA Francisella tularensis ssrA SEQ ID NO: 163 GGGGGCGAATATGGTTTCGACATGAATGTCAAAATCTAAGGT GCATGCCGAGGAAGTACCGTAACCTCGTTAATAACAGTACAA ATGCCAATAATAACTGGCAACAAAAAAGCAAACCGCGTAGCG GCTAACGACAGCAACTTTGCTGCTGTTGCTAAAGCTGCCTAGT CTAGCTTAATAATCTAGATGCGCACGGATATGATAGTCTTTCT TATGACACTATCTATACATCCGTTCATATTCCGCATAAGACGG TCTTTGCTTTTTGTCTGGGAGTTAAGGCTGTATTTAACAGACTC GCTAACTATTACCCTGGCTAATTGGGGAATAGTCAAGCTAAAC TCAAATAGATTAGCCTAAGCATGTAGATCCAAAGATCTAGAG TTTGTGGACGCGGGTTCAAATCCCGCCGCCTCCACCA Francisella tularensis tmRNA SEQ ID NO: 164 GGGGGCGAAUAUGGUUUCGACAUGAAUGUCAAAAUCUAAGG UGCAUGCCGAGGAAGUACCGUAACCUCGUUAAUAACAGUAC AAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUA GCGGCUAACGACAGCAACUUUGCUGCUGUUGCUAAAGCUGC CUAGUCUAGCUUAAUAAUCUAGAUGCGCACGGAUAUGAUAG UCUUUCUUAUGACACUAUCUAUACAUCCGUUCAUAUUCCGC AUAAGACGGUCUUUGCUUUUUGUCUGGGAGUUAAGGCUGUA UUUAACAGACUCGCUAACUAUUACCCUGGCUAAUUGGGGAA UAGUCAAGCUAAACUCAAAUAGAUUAGCCUAAGCAUGUAGA UCCAAAGAUCUAGAGUUUGUGGACGCGGGUUCAAAUCCCGC CGCCUCCACCA Guillardia theta (plastid) ssrA SEQ ID NO: 165 GGGGCTGATTTGGATTCGACATATAAATTTGCGTGTTTCATTA TGAAGCAAGTCAAGTTTAATGATCTTGTAAAAAACATTAAAG TACAAATAAATGCAAGCAATATAGTTTCATTTAGTTCAAAACG TTTAGTCTCTTTTGCATAAGCAAAATGTGTTAATAACTTTCTTA GTAGAAATTGGAGAAGTTTACTAAGATTTATATTTACTCCATA ATTATTTTAAAGATGGTAAAAAGGTGATTCATCATTTGTATGT TTCTAAACTTTGTGAAAGAATAGTGGGCTCCATTTATAATGAA CGTGGGTTCAAATCCCACCAGCTCCACCA Guillardia theta (plastid) tmRNA SEQ ID NO: 166 GGGGCUGAUUUGGAUUCGACAUAUAAAUUUGCGUGUUUCAU UAUGAAGCAAGUCAAGUUUAAUGAUCUUGUAAAAAACAUU AAAGUACAAAUAAAUGCAAGCAAUAUAGUUUCAUUUAGUUC AAAACGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUA ACUUUCUUAGUAGAAAUUGGAGAAGUUUACUAAGAUUUAU AUUUACUCCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAU UCAUCAUUUGUAUGUUUCUAAACUUUGUGAAAGAAUAGUG GGCUCCAUUUAUAAUGAACGUGGGUUCAAAUCCCACCAGCU CCACCA Thalassiosira Weissflogii (plastid) ssrA SEQ ID NO: 167 GGGGCTGATTTGGTTTCGACATTTAAAACTTCTTTCTATGTGTC AGGTCAAAGTTTGTATTCTTTGTAAAAAAATACTAAAATACTA ATAAATGCTAATAATATAATACCGTTTATTTTTAAAGCAGTAA AAACAAAAAAAGAAGCAATGGCTTTAAATTTTGCTGTATAGT TCATTAACTTAGGTTATTAAATATTTTTTCATTATAACTGGACT TTTCTCTAGTTTATAGTTTAGAATAAATTTAAATTTTGCAAAAC TCGTTCGAAAATTTTCGGGCTAAACCTGTAAACGCAAATACTA AGAAATTTTAGATGGACATGGGTTCAATTCCCATCAGTTCCAC CA Thalassiosira Weissflogii (plastid) tmRNA SEQ ID NO: 168 GGGGCUGAUUUGGUUUCGACAUUUAAAACUUCUUUCUAUGU GUCAGGUCAAAGUUUGUAUUCUUUGUAAAAAAAUACUAAA AUACUAAUAAAUGCUAAUAAUAUAAUACCGUUUAUUUUUA AAGCAGUAAAAACAAAAAAAGAAGCAAUGGCUUUAAAUUU UGCUGUAUAGUUCAUUAACUUAGGUUAUUAAAUAUUUUUU CAUUAUAACUGGACUUUUCUCUAGUUUAUAGUUUAGAAUAA AUUUAAAUUUUGCAAAACUCGUUCGAAAAUUUUCGGGCUAA ACCUGUAAACGCAAAUACUAAGAAAUUUUAGAUGGACAUGG GUUCAAUUCCCAUCAGUUCCACCA Helicobacter pylori ssrA, (clinical isolate 1), internal partial SEQ ID NO: 176 TGGGGATGTTACGGTTTCGACAGGGGTAGTTCGAGCTTAGGTG
GCGAGTCGAGGGGATCGGCCTCGTTAAAACGTCAAAGCCTAT AACTGGCAAACAACAAAACAACTTCGCTTTAGCAGCTTAATA AGCTCTTAGCGGTTCCTCCCTCCATCGCCCATGTGGTAGGGTA AGGGACTCAAATTAAGTGGGCTACGCTGGATTCCACCGTCTG AGGATGAAAGAAGAGAACAACCAGACTAGCTACCCGGACGC CCGTCGATAGGCAGATGGAGTAGCGAATCGCGAATATATCGA CTACACTCGTAGAAGCTTAAGTGCCGATATTCTTGGACGTGGG TTCGACTCCC Helicobacter pylori tmRNA, (clinical isolate 1), internal partial SEQ ID NO: 177 UGGGGAUGUUACGGUUUCGACAGGGGUAGUUCGAGCUUAGG UGGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCC UAUAACUGGCAAACAACAAAACAACUUCGCUUUAGCAGCUU AAUAAGCUCUUAGCGGUUCCUCCCUCCAUCGCCCAUGUGGU AGGGUAAGGGACUCAAAUUAAGUGGGCUACGCUGGAUUCCA CCGUCUGAGGAUGAAAGAAGAGAACAACCAGACUAGCUACC CGGACGCCCGUCGAUAGGCAGAUGGAGUAGCGAAUCGCGAA UAUAUCGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUCU UGGACGUGGGUUCGACUCCC Helicobacter pylori ssrA, (clinical isolate 2), internal partial SEQ ID NO: 178 TGGGGACGTTACGGTTTCGACAGGGATAGTTCGAGCTTAGGTT GCGAGTCGAGGGGATCGGCCTCGTTAAAACGTCAAAGCCTAT AATTGGCAAACAAAACAATCTTTCTTTAGCTGCTTAATTGCAC TAAAGGTTCCTCCCTCCATCGTCCATGTGGTAGGGTAAGGGAC TCAAACTAAGTGGACTACGCCGGAGTTCGCCGTCTGAGGACA AAGGAAGAGAACAACCAGACTAGCAACTTGGAAGCCTGTCGA TAGGCCGAAGAGTTCGCGAAATGCTAATATATCGACTACACT CGTAGAAGCTTAAGTGCCGATATTTTTGGACGTGGGTTCGATT CCCT Helicobacter pylori tmRNA, (clinical isolate 2), internal partial SEQ ID NO: 179 UGGGGACGUUACGGUUUCGACAGGGAUAGUUCGAGCUUAGG UUGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCC UAUAAUUGGCAAACAAAACAAUCUUUCUUUAGCUGCUUAAU UGCACUAAAGGUUCCUCCCUCCAUCGUCCAUGUGGUAGGGU AAGGGACUCAAACUAAGUGGACUACGCCGGAGUUCGCCGUC UGAGGACAAAGGAAGAGAACAACCAGACUAGCAACUUGGAA GCCUGUCGAUAGGCCGAAGAGUUCGCGAAAUGCUAAUAUAU CGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUUUUGGAC GUGGGUUCGAUUCCCU Listeria seeligeri (NCTC 11856) ssrA, internal partial SEQ ID NO: 180 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATACTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCCATATTTCTGG Listeria seeligeri (NCTC 11856) tmRNA, internal partial SEQ ID NO: 181 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUACUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCCAUAUUUCUGG Listeria ivanovii (NCTC 11846) ssrA, internal partial SEQ ID NO: 182 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATTAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria ivanovii (NCTC 11846) tmRNA, internal partial SEQ ID NO: 183 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUUAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UCGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Mycobacterium africanum (clinical isolate) ssrA, internal partial SEQ ID NO: 184 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTC GGGACAACCACAGCGACTGGGATCGTCATCTCGGCTAGTTCG CGTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium africanum (clinical isolate) tmRNA, internal partial SEQ ID NO: 185 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGG CAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UCCUCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCU AGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium gordonae (clinical isolate)ssrA, internal partial SEQ ID NO: 186 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCATATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCGGACCGGGAACGCCCTCGCCCCGGACCCCGGCATC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTCCG TGTGACCAGGAGATCCGAGCAGAGACATAGCGGACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium gordonae (clinical isolate) tmRNA, internal partial SEQ ID NO: 187 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGC AUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGACU CAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUA GUCCGUGUGACCAGGAGAUCCGAGCAGAGACAUAGCGGACU GCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium kansasii (clinical isolate) ssrA, internal partial SEQ ID NO: 188 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGACCGCCCTCGACCCGGACTCTGGCATCA GCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCGTCG GGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCGC GTGACCAGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAATGCCGTA
Mycobacterium kansasii (clinical isolate) tmRNA, internal partial SEQ ID NO: 189 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGACCGCCCUCGACCCGGACUCUGG CAUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGAC UCGUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUUCGCGUGACCAGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium chelonae ssrA, internal partial SEQ ID NO: 190 ACAGCGAGTCTCGACTTAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCATTGCAACCAATTAAGCGCCGATT CTCATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGTG TCTGTCAGACCGGGAGCGCCCTCAGCCCGGACCCTGGCATCA GCTAGAGGGACAAACTACGGGTTCGGTCGCGGGACCCGTAGG GACATCAAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGCG GGACCGAGAGATCCAAGTAGAGGCATAGCGAACTGCGCACGG AGAAGCCTTAATGAACGGCCGTTG Mycobacterium chelonae tmRNA, internal partial SEQ ID NO: 191 ACAGCGAGUCUCGACUUAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCAUUGCAACCAAUUAAGCGCCGA UUCUCAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUG CGUGUCUGUCAGACCGGGAGCGCCCUCAGCCCGGACCCUGG CAUCAGCUAGAGGGACAAACUACGGGUUCGGUCGCGGGACC CGUAGGGACAUCAAACAGCGACUGGGAUCGUCAUCUCGGCU UGUUCGCGGGACCGAGAGAUCCAAGUAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUAAUGAACGGCCGUUG Mycobacterium szulgai (ATCC 35799) ssrA, internal partial SEQ ID NO: 192 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGAGA ACACTCAGCGCGACTTCGCTCTCGCTGCCTAAGCGACAGCAA GTCCGTCAGACCGGGAAAGCCCTCGACCCGGACCCTGGCGTC ATCTAGAGGGATCCACCGGTGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCG CGTGACCAGGAGATCCGAGTAGAGACATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium szulgai (ATCC 35799) tmRNA, internal partial SEQ ID NO: 193 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA GAACACUCAGCGCGACUUCGCUCUCGCUGCCUAAGCGACAG CAAGUCCGUCAGACCGGGAAAGCCCUCGACCCGGACCCUGG CGUCAUCUAGAGGGAUCCACCGGUGAGUUCGGUCGCGGGAC UCAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUUCGCGUGACCAGGAGAUCCGAGUAGAGACAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium malmoense (clinical isolate) ssrA, internal partial SEQ ID NO: 194 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCATATAAGCGCCGTTTC AACACAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTAG TCCGTCAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTCA GCTGGAGGGATCCACCGGTGAGTCCGGTCGCGGGACTCATCG GGACATACACAGCGACTGGGATCGTCATCCTGGCTGGTTCGC GTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium malmoense (clinical isolate) tmRNA, internal partial SEQ ID NO: 195 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGU UUCAACACAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGG CGUCAGCUGGAGGGAUCCACCGGUGAGUCCGGUCGCGGGAC UCAUCGGGACAUACACAGCGACUGGGAUCGUCAUCCUGGCU GGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium flavescens ssrA, internal partial SEQ ID NO: 196 ACTTCGAGCGTCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CCAATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGT GTCTGTCAGCCCGGGAGAGCCCTCGACCCGGTGTCTGGCATCA GCTAGAGGGATAAACCGGTGGGTCCGGTCGCGGGACTCATCG GGACATCAAACAGCGACTGGGATCGTCATCCTGACTTGTTCGC GTGATCAGGAGATCCGAGTAGAGACATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAACGCCGTAG Mycobacterium flavescens tmRNA, internal partial SEQ ID NO: 197 ACUUCGAGCGUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCCAAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUG CGUGUCUGUCAGCCCGGGAGAGCCCUCGACCCGGUGUCUGG CAUCAGCUAGAGGGAUAAACCGGUGGGUCCGGUCGCGGGAC UCAUCGGGACAUCAAACAGCGACUGGGAUCGUCAUCCUGAC UUGUUCGCGUGAUCAGGAGAUCCGAGUAGAGACAUAGCGAA CUGCGCACGGAGAAGCCUUGAGGGAACGCCGUAG Mycobacterium marinum ssrA, internal partial SEQ ID NO: 198 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGATGCAACTAGATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCGGACCGGGAACGCCCTCGCCCCGGACCCCGGCATC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGGCTCATC GGGACATCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCG CGTGACCAGGAGATCCGAGCAGAGACCTAGCGGACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium marinum tmRNA, internal partial SEQ ID NO: 199 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGAUGCAACUAGAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGC AUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGGCU CAUCGGGACAUCAACAGCGACUGGGAUCGUCAUCCUGGCUA GUUCGCGUGACCAGGAGAUCCGAGCAGAGACCUAGCGGACU GCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium microti (environmental isolate) ssrA, internal partial SEQ ID NO: 200 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTC GGGACAGCCACAGCGACTGGGATCGTCATCTCGGCTAGTTCG CGTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium microti (environmental isolate) tmRNA, internal partial SEQ ID NO: 201 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGG CAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UCCUCGGGACAGCCACAGCGACUGGGAUCGUCAUCUCGGCU AGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial SEQ ID NO: 202 ACTTCGAGCATCGAATCCAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CCAATCAGCGCGACTACGCCCTCGCTGCCTAAGCGACGGCTG GTCTGTCAGACCGGGAGTGCCCTCGGCCCGGATCCTGGCATCA
GCTAGAGGGACCCACCCACGGGTTCGGTCGCGGGACCTGTGG GGACATCAAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGT GTGACCGGGAGATCCGAGTAGAGACATAGCGAACTGCGCACG GAGAAGCCTCGAGGACATGCCGTAG Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial SEQ ID NO: 203 ACUUCGAGCAUCGAAUCCAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCCAAUCAGCGCGACUACGCCCUCGCUGCCUAAGCGACGG CUGGUCUGUCAGACCGGGAGUGCCCUCGGCCCGGAUCCUGG CAUCAGCUAGAGGGACCCACCCACGGGUUCGGUCGCGGGAC CUGUGGGGACAUCAAACAGCGACUGGGAUCGUCAUCUCGGC UUGUUCGUGUGACCGGGAGAUCCGAGUAGAGACAUAGCGAA CUGCGCACGGAGAAGCCUCGAGGACAUGCCGUAG Mycobacterium xenopi (clinical isolate) ssrA, internal partial SEQ ID NO: 204 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACTAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGGCCGGGAGTTCCCTCGACCCGGATCCTGGCGTCA GCTAGAGGGATCCACCGATGGGTTCGGTCGCGGGACCCATCG GGACACCACACAGCGACTGGGATCGCCGTCCCGGCTAGTTCG CGAGACCGGGAGATCCGAGTAAGGGCAAAGCGAACTGCGCA CGGAGAAGCCTTGAGGGTATGCCGTA Mycobacterium xenopi (clinical isolate) tmRNA, internal partial SEQ ID NO: 205 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACUAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGGCCGGGAGUUCCCUCGACCCGGAUCCUGG CGUCAGCUAGAGGGAUCCACCGAUGGGUUCGGUCGCGGGAC CCAUCGGGACACCACACAGCGACUGGGAUCGCCGUCCCGGC UAGUUCGCGAGACCGGGAGAUCCGAGUAAGGGCAAAGCGAA CUGCGCACGGAGAAGCCUUGAGGGUAUGCCGUA Mycobacterium intracellulare (NCTC 10425) ssrA, internal partial SEQ ID NO: 206 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA CCGACCACCGTAAGCGTCGTTGCAAACAGATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTTATC GGGACACCAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGC GTGACCGGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACG GAGAAGTCTTGAGGGAATGCCGTAG Mycobacterium intracellulare (NCTC 10425) tmRNA, internal partial SEQ ID NO: 207 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA ACCGACCACCGUAAGCGUCGUUGCAAACAGAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGG CGUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UUAUCGGGACACCAACAGCGACUGGGAUCGUCAUCUCGGCU UGUUCGCGUGACCGGGAGAUCCGAGUAGAGGCAUAGCGAAC UGCGCACGGAGAAGUCUUGAGGGAAUGCCGUAG Mycobacterium scrofulaceum (NCTC 10803) ssrA, internal partial SEQ ID NO: 208 ACATCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGACCGGGAAAGCCCTCGACCCGGAGCCTGGCGTC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTCCG CGTGACCAGGAGATCCGAGCAGAGGCATAGCGGACTGCGCAC GGAGAAGTCTTGAGGGAATGCCGTTG Mycobacterium scrofulaceum (NCTC 10803) tmRNA, internal partial SEQ ID NO: 209 ACAUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAAAGCCCUCGACCCGGAGCCUGG CGUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGAC UCAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUCCGCGUGACCAGGAGAUCCGAGCAGAGGCAUAGCGGAC UGCGCACGGAGAAGUCUUGAGGGAAUGCCGUUG Nocardia asteroides ssrA, internal partial SEQ ID NO: 210 ACTGTGTGCGCCGAGGTAGGGGAAGCGTGTCGGTGCAGGCTG GAGACCACCGTTAAGCGTCGCGGCAACCAATTAAGCGCCGAT TCCAATCAGCGCGACTACGCCCTCGCTGCCTGATCAGCGACGG CTAGCTGTCGGCCCGGGTTGTGTTCCCGAACCCGGATGCCGGC ATCATCTCAGGGAACTCACCGTGTTCGCCGGTCGCGGACGGA CACGGGACAGCAAACAGCGACTGGGATCGTCATCTCGGCTTG TTCGCGTGACCGGGAGATCCAAGTAGAGACATAGCGGACTGC ACACGGAGAAGCCCTACTGACTCGACACAG Nocardia asteroides tmRNA, internal partial SEQ ID NO: 211 ACUGUGUGCGCCGAGGUAGGGGAAGCGUGUCGGUGCAGGCU GGAGACCACCGUUAAGCGUCGCGGCAACCAAUUAAGCGCCG AUUCCAAUCAGCGCGACUACGCCCUCGCUGCCUGAUCAGCG ACGGCUAGCUGUCGGCCCGGGUUGUGUUCCCGAACCCGGAU GCCGGCAUCAUCUCAGGGAACUCACCGUGUUCGCCGGUCGC GGACGGACACGGGACAGCAAACAGCGACUGGGAUCGUCAUC UCGGCUUGUUCGCGUGACCGGGAGAUCCAAGUAGAGACAUA GCGGCUGCACACGGAGAAGCCCUACUGACUCGACACAG Salmonella enteritidis ssrA, internal partial SEQ ID NO: 212 ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTG GCCTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAA CCTACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTC CCTAGCCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAAC CCAAAAGAGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGT TAAAACGAATCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGC AGGTGCCAGGCGAATGTAAAGACTGACTAAGCATGTAGTACC GAGGATGTAGGAATTTCGG Salmonella enteritidis tmRNA, internal partial SEQ ID NO: 213 ACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUU GGCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGA AACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUC UCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGU CAAACCCAAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUG AAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUC CGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAU GUAGUACCGAGGAUGUAGGAAUUUCGG Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial SEQ ID NO: 214 ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGC TCCGTCATCAACACATTTCGGTTAAATATAACTGACAAATCAA ACAATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCT AACAGCATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTA GGATATGCTAAACACTGCCGCTTGAAGTCTGTTTAGATGAAAT ATAATCAAGCTAGTATCATGTTGGTTGTTTATTGCTTAGCATG ATGCGAAAATTATCAATAAACTACACACGTAGAAAGATTTGT ATCAGGACCTCTGG Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial SEQ ID NO: 215 ACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGG CUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAU CAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAU CGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAAC CCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUU AGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUA UUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACG UAGAAAGAUUUGUAUCAGGACCUCUGG
Streptococcus agalactiae (NCTC 8181) ssrA, internal partial SEQ ID NO: 216 ACAGGCATTATGAGGTATATTTTGCGACTCATCGGCAGATGTA AAATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTAC GCATTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGAT TGTTTGCGTTTTGCTAGAAGGTCTTATTTATCAGCAAACTACG TTTGGCTACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCG CTATGTGAGGGCTTGAGTTATGTGTCATCACCTAGTTAAATCA ATACATAACCTATAGTTGTAGACAAATATATTAGCAGATGTTT GG Streptococcus agalactiae (NCTC 8181) tmRNA, internal partial SEQ ID NO: 217 ACAGGCAUUAUGAGGUAUAUUUUGCGACUCAUCGGCAGAUG UAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCU UACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCAC AAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCA AACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUU AUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACC UAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUA UUAGCAGAUGUUUGG
[0048] Of the above sequences SEQ ID NOs 47 to 62, 65 to 68, 71 and 72, 98 and 99, 159 to 168 and 176-217 are novel sequences.
[0049] The above mentioned sequences can be used to form a database of ssrA gene sequences which can be used to identify a bacterial species, or for the generation of nucleic acid diagnostic assays.
[0050] Representative probes identified in accordance with the invention are as follows:
Salmonella:
[0051] 1) Genius specific probe:
TABLE-US-00002 5'-CGAATCAGGCTAGTCTGGTAG-3' SEQ ID NO: 218
Mycobacteria:
[0052] 2) Oligonucleotide probe for detection of tuberculosis complex
TABLE-US-00003 SEQ ID NO: 219 TB01 5'-ACTCCTCGGACA (A/G) CCACAGCGA-3'
3) Oligonucleotide probes for detection of M. avium and M. paratuberculosis sequences
TABLE-US-00004 SEQ ID NO: 220 Probe 1: PAV1-5'-GTTGCAAATAGATAAGCGCC-3' SEQ ID NO: 221 Probe 2: PAV2-5'-TCCGTCAGCCCGGGAACGCC-3'
Listeria:
[0053] 4) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells:
TABLE-US-00005 LVtm: 5'-TTTTGTTTTTCTTTGCCA-3' SEQ ID NO: 222
Escherichia coli: 5) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells:
TABLE-US-00006 Evtm: 5'-AGTTTTCGTCGTTTGCGA-3' SEQ ID NO: 223
Further representative primers identified in accordance with the invention are as follows:
Mycobacteria:
[0054] 1) Degenerative oligonucleotide primers for the amplification of all mycobacterial sequences
TABLE-US-00007 5' Primer SEQ ID NO: 224 10SAAM3-5'-CAGGCAA (G/C) (A/T/C) GACCACCGTAA-3' 3' Primer SEQ ID NO: 225 10SAAM4-5' GGATCTCC(C/T)G(A/G)TC(A/T)C(A/G)CG(A/G) AC(A/T)A-3'
2) Oligonucleotide primers for the amplification of M. avium and M. paratuberculosis
TABLE-US-00008 SEQ ID NO: 226 5' Primer: AP1for-5'-TGCCGGTGCAGGCAACTG-3' SEQ ID NO: 227 3' Primer: AP2rev-5'-CACGCGAACAAGCCAGGA-3'
BRIEF DESCRIPTION OF THE DRAWINGS
[0055] In the accompanying drawings:
[0056] FIG. 1 is a clustal alignment of E. coli and V. cholerae ssrA gene sequences;
[0057] FIG. 2 is a photograph of an agarose gel of total cellular RNA prepared from E. coli and V. cholerae cells;
[0058] FIG. 3 is a photograph of an autoradiogram of hybridisation of a V. cholerae oligonucleotide probe to tmRNA transcripts of E. coli and V. cholerae;
[0059] FIG. 4 is a photograph of an agarose gel of the amplified products of universal ssrA gene amplification primers from a panel of organisms;
[0060] FIG. 5 is a clustal alignment of the ssrA gene sequences from the Listeria species;
[0061] FIG. 6 is a clustal alignment of the L. monocytogenes and B. subtilus ssrA/tmRNA gene sequences;
[0062] FIG. 7 is a photograph of an agarose gel of the amplified products of Listeria genus specific PCR amplification primers from a panel of organisms;
[0063] FIG. 8 is a photograph of an autoradiogram of hybridised Listeria genus specific oligonucleotide probe to a panel of organisms as prepared in Example 4;
[0064] FIG. 9 is a photograph of an autoradiogram of hybridised L. monocytogenes species specific probe to a panel of organisms as prepared in Example 7;
[0065] FIG. 10 is a computer scanned image of a nylon membrane strip used in the multiple colorimetric probe detection of Listeria ssrA gene sequences as described in Example 6.
[0066] FIG. 11 is a clustal alignment of ssrA gene sequences from C. trachomatis strains;
[0067] FIG. 12 is a clustal alignment of ssrA gene sequences from H. pylori strains;
[0068] FIG. 13 is a clustal alignment of ssrA gene sequences from M. genitalium strains;
[0069] FIG. 14 is a clustal alignment of ssrA gene sequences from N. gonorrhoeae strains;
[0070] FIG. 15 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains;
[0071] FIG. 16 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains and the L. innocua strain;
[0072] FIG. 17 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after medium heat treatment of E. coli cells;
[0073] FIG. 18 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after extreme heat treatment of E. coli cells;
[0074] FIG. 19 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after medium heat treatment of L. monocytogenes cells;
[0075] FIG. 20 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after extreme heat treatment of L. monocytogenes cells; and
[0076] FIG. 21 is a photograph of an agarose gel of RT-PCR generated tmRNA products at various time points post heat treatment.
[0077] The invention will be further illustrated by the following Examples.
MODES FOR CARRYING OUT THE INVENTION
Example 1
Examination of the Primary Nucleotide Sequences of Available tmRNA Sequences
[0078] A comparative primary nucleotide sequence alignment of available tmRNA sequences using the Clustal W nucleic acid alignment programme demonstrated that tmRNA sequences from prokaryotes show a more significant degree of nucleotide sequence variability and non-homology than other bacterial high copy number RNA, as demonstrated in Table 1.
TABLE-US-00009 TABLE 1 Percentage nucleotide sequence homology between RNA molecules from different bacteria. Escherichia coli vs. Bacillus subtilus vs. Vibrio cholerae Mycobacterium tuberculosis rRNA % 88 66 homology tmRNA % 68 25 homology
[0079] These regions of non-homology between tmRNA sequences from different bacteria are located in the middle of the molecule, and the extent of nucleotide sequence non-homology within the tmRNA molecule indicated that genus as well as species specific probes could be generated to distinguish between and/or detect bacteria.
[0080] Nucleotide sequence alignments had previously shown that the 5' and 3' flanking regions of the tmRNA molecules share a high degree of homology both within species and within genus. This observation indicated that universal oligonucleotide primers could be generated to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria.
[0081] We have now demonstrated that these regions of homology and non-homology within the nucleotide sequence of tmRNA molecules from different organisms can be used as the basis of identifying and detecting organisms at the molecular level.
Example 2
Development of a V. cholerae tmRNA Specific Probe
[0082] A nucleotide sequence alignment of the E. coli (SEQ ID NO. 37) and V. cholerae (SEQ ID NO. 127) ssrA sequences as depicted in FIG. 1, shows that these two bacterial species are phylogenetically closely related. There are however, regions of non-homology between the sequences as evidenced by the absence of asterix marks. An oligonucleotide probe, complementary to the variable region of the V. cholerae ssrA nucleotide sequence underlined in FIG. 1, was synthesised.
[0083] The sequence of the V. cholerae tmRNA specific probe is
TABLE-US-00010 5'-AACGAATGGCTAACCTGAA-3' SEQ ID NO. 169
[0084] Total RNA was isolated from liquid cultures of E. coli and V. cholerae at the mid-exponential phase and the stationary phase of growth. Equivalent amounts of the isolated total RNA were electrophoresed on a denaturing formaldehyde agarose gel and blotted onto HYBOND-N nylon membrane as shown in FIG. 2 in which the Lanes 1-4 represent the following:
Lane 1: Total E. coli RNA mid-log phase Lane 2: Total V. cholerae RNA mid-log phase Lane 3: Total E. coli RNA stationary phase Lane 4: Total V. cholerae RNA stationary phase
[0085] The resulting Northern blot was then hybridised with the V. cholerae tmRNA specific probe end-labelled with γP32. The results of the hybridisation experiment shown in FIG. 3 demonstrate the specificity of the probe as only V. cholerae tmRNAs were detected. Moreover, a greater degree of hybridisation signal intensity was observed with the V. cholerae tmRNA isolated from cultures during the stationary phase of growth, indicating that a higher copy number of the tmRNA molecule is present in V. cholerae cells during this phase.
Example 3
Generation of Universal ssrA/tmRNA Oligonucleotide Amplification Primers for the Characterisation of Unknown ssrA Gene and tmRNA Sequences
[0086] Clustal W alignment of all available ssrA gene and tmRNA sequences indicated that degenerate oligonucleotide primers could be designed to amplify ssrA gene and tmRNA nucleotide sequences for a wide variety of organisms.
[0087] Degenerate oligonucleotide primers were synthesised to PCR amplify ssrA gene sequences from total genomic DNA preparations from a broad range of bacteria.
[0088] The sequences of the synthesised degenerate oligonucleotides are as follows: [0089] (a) tmU5': 5' in vitro PCR amplification primer
TABLE-US-00011 [0089] 5'-GGG(A/C)(C/T)TACGG(A/T)TTCGAC-3' SEQ ID NO: 170
[0090] (b) tmU3': 3' in vitro PCR amplification primer
TABLE-US-00012 [0090] 5'-GGGA(A/G)TCGAACC(A/G)(C/G)GTCC-3' SEQ ID NO: 171
[0091] Degenerate base positions are in parentheses.
[0092] The products of PCR reactions were electrophoresed on an agarose gel and a 350 base pair (approx.) PCR product was amplified in all cases, as shown in FIG. 4, demonstrating the "universality" of the degenerate tmRNA primers.
[0093] In FIG. 4 the lanes represent the following:
Lane A: Molecular weight marker V Lane 1: Escherichia coli Lane 2: Salmonella poona Lane 3: Klebsiella aerogenes Lane 4: Proteus mirabilis Lane 5: Proteus rettgeri Lane 6: Aeromonas hydrophilia Lane 7: Staphyloccus aureus Lane 8: Enterococcus faecalis Lane 9: Lactobacillus lactis Lane 10: Bacillus subtilus Lane 11: Listeria monocytogenes Lane 12: Listeria innocua Lane 13: Listeria murrayi Lane 14: Listeria welshimeri Lane 15: Listeria grayi Lane 16: Mycobacterium bovis Lane B: Molecular weight marker V
[0094] The universal primers amplified the ssrA gene from both Gram positive and Gram negative bacteria, as shown in Table 2.
TABLE-US-00013 TABLE 2 Bacterial species tested with universal amplification primers. PCR Product Gram negative Escherichia coli + bacteria Salmonella poona + Klebsiella aerogenes + Proteus mirabilis + Proteus rettgeri + Aeromonas hydrophilia + Gram positive Staphyloccus aureus + bacteria Enterococcus faecalis + Lactobacillus lactis + Bacillus subtilus + Listeria monocytogenes + Listeria innocua + Listeria murrayi + Listeria welshimeri + Listeria grayi + Mycobacterium bovis +
Example 4
Isolation and Characterisation of Previously Unknown Bacterial ssrA/tmRNA Nucleotide Sequences
[0095] The PCR products amplified from genomic DNA from the Listeria species of bacteria and that from the M. bovis bacterium, from Example 2, were subcloned into a T-tailed plasmid vector for the purposes of DNA sequencing. Three recombinant clones were selected for each species and sequenced by the di-deoxy sequencing method. The sequence of both DNA strands for each subclone was determined.
[0096] The nucleotide sequence determined for the M. bovis ssrA gene shared 100% homology with the Mycobacterium tuberculosis ssrA gene sequence.
[0097] A clustal W alignment of the novel ssrA gene sequences obtained for the Listeria species (SEQ ID NOS 51, 53, 55, 59 and 61) is shown in FIG. 5. This analysis indicated that genus-specific probes and oligonucleotide amplification primers can be generated for Listeria bacteria. Furthermore, the alignment also indicated that a species specific oligonucleotide probe can be generated which will distinguish L. monocytogenes from the other Listeria species.
[0098] In FIG. 5 the proposed genus specific oligonucleotide primers, Ltm 1 and Ltm 2, are boxed, as is the genus specific Listeria oligonucleotide probe, LGtm. The proposed L. monocytogenes species specific oligonucleotide probe sequence, LStm, is underlined and italicised.
[0099] To further illustrate that the ssrA gene/tmRNA nucleic acid target is a suitable target for bacterial diagnostics, a comparative alignment of the L. monocytogenes ssrA gene nucleotide sequence (SEQ ID NO. 55) with the available B. subtilis ssrA gene nucleotide sequence (SEQ ID NO. 11) (a phylogenetically closely related bacteria to Listeria) was carried out as shown in FIG. 6. Analysis of the sequence alignment showed a percentage nucleotide sequence homology of 41%, whereas the corresponding 16S rRNA alignment exhibits a nucleotide sequence percentage homology of 87%, (data not shown).
Example 5
Generation and Application of ssrA Gene/tmRNA Genus-Specific Amplification Primers, Genus-Specific and Species-Specific Probes for the Listeria Bacterial Species
[0100] Using the Listeria genus ssrA gene/tmRNA nucleotide sequence alignment of Example 4, regions of the ssrA gene/tmRNA nucleotide sequence were analysed to determine their suitability for the generation of genus-specific amplification primers, and genus-specific and species-specific oligonucleotide probes. In this analysis, regions which demonstrated the greatest sequence differences to B. subtilis, were selected in the design of these amplification primers and probes.
[0101] The sequences of the synthesised oligonucleotides are as follows: [0102] (a) Ltm1: 5' Listeria genus specific amplification primer
TABLE-US-00014 [0102] 5'-AAAGCCAATAATAACTGG-3' SEQ ID NO: 172
[0103] (b) Ltm2: 3' Listeria genus specific amplification primer
TABLE-US-00015 [0103] 5'-CCAGAAATATCGGCACTT-3' SEQ ID NO: 173
[0104] (c) LGtm: Listeria genus specific hybridisation probe
TABLE-US-00016 [0104] 5'-GTGAGACCCTTACCGTAG-3' SEQ ID NO: 174
[0105] (d) LStm: L. monocytogenes species specific hybridisation probe
TABLE-US-00017 [0105] 5'-TCTATTTAACCCCAGACG-3' SEQ ID NO: 175
[0106] The genus specific amplification primers Ltm1 and Ltm2 were used in a series of PCR reactions with total genomic DNA from twenty different strains as the template in each case. Only ssrA gene sequences from the Listeria species were amplified (260 base pair product) with these primers (FIG. 7 and Table 3) demonstrating that the ssrA gene/tmRNA is a suitable target for specific in vitro amplification of a bacterial genus. No amplification products were observed for any other bacterial species tested, although PCR products were obtained from the DNA from these bacterial species using the universal primers (tmU5' and tmU3') described in Example 2.
[0107] In FIG. 7 the lanes represent the following:
Lane A: Molecular weight marker V Lane 1: E. coli Lane 2: S. poona Lane 3: K. aerogenes Lane 4: P. mirabilis Lane 5: P. rettgeri Lane 6: A. hydrophilia Lane 7: S. aureus Lane 8: E. faecalis Lane 9: L. lactis Lane 10: B. subtilus Lane 11: L. monocytogenes strain 1 Lane 12: L. monocytogenes strain 2 Lane 13: L. monocytogenes strain 3 Lane 14: L. monocytogenes strain 4 Lane 15: L. monocytogenes clinical isolate Lane 16: L. innocua Lane 17: L. murrayi Lane 18: L. welshimeri Lane 19: L. grayi Lane 20: M. bovis Lane B: Molecular weight marker V
TABLE-US-00018 TABLE 3 Bacterial species tested with Listeria specific amplification primers. PCR Product Gram negative Escherichia coli - bacteria Salmonella poona - Klebsiella aerogenes - Proteus mirabilis - Proteus rettgeri - Aeromonas hydrophilia - Gram positive Staphyloccus aureus - bacteria Entrococcus faecalis - Lactobacillus lactis - Bacillus subtilus - Listeria monocytogenes strain 1 + Listeria monocytogenes strain 2 + Listeria monocytogenes strain 3 + Listeria monocytogenes strain 4 + Listeria monocytogenes clinical + isolate Listeria innocua + Listeria murrayi + Listeria welshimeri + Listeria grayi + Mycobacterium bovis -
[0108] The Listeria genus specific oligonucleotide probe, LGtm, was hybridised to the Southern blot depicted in FIG. 4. Positive hybridisation signals were observed only with Listeria species as shown in FIG. 8 and Table 4, demonstrating the utility of the tmRNA sequence as a target in detecting a specific genus.
[0109] In FIG. 8 the lanes represent the following:
Lane A: Molecular weight marker V Lane 1: Escherichia coli Lane 2: Salmonella poona Lane 3: Klebsiella aerogenes Lane 4: Proteus mirabilis Lane 5: Proteus rettgeri Lane 6: Aeromonas hydrophilia Lane 7: Staphyloccus aureus Lane 8: Enterococcus faecalis Lane 9: Lactobacillus lactis Lane 10: Bacillus subtilus Lane 11: Listeria monocytogenes Lane 12: Listeria innocua Lane 13: Listeria murrayi Lane 14: Listeria welshimeri Lane 15: Listeria grayi Lane 16: Mycobacterium bovis Lane B: Molecular weight marker V
[0110] The PCR products generated using the genus-specific amplification described in this Example, and shown in FIG. 7, were Southern blotted and hybridised to the L. monocytogenes species-specific oligonucleotide probe. A positive hybridisation signal was observed with three of the four typed strains and the clinical isolate of L. monocytogenes as shown in FIG. 9 and Table 4.
[0111] In FIG. 9 the lanes represent the following:
Lane A: Molecular weight marker V Lane 1: E. coli Lane 2: S. poona Lane 3: K. aerogenes Lane 4: P. mirabilis Lane 5: P. rettgeri Lane 6: A. hydrophilia Lane 7: S. aureus Lane 8: E. faecalis Lane 9: L. lactis Lane 10: B. subtilus Lane 11: L. monocytogenes strain 1 Lane 12: L. monocytogenes strain 2 Lane 13: L. monocytogenes strain 3 Lane 14: L. monocytogenes strain 4 Lane 15: L. monocytogenes clinical isolate Lane 16: L. innocua Lane 17: L. murrayi Lane 18: L. welshimeri Lane 19: L. grayi Lane 20: M. bovis Lane B: Molecular weight marker V
TABLE-US-00019 TABLE 4 Specificity of the Listeria genus-specific probe and the L. monocytogenes species-specific probe. LGtm LStm Genus- Species- specific specific probe probe Gram negative Escherichia coli - - bacteria Salmonella poona - - Klebsiella aerogenes - - Proteus mirabilis - - Proteus rettgeri - - Aeromonas hydrophilia - - Gram positive Staphyloccus aureus - - bacteria Entrococcus faecalis - - Lactobacillus lactis - - Bacillus subtilus - - Listeria monocytogenes strain 1 + + Listeria monocytogenes strain 2 + + Listeria monocytogenes strain 3 + + Listeria monocytogenes strain 4 + - Listeria monocytogenes clinical + + isolate Listeria innocua + - Listeria murrayi + - Listeria welshimeri + - Listeria grayi + - Mycobacterium bovis - -
[0112] One of the typed L. monocytogenes strains, strain 4, failed to generate a positive signal with this probe. DNA sequencing of the PCR amplified ssrA gene from this strain demonstrated that it contained a probe target region identical to L. innocua. It should be noted however that the ssrA gene from this strain contains other regions where the sequence is identical to the previously characterised L. monocytogenes strain and that these sequences are different to the L. innocua sequence, as shown in FIG. 15. Therefore a species specific oligonucleotide directed to one of these variable regions can be synthesised which would recognise each strain type (isolate) within the species, for example L. monocytogenes.
Example 6
Multiple Colorimetric Probe Detection of Listeria ssrA Gene Sequences
[0113] LGTm (A), LStm (B) and a Campylobacter upsaliensis 16S-23S rRNA spacer (C-5' CATTAAACTTTAGCAAGGAAGTG 3') SEQ ID NO: 228 oligonucleotide probe were irreversibly bound to nylon membrane strips and hybridised to with amplified ssrA PCR product, using the genus specific primers Ltm1 and Ltm2 (Ltm1 was labelled with biotin at the 5' end), from L. monocytogenes (1-6), L. innocua (7-10), L. ivanovii (11), L. murrayi (12), L. seeligeri (13), L. welshmeri (14) and L. grayii (15). The ssrA amplified PCR products, using tmU5' and tmU3' (tmU5' was labelled with biotin at the 5' end), were also hybridised to the nylon membrane strips from the Gram-positive bacteria, B. subtilus, L. lactis, S. aureus, S. epidermis, E. faecalis, C. perfringins (16-21) and the Gram-negative bacteria E. coli, S. enteritidis, P. Rettgeri, K. aerogenes (22-25). As shown in FIG. 10 after hybridisation, development of the colorimetric assay to biotin revealed the following: Strips 1-6 demonstrates that the ssrA amplified PCR product originated from L. monocytogenes combined with the confirmation that the PCR product amplified is from the genus Listeria--A and B give colour detection; Strips 7-15 demonstrate that these PCR products originated from the genus Listeria--only A gives colour detection; and Strips 16-25 demonstrate that the PCR products are not from the genus Listeria--no colour detection. C is a negative oligonucleotide control probe and D is a positive control colorimetric detection assay for all samples.
Example 7
Use of ssrA/tmRNA Sequences to Distinguish Between Species of Organisms
[0114] Clustal W alignments as shown in FIGS. 11 (SEQ ID NOS. 19 and 21), 12 (SEQ ID NOS. 41 and 43), 13 (SEQ ID NOS. 77 and 79), 14 (SEQ ID NOS. 83 and 85), 15 and 16 (SEQ ID NO. 53, 55 and 57), indicate that there are nucleotide differences within the ssrA/tmRNA sequences of different strains of the same bacteria. This suggests that the ssrA/tmRNA sequences could potentially be used to discriminate between individual and/or groups of strains within a bacterial species. This may have useful applications in epidemiology and bacterial population analysis.
Example 8
tmRNA Integrity Analysis after Medium and Extreme Heat Treatment of Bacterial Cells
[0115] E. coli and L. monocytogenes cultures were heat treated at 80° C., for 20 min. in the case of E. coli and 40 min. in the case of L. monocytogenes and at 120° C. for 15 min. (autoclaving) after overnight growth and tested for viability at Oh, 1 h, 2 h, 6 h, 12 h, 24 h and 48 h after heat treatment. No viability was observed at each time period tested. Total RNA was also isolated at these time periods and electrophoresed on denaturing 1.2% agarose gels and Northern blotted. Each blot was hybridised to, in the case of E. coli (FIGS. 17 and 18) with a radioactively labelled oligonucleotide probe Evtm and in the case of L. monocytogenes (FIGS. 19 and 20) with a radiolabelled LVtm. No tmRNA transcript was detected with each sample tested, demonstrating that tmRNA transcript is degraded after heat treatment. The lanes represented with the notation +ve is a positive control total RNA sample.
Example 9
Use of the tmRNA Transcript in Distinguishing Between Viable and Non-Viable Bacteria
[0116] A 100 ml culture of L. monocytogenes was grown overnight in liquid culture. After growth, serial dilutions of the cells were carried out and viability was determined by spread plating on nutrient agar plates. Simultaneously, total RNA was isolated from a 1 ml aliquot of these cells. The remainder of the cells were heated at 65° C. for 20 min. Cells were then removed for both viability analysis and total RNA isolation. Samples were taken for viability and RNA isolation at time periods of 0 h, 2 h, 6 h and 24 h after treatment.
[0117] Spread plating on nutrient agar plates indicated that heat treatment killed L. monocytogenes cells, with no viable colony forming units observed. Each RNA sample isolated was then treated with DNase to remove any contaminating DNA and total RNA samples (100 ng) were subjected to Reverse Transcriptase-PCR amplification using the Listeria genus specific ssrA/tmRNA oligonucleotide primers Ltm1 and Ltm2. Negative control amplification reactions included primers, target, and Taq polymerase, but no Reverse Transcriptase. The results of the amplification reactions are shown in FIG. 12.
[0118] Amplified tmRNA RT-PCR products were only observed with the RNA sample which was not heat treated. All other samples gave no RT-PCR product indicating that the tmRNA molecules in these samples may have been degraded in the non-viable heat treated cells.
In FIG. 21 the lanes represent the following: Lane A: Molecular weight marker V; Lane 1: PCR amplification of RNA (no heat treatment of cells) [0119] -Reverse Transcriptase (RT), +Taq polymerase (TP); Lane 2: RT-PCR of RNA (no heat treatment of cells), +RT, +TP; Lane 3: PCR amplification of RNA (at 0 time after heat treatment), [0120] --RT, +TP; Lane 4: RT-PCR of RNA (at 0 time after heat treatment), +RT, +TP; Lane 5: PCR amplification of RNA (at 1 h time after heat treatment), [0121] -RT, +TP; Lane 6: RT-PCR of RNA (at 1 h time after heat treatment), [0122] +RT, +TP; Lane 7: PCR amplification of RNA (at 2 h time after heat treatment), [0123] -RT, +TP; Lane 8: RT-PCR of RNA (at 2 h time after heat treatment), [0124] +RT, +TP; Lane 9: PCR amplification of RNA (at 6 h time after heat treatment), [0125] -RT, +TP; Lane 10: RT-PCR of RNA (at 6 h time after heat treatment), [0126] +RT, +TP; Lane 11: PCR amplification of RNA (at 24 h time after heat treatment), [0127] -RT, +TP; Lane 12: RT-PCR of RNA (at 24 h time after heat treatment), [0128] +RT, +TP; Lane B: Molecular weight marker V.
Sequence CWU
1
2391366DNAActinobacillus actinomycetemcomitans 1ggggctgatt ctggattcga
cgggattagc gaagcccgaa gtgcacgtcg aggtgcggta 60ggcctcgtaa ataaaccgca
aaaaaatagt cgcaaacgac gaacaatacg ctttagcagc 120ttaataacct gcctttagcc
ttcgctcccc agcttccgct cgtaagacgg ggataaagcg 180gagtcaaacc aaaacgagat
cgtgtggaag ccaccgtttg aggatcgaag cattaaatta 240aatcaaagta gcttaattgt
cgcgtgtccg tcagcaggat taagtgaatt taaagaccgg 300actaaacgtg tagtgctaac
ggcagaggaa tttcggacgg gggttcaact ccccccagct 360ccacca
3662366RNAActinobacillus
actinomycetemcomitans 2ggggcugauu cuggauucga cgggauuagc gaagcccgaa
gugcacgucg aggugcggua 60ggccucguaa auaaaccgca aaaaaauagu cgcaaacgac
gaacaauacg cuuuagcagc 120uuaauaaccu gccuuuagcc uucgcucccc agcuuccgcu
cguaagacgg ggauaaagcg 180gagucaaacc aaaacgagau cguguggaag ccaccguuug
aggaucgaag cauuaaauua 240aaucaaagua gcuuaauugu cgcguguccg ucagcaggau
uaagugaauu uaaagaccgg 300acuaaacgug uagugcuaac ggcagaggaa uuucggacgg
ggguucaacu ccccccagcu 360ccacca
3663315DNAAeromonas salmonicida 3aagattcacg
aaacccaagg tgcatgccga ggtgcggtag gcctcgttaa caaaccgcaa 60aaaaatagtc
gcaaacgacg aaaactacgc actagcagct taataacctg catagagccc 120ttctacccta
gcttgcctgt gtcctaggga atcggaaggt catccttcac aggatcgtgt 180ggaagtcctg
ctcggggcgg aagcattaaa accaatcgag ctagtcaatt cgtggcgtgt 240ctctccgcag
cgggttggcg aatgtaaaga gtgactaagc atgtagtacc gaggatgtag 300taattttgga
cgggg
3154315RNAAeromonas salmonicida 4aagauucacg aaacccaagg ugcaugccga
ggugcgguag gccucguuaa caaaccgcaa 60aaaaauaguc gcaaacgacg aaaacuacgc
acuagcagcu uaauaaccug cauagagccc 120uucuacccua gcuugccugu guccuaggga
aucggaaggu cauccuucac aggaucgugu 180ggaaguccug cucggggcgg aagcauuaaa
accaaucgag cuagucaauu cguggcgugu 240cucuccgcag cggguuggcg aauguaaaga
gugacuaagc auguaguacc gaggauguag 300uaauuuugga cgggg
3155349DNAAlcaligenes eutrophus
5tgggccgacc tggtttcgac gtggttacaa agcagtgagg cataccgagg acccgtcacc
60tcgttaatca atggaatgca ataactgcta acgacgaacg ttacgcactc gcttaattgc
120ggccgtcctc gcactggctc gctgacgggc tagggtcgca agaccacgcg aggtatttac
180gtcagataag ctccggaagg gtcacgaagc cggggacgaa aacctagtga ctcgccgtcg
240tagagcgtgt tcgtccgatg cgccggttaa atcaaatgac agaactaagt atgtagaact
300ctctgtggag ggcttacgga cgcgggttcg attcccgccg gctccacca
3496349RNAAlcaligenes eutrophus 6ugggccgacc ugguuucgac gugguuacaa
agcagugagg cauaccgagg acccgucacc 60ucguuaauca auggaaugca auaacugcua
acgacgaacg uuacgcacuc gcuuaauugc 120ggccguccuc gcacuggcuc gcugacgggc
uagggucgca agaccacgcg agguauuuac 180gucagauaag cuccggaagg gucacgaagc
cggggacgaa aaccuaguga cucgccgucg 240uagagcgugu ucguccgaug cgccgguuaa
aucaaaugac agaacuaagu auguagaacu 300cucuguggag ggcuuacgga cgcggguucg
auucccgccg gcuccacca 3497347DNAAquifex aeolicus
7gggggcggaa aggattcgac ggggacaggc ggtccccgag gagcaggccg ggtggctccc
60gtaacagccg ctaaaacagc tcccgaagct gaactcgctc tcgctgccta attaaacggc
120agcgcgtccc cggtaggttt gcgggtggcc taccggaggg cgtcagagac acccgctcgg
180gctactcggt cgcacggggc tgagtagctg acacctaacc cgtgctaccc tcggggagct
240tgcccgtggg cgacccgagg ggaaatcctg aacacgggct aagcctgtag agcctcggat
300gtggccgccg tcctcggacg cgggttcgat tcccgccgcc tccacca
3478347RNAAquifex aeolicus 8gggggcggaa aggauucgac ggggacaggc gguccccgag
gagcaggccg gguggcuccc 60guaacagccg cuaaaacagc ucccgaagcu gaacucgcuc
ucgcugccua auuaaacggc 120agcgcguccc cgguagguuu gcggguggcc uaccggaggg
cgucagagac acccgcucgg 180gcuacucggu cgcacggggc ugaguagcug acaccuaacc
cgugcuaccc ucggggagcu 240ugcccguggg cgacccgagg ggaaauccug aacacgggcu
aagccuguag agccucggau 300guggccgccg uccucggacg cggguucgau ucccgccgcc
uccacca 3479316DNABacillus megaterium 9agggtagttc
gagcttaggt tgcgagtcga ggagatggcc tcgttaaaac atcaacgcca 60ataataactg
gcaaatctaa caataacttc gctttagctg cataatagta gcttagcgtt 120cctccctcca
tcgcccatgt ggtagggtaa gggactcact ttaagtgggc tacgccggag 180ttcgccgtct
gaggacgaag gaagagaata atcagactag cgactgggac gcctgttggt 240aggcagaaca
gctcgcgaat gatcaatatg ccaactacac tcgtagacgc ttaagtggcc 300atatttctgg
acgtgg
31610316RNABacillus megaterium 10aggguaguuc gagcuuaggu ugcgagucga
ggagauggcc ucguuaaaac aucaacgcca 60auaauaacug gcaaaucuaa caauaacuuc
gcuuuagcug cauaauagua gcuuagcguu 120ccucccucca ucgcccaugu gguaggguaa
gggacucacu uuaagugggc uacgccggag 180uucgccgucu gaggacgaag gaagagaaua
aucagacuag cgacugggac gccuguuggu 240aggcagaaca gcucgcgaau gaucaauaug
ccaacuacac ucguagacgc uuaaguggcc 300auauuucugg acgugg
31611363DNABacillus subtilis
11ggggacgtta cggattcgac agggatggat cgagcttgag ctgcgagccg agaggcgatc
60tcgtaaacac gcacttaaat ataactggca aaactaacag ttttaaccaa aacgtagcat
120tagctgccta ataagcgcag cgagctcttc ctgacattgc ctatgtgtct gtgaagagca
180catccaagta ggctacgctt gcgttcccgt ctgagaacgt aagaagagat gaacagacta
240gctctcggaa ggcccgcccg caggcaagaa gatgagtgaa accataaata tgcaggctac
300gctcgtagac gcttaagtaa tcgatgtttc tggacgtggg ttcgactccc accgtctcca
360cca
36312363RNABacillus subtilis 12ggggacguua cggauucgac agggauggau
cgagcuugag cugcgagccg agaggcgauc 60ucguaaacac gcacuuaaau auaacuggca
aaacuaacag uuuuaaccaa aacguagcau 120uagcugccua auaagcgcag cgagcucuuc
cugacauugc cuaugugucu gugaagagca 180cauccaagua ggcuacgcuu gcguucccgu
cugagaacgu aagaagagau gaacagacua 240gcucucggaa ggcccgcccg caggcaagaa
gaugagugaa accauaaaua ugcaggcuac 300gcucguagac gcuuaaguaa ucgauguuuc
uggacguggg uucgacuccc accgucucca 360cca
36313387DNABordetella pertussis
13ggggccgatc cggattcgac gtgggtcatg aaacagctca gggcatgccg agcaccagta
60agctcgttaa tccactggaa cactacaaac gccaacgacg agcgtctcgc tctcgccgct
120taagcggtga gccgctgcac tgatctgtcc ttgggtcagg cgggggaagg caacttcaca
180gggggcaacc ccgaaccgca gcagcgacat tcacaaggaa tcggccaccg ctggggtcac
240acggcgttgg tttaaattac gtgaatcgcc ctggtccggc ccgtcgatcg gctaagtcca
300gggttaaatc caaatagatc gactaagcat gtagaactgg ttgcggaggg cttgcggacg
360ggggttcaat tccccccggc tccacca
38714387RNABordetella pertussis 14ggggccgauc cggauucgac gugggucaug
aaacagcuca gggcaugccg agcaccagua 60agcucguuaa uccacuggaa cacuacaaac
gccaacgacg agcgucucgc ucucgccgcu 120uaagcgguga gccgcugcac ugaucugucc
uugggucagg cgggggaagg caacuucaca 180gggggcaacc ccgaaccgca gcagcgacau
ucacaaggaa ucggccaccg cuggggucac 240acggcguugg uuuaaauuac gugaaucgcc
cugguccggc ccgucgaucg gcuaagucca 300ggguuaaauc caaauagauc gacuaagcau
guagaacugg uugcggaggg cuugcggacg 360gggguucaau uccccccggc uccacca
38715362DNABorrelia burgdorferi
15ggggatgttt tggatttgac tgaaaatgtt aatattgtaa gttgcaggca gagggaatct
60cttaaaactt ctaaaataaa tgcaaaaaat aataacttta caagctcaaa tcttgtaatg
120gctgcttaag ttagcagagg gttttgttga atttggcttt gaggttcact tatactcttt
180tcgacatcaa agcttgctta aaaatgtttt caagttgatt tttagggact tttatacttg
240agagcaattt ggtggtttgc tagtatttcc aaaccatatt gcttaataaa atactagata
300agcttgtaga agcttatagt attattttta ggacgcgggt tcaattcccg ccatctccac
360ca
36216362RNABorrelia burgdorferi 16ggggauguuu uggauuugac ugaaaauguu
aauauuguaa guugcaggca gagggaaucu 60cuuaaaacuu cuaaaauaaa ugcaaaaaau
aauaacuuua caagcucaaa ucuuguaaug 120gcugcuuaag uuagcagagg guuuuguuga
auuuggcuuu gagguucacu uauacucuuu 180ucgacaucaa agcuugcuua aaaauguuuu
caaguugauu uuuagggacu uuuauacuug 240agagcaauuu ggugguuugc uaguauuucc
aaaccauauu gcuuaauaaa auacuagaua 300agcuuguaga agcuuauagu auuauuuuua
ggacgcgggu ucaauucccg ccaucuccac 360ca
36217359DNACampylobacter jejuni
17gggagcgact tggcttcgac aggagtaagt ctgcttagat ggcatgtcgc tttgggcaaa
60gcgtaaaaag cccaaataaa attaaacgca aacaacgtta aattcgctcc tgcttacgct
120aaagctgcgt aagttcagtt gagcctgaaa tttaagtcat actatctagc ttaattttcg
180gtcatttttg atagtgtagc cttgcgtttg acaagcgttg aggtgaaata aagtcttagc
240cttgcttttg agttttggaa gatgagcgaa gtagggtgaa gtagtcatct ttgctaagca
300tgtagaggtc tttgtgggat tatttttgga caggggttcg attcccctcg cttccacca
35918359RNACampylobacter jejuni 18gggagcgacu uggcuucgac aggaguaagu
cugcuuagau ggcaugucgc uuugggcaaa 60gcguaaaaag cccaaauaaa auuaaacgca
aacaacguua aauucgcucc ugcuuacgcu 120aaagcugcgu aaguucaguu gagccugaaa
uuuaagucau acuaucuagc uuaauuuucg 180gucauuuuug auaguguagc cuugcguuug
acaagcguug aggugaaaua aagucuuagc 240cuugcuuuug aguuuuggaa gaugagcgaa
guagggugaa guagucaucu uugcuaagca 300uguagagguc uuugugggau uauuuuugga
cagggguucg auuccccucg cuuccacca 35919420DNAChlamydia trachomatis
(D/UW-3/CX) 19gggggtgtaa aggtttcgac ttagaaatga agcgttaatt gcatgcggag
ggcgttggct 60ggcctcctaa aaagccgaca aaacaataaa tgccgaacct aaggctgaat
gcgaaattat 120cagcttcgct gatctcgaag atctaagagt agctgcttaa ttagcaaagt
tgttacctaa 180atacgggtga cccggtgttc gcgagctcca ccagaggttt tcgaaacacc
gtcatgtatc 240tggttagaac ttaggtcctt taattctcga ggaaatgagt ttgaaattta
atgagagtcg 300ttagtctcta taggggtttc tagctgagga gacataacgt atagtaccta
ggaactaagc 360atgtagaggt tagcggggag tttactaagg acgagagttc gactctctcc
acctccacca 42020420RNAChlamydia trachomatis (D/UW-3/CX) 20ggggguguaa
agguuucgac uuagaaauga agcguuaauu gcaugcggag ggcguuggcu 60ggccuccuaa
aaagccgaca aaacaauaaa ugccgaaccu aaggcugaau gcgaaauuau 120cagcuucgcu
gaucucgaag aucuaagagu agcugcuuaa uuagcaaagu uguuaccuaa 180auacggguga
cccgguguuc gcgagcucca ccagagguuu ucgaaacacc gucauguauc 240ugguuagaac
uuagguccuu uaauucucga ggaaaugagu uugaaauuua augagagucg 300uuagucucua
uagggguuuc uagcugagga gacauaacgu auaguaccua ggaacuaagc 360auguagaggu
uagcggggag uuuacuaagg acgagaguuc gacucucucc accuccacca
42021421DNAChlamydia trachomatis (mouse pneumonitis) 21gggggtgtaa
aggtttcgac ttagaaatga agcgttaatt gcatgcggag ggcgttggct 60ggcctcctaa
aaagccgaca aaacaataaa tgccgaacct aaggctgaat gcgaaattat 120cagcttcgct
gatcttaatg atctaagagt tgctgcttaa ttagcaaagt tgttacctaa 180gtactggtaa
cccggtgttc gcgagctcca ccagaggttt tcgaaacgcc gtcatttatc 240tggttagaat
tagggccttt taactctcaa gggaactaat ttgaatttta atgagagtcg 300ttggtctcta
tagaggtttc tagctgagga gatataacgt aaaatattct agaaactaag 360catgtagagg
ttagcgggga gtttactaag gacgagagtt cgaatctctc cacctccacc 420a
42122421RNAChlamydia trachomatis (mouse pneumonitis) 22ggggguguaa
agguuucgac uuagaaauga agcguuaauu gcaugcggag ggcguuggcu 60ggccuccuaa
aaagccgaca aaacaauaaa ugccgaaccu aaggcugaau gcgaaauuau 120cagcuucgcu
gaucuuaaug aucuaagagu ugcugcuuaa uuagcaaagu uguuaccuaa 180guacugguaa
cccgguguuc gcgagcucca ccagagguuu ucgaaacgcc gucauuuauc 240ugguuagaau
uagggccuuu uaacucucaa gggaacuaau uugaauuuua augagagucg 300uuggucucua
uagagguuuc uagcugagga gauauaacgu aaaauauucu agaaacuaag 360cauguagagg
uuagcgggga guuuacuaag gacgagaguu cgaaucucuc caccuccacc 420a
42123404DNAChlorobium tepidum 23ggggatgaca ggctatcgac aggataggtg
tgagatgtcg ttgcactccg agtttcagca 60tggacggact cgttaaacaa gtctatgtac
caatagatgc agacgattat tcgtatgcaa 120tggctgcctg attagcacaa gttaattcag
aagccatcgt cctgcggtga atgcgcttac 180tctgaagccg ccggatggca taacccgcgc
ttgagcctac gggttcgcgc aagtaagctc 240cgtacattca tgcccgaggg ggtgtgcggg
taaccaatcg ggataagggg acgaacgctg 300ctggcggtgt aatcggacca cgaaaaacca
accaccagag atgagtgtgg taactgcatc 360gagcagtgtc ctggacgcgg gttcaagtcc
cgccatctcc acca 40424404RNAChlorobium tepidum
24ggggaugaca ggcuaucgac aggauaggug ugagaugucg uugcacuccg aguuucagca
60uggacggacu cguuaaacaa gucuauguac caauagaugc agacgauuau ucguaugcaa
120uggcugccug auuagcacaa guuaauucag aagccaucgu ccugcgguga augcgcuuac
180ucugaagccg ccggauggca uaacccgcgc uugagccuac ggguucgcgc aaguaagcuc
240cguacauuca ugcccgaggg ggugugcggg uaaccaaucg ggauaagggg acgaacgcug
300cuggcggugu aaucggacca cgaaaaacca accaccagag augagugugg uaacugcauc
360gagcaguguc cuggacgcgg guucaagucc cgccaucucc acca
40425294DNACyanophora paradoxa (alga) cyanelle 25ggggctgttt aggtttcgac
gtttttttct aattatgttt gttaagcaag tcgaggattt 60gttctatctc gaaaatcaag
aactctcaaa atttaaacgc aactaatatt gtacgtttta 120accgtaaagc agctttcgct
gtttaataat tacttttaat ttaaaaacct aattttttta 180ggaatttatt tatttattgt
ttatcctgct taatgaatta aaaaaagcta tacttgtgaa 240taaacgcata atttaaaaaa
acggacgtgg gttcaaatcc caccagctcc acca 29426294RNACyanophora
paradoxa (alga) cyanelle 26ggggcuguuu agguuucgac guuuuuuucu aauuauguuu
guuaagcaag ucgaggauuu 60guucuaucuc gaaaaucaag aacucucaaa auuuaaacgc
aacuaauauu guacguuuua 120accguaaagc agcuuucgcu guuuaauaau uacuuuuaau
uuaaaaaccu aauuuuuuua 180ggaauuuauu uauuuauugu uuauccugcu uaaugaauua
aaaaaagcua uacuugugaa 240uaaacgcaua auuuaaaaaa acggacgugg guucaaaucc
caccagcucc acca 29427189DNAClostridium acetobutylicum
27aatctggcgt cgagagcggg gaaacgagcc ttacaaagct ttgagtaagg aacggaattt
60atgaagctac tgaagtgaaa agcttgtttg taggcgtttc atggagggaa tgttaaaata
120caaactgcac tcggagatgc ttaatgaaac cattttcgga caggggttcg attcccctcg
180cctccacca
18928189RNAClostridium acetobutylicum 28aaucuggcgu cgagagcggg gaaacgagcc
uuacaaagcu uugaguaagg aacggaauuu 60augaagcuac ugaagugaaa agcuuguuug
uaggcguuuc auggagggaa uguuaaaaua 120caaacugcac ucggagaugc uuaaugaaac
cauuuucgga cagggguucg auuccccucg 180ccuccacca
18929349DNADeinococcus radiodurans
29gggggtgacc cggtttcgac aggggaactg aaggtgatgt tgcgtgtcga ggtgccgttg
60gcctcgtaaa caaacggcaa agccatttaa ctggcaacca gaactacgct ctcgctgctt
120aagtgagatg acgaccgtgc agcccggcct ttggcgtcgc ggaagtcact aaaaaagaag
180gctagcccag gcgattctcc atagccgacg gcgaaacttt atggagctac ggcctgcgag
240aacctgccca ctggtgagcg ccggcccgac aatcaaacag tgggatacac acgtagacgc
300acgctggacg gacctttgga cggcggttcg actccgccca cctccacca
34930349RNADeinococcus radiodurans 30gggggugacc cgguuucgac aggggaacug
aaggugaugu ugcgugucga ggugccguug 60gccucguaaa caaacggcaa agccauuuaa
cuggcaacca gaacuacgcu cucgcugcuu 120aagugagaug acgaccgugc agcccggccu
uuggcgucgc ggaagucacu aaaaaagaag 180gcuagcccag gcgauucucc auagccgacg
gcgaaacuuu auggagcuac ggccugcgag 240aaccugccca cuggugagcg ccggcccgac
aaucaaacag ugggauacac acguagacgc 300acgcuggacg gaccuuugga cggcgguucg
acuccgccca ccuccacca 34931330DNADesulfovibrio
desulfuricans 31gggactggaa ccgtagcggc aggtcgaggc gccgctggcc tcgtaaaaag
cggcacaaaa 60gtaattgcca acaacgatta cgactacgct tacgctgcct aataacagcg
aggcaatgac 120cgtttaacgg tcgcgccgat cagggccatg cctgataacc ctgattggcg
acacttatca 180ggctggcgaa aaccggctct cgccggggtt tttcgcgagg agtttaccgg
cgggattgct 240gcgttgtgcc tggtcagggg ccaacagcgc ggtgaaatac atacttgacc
taaacctgta 300atgcttcgtg tggaatgttc tcggacgggg
33032330RNADesulfovibrio desulfuricans 32gggacuggaa
ccguagcggc aggucgaggc gccgcuggcc ucguaaaaag cggcacaaaa 60guaauugcca
acaacgauua cgacuacgcu uacgcugccu aauaacagcg aggcaaugac 120cguuuaacgg
ucgcgccgau cagggccaug ccugauaacc cugauuggcg acacuuauca 180ggcuggcgaa
aaccggcucu cgccgggguu uuucgcgagg aguuuaccgg cgggauugcu 240gcguugugcc
uggucagggg ccaacagcgc ggugaaauac auacuugacc uaaaccugua 300augcuucgug
uggaauguuc ucggacgggg
33033318DNADichelobacter nodosus 33ctcgaggtgc atgtcgagaa tgagagaatc
tcgttaaata ctttcaaaac ttatagttgc 60aaacgacgac aactacgctt tagcggctta
attcccgctt tcgcttacct agatttgtct 120gtgggtttac cgtaagcgac attaacacag
aatcgctggt taacgcgtcc gctgttaatc 180ggttaaatta agcggaatcg cttgtaaaat
gcctgagcgt tggctgttta tgagttaaac 240ctaattaact gctctaaaca tgtagtacca
aaagttaagg attcgcggac gggggttcaa 300atccccccgc ctccacca
31834318RNADichelobacter nodosus
34cucgaggugc augucgagaa ugagagaauc ucguuaaaua cuuucaaaac uuauaguugc
60aaacgacgac aacuacgcuu uagcggcuua auucccgcuu ucgcuuaccu agauuugucu
120guggguuuac cguaagcgac auuaacacag aaucgcuggu uaacgcgucc gcuguuaauc
180gguuaaauua agcggaaucg cuuguaaaau gccugagcgu uggcuguuua ugaguuaaac
240cuaauuaacu gcucuaaaca uguaguacca aaaguuaagg auucgcggac ggggguucaa
300auccccccgc cuccacca
31835367DNAEnterococcus faecalis 35gggggcgtta cggattcgac aggcatagtt
gagcttgaat tgcgtttcgt aggttacggc 60tacgttaaaa cgttacagtt aaatataact
gctaaaaacg aaaacaattc tttcgcttta 120gctgcctaaa aaccagctag cgaagatcct
cccggcatcg cccatgtgct cgggtcaggg 180tcctaatcga agtgggatac gctaaatttt
tccgtctgta aaatttagag gagcttacca 240gactagcaat acagaatgcc tgtcactcgg
cacgctgtaa agcgaacctt taaatgagtg 300tctatgaacg tagagattta agtggcaata
tgtttggacg cgggttcgac tcccgccgtc 360tccacca
36736367RNAEnterococcus faecalis
36gggggcguua cggauucgac aggcauaguu gagcuugaau ugcguuucgu agguuacggc
60uacguuaaaa cguuacaguu aaauauaacu gcuaaaaacg aaaacaauuc uuucgcuuua
120gcugccuaaa aaccagcuag cgaagauccu cccggcaucg cccaugugcu cgggucaggg
180uccuaaucga agugggauac gcuaaauuuu uccgucugua aaauuuagag gagcuuacca
240gacuagcaau acagaaugcc ugucacucgg cacgcuguaa agcgaaccuu uaaaugagug
300ucuaugaacg uagagauuua aguggcaaua uguuuggacg cggguucgac ucccgccguc
360uccacca
36737363DNAEscherichia coli 37ggggctgatt ctggattcga cgggatttgc gaaacccaag
gtgcatgccg aggggcggtt 60ggcctcgtaa aaagccgcaa aaaatagtcg caaacgacga
aaactacgct ttagcagctt 120aataacctgc ttagagccct ctctccctag cctccgctct
taggacgggg atcaagagag 180gtcaaaccca aaagagatcg cgtggaagcc ctgcctgggg
ttgaagcgtt aaaacttaat 240caggctagtt tgttagtggc gtgtccgtcc gcagctggca
agcgaatgta aagactgact 300aagcatgtag taccgaggat gtaggaattt cggacgcggg
ttcaactccc gccagctcca 360cca
36338363RNAEscherichia coli 38ggggcugauu
cuggauucga cgggauuugc gaaacccaag gugcaugccg aggggcgguu 60ggccucguaa
aaagccgcaa aaaauagucg caaacgacga aaacuacgcu uuagcagcuu 120aauaaccugc
uuagagcccu cucucccuag ccuccgcucu uaggacgggg aucaagagag 180gucaaaccca
aaagagaucg cguggaagcc cugccugggg uugaagcguu aaaacuuaau 240caggcuaguu
uguuaguggc guguccgucc gcagcuggca agcgaaugua aagacugacu 300aagcauguag
uaccgaggau guaggaauuu cggacgcggg uucaacuccc gccagcucca 360cca
36339366DNAHaemophilus influenzae 39ggggctgatt ctggattcga cgggattagc
gaagcccaag gtgcacgtcg aggtgcggta 60ggcctcgtaa ataaaccgca aaaaaatagt
cgcaaacgac gaacaatacg ctttagcagc 120ttaataacct gcatttagcc ttcgcgctcc
agcttccgct cgtaagacgg ggataacgcg 180gagtcaaacc aaaacgagat cgtgtggaag
ccaccgtttg aggatcgaag cactaaattg 240aatcaaacta gcttaagttt agcgtgtctg
tccgcatgct taagtgaaat taaagacgag 300actaaacgtg tagtactgaa ggtagagtaa
tttcggacgg gggttcaact ccccccagct 360ccacca
36640366RNAHaemophilus influenzae
40ggggcugauu cuggauucga cgggauuagc gaagcccaag gugcacgucg aggugcggua
60ggccucguaa auaaaccgca aaaaaauagu cgcaaacgac gaacaauacg cuuuagcagc
120uuaauaaccu gcauuuagcc uucgcgcucc agcuuccgcu cguaagacgg ggauaacgcg
180gagucaaacc aaaacgagau cguguggaag ccaccguuug aggaucgaag cacuaaauug
240aaucaaacua gcuuaaguuu agcgugucug uccgcaugcu uaagugaaau uaaagacgag
300acuaaacgug uaguacugaa gguagaguaa uuucggacgg ggguucaacu ccccccagcu
360ccacca
36641340DNAHelicobacter pylori (ATC 43504) 41agatttcttg tcgcgcagat
agcatgccaa gcgctgcttg taaaacagca acaaaaataa 60ctgtaaacaa cacagattac
gctccagctt acgctaaagc tgcgtgagtt aatctccttt 120tggagctgga ctgattagaa
tttctagcgt tttaatcgct ccataacctt aagctagacg 180cttttaaaag gtggttcgcc
ttttaaacta agaaacaaga actcttgaaa ctatcttaag 240gttttagaaa gttggaccag
agctagtttt aaggctaaaa actaaccaat tttctaagca 300ttgtagaagt ttgtgtttag
ggcaagattt ttggactggg 34042340RNAHelicobacter
pylori (ATC 43504) 42agauuucuug ucgcgcagau agcaugccaa gcgcugcuug
uaaaacagca acaaaaauaa 60cuguaaacaa cacagauuac gcuccagcuu acgcuaaagc
ugcgugaguu aaucuccuuu 120uggagcugga cugauuagaa uuucuagcgu uuuaaucgcu
ccauaaccuu aagcuagacg 180cuuuuaaaag gugguucgcc uuuuaaacua agaaacaaga
acucuugaaa cuaucuuaag 240guuuuagaaa guuggaccag agcuaguuuu aaggcuaaaa
acuaaccaau uuucuaagca 300uuguagaagu uuguguuuag ggcaagauuu uuggacuggg
34043386DNAHelicobacter pylori (strain 26695)
43ggggctgact tggatttcga cagatttctt gtcgcacaga tagcatgcca agcgctgctt
60gtaaaacagc aacaaaaata actgtaaaca acacagatta cgctccagct tacgctaaag
120ctgcgtgagt taatctcctt ttggagctgg actgattaga atttctagcg ttttaatcgc
180tccataacct taagctagac gcttttaaaa ggtggttcgc cttttaaact aagaaacaag
240aactcttgaa actatctcaa ggttttagaa agttggacca gagctagttt taaggctaaa
300aaaccaacca attttctaag cattgtagaa gtttgtgttt agggcaagat ttttggactg
360gggttcgatt ccccacagct ccacca
38644386RNAHelicobacter pylori (strain 26695) 44ggggcugacu uggauuucga
cagauuucuu gucgcacaga uagcaugcca agcgcugcuu 60guaaaacagc aacaaaaaua
acuguaaaca acacagauua cgcuccagcu uacgcuaaag 120cugcgugagu uaaucuccuu
uuggagcugg acugauuaga auuucuagcg uuuuaaucgc 180uccauaaccu uaagcuagac
gcuuuuaaaa ggugguucgc cuuuuaaacu aagaaacaag 240aacucuugaa acuaucucaa
gguuuuagaa aguuggacca gagcuaguuu uaaggcuaaa 300aaaccaacca auuuucuaag
cauuguagaa guuuguguuu agggcaagau uuuuggacug 360ggguucgauu ccccacagcu
ccacca 38645312DNAKlebsiella
aerogenes (NCTC 9528) 45gggattcgcg aaacccaagg tgcatgccga ggggcggttg
gcctcgtaaa aagccgcaaa 60aaaatagtcg caaacgacga aaactacgct ttagcagctt
aataacctgc taagagccct 120ctctccctag cttccgctcc taagacgggg aataaagaga
ggtcaaaccc aaaagagatc 180gcgtggaagc cctgcctggg gttgaagcgt taaaactaat
caggctagtt tgtcagtggc 240gtgtccgtcc gcagctggcc agcgaatgta aagactggac
taagcatgta gtgccgagga 300tgtaggaatt tc
31246312RNAKlebsiella aerogenes (NCTC 9528)
46gggauucgcg aaacccaagg ugcaugccga ggggcgguug gccucguaaa aagccgcaaa
60aaaauagucg caaacgacga aaacuacgcu uuagcagcuu aauaaccugc uaagagcccu
120cucucccuag cuuccgcucc uaagacgggg aauaaagaga ggucaaaccc aaaagagauc
180gcguggaagc ccugccuggg guugaagcgu uaaaacuaau caggcuaguu ugucaguggc
240guguccgucc gcagcuggcc agcgaaugua aagacuggac uaagcaugua gugccgagga
300uguaggaauu uc
31247316DNALactobacillus lactis (NCTC 662) 47aagcacagtt cgagcttgaa
ttgcgtttcg taggttacgt ctacgttaaa acgttacagt 60taaatataac tgctaaaaac
gaaaacaact cttacgcttt agctgcctaa aaacagttag 120cgtagatcct ctcggcatcg
cccatgtgct cgagtaaggg tctcaaattt agtgggatac 180gttaaacttt tccgtctgta
aagtttaaaa gagatcatca gactagcgat acagaatgcc 240tgtcactcgg caagctgtaa
agcgaaacct caaatgagtt gactatgaac gtagattttt 300aagtgtcgat gtgttt
31648316RNALactobacillus
lactis (NCTC 662) 48aagcacaguu cgagcuugaa uugcguuucg uagguuacgu
cuacguuaaa acguuacagu 60uaaauauaac ugcuaaaaac gaaaacaacu cuuacgcuuu
agcugccuaa aaacaguuag 120cguagauccu cucggcaucg cccaugugcu cgaguaaggg
ucucaaauuu agugggauac 180guuaaacuuu uccgucugua aaguuuaaaa gagaucauca
gacuagcgau acagaaugcc 240ugucacucgg caagcuguaa agcgaaaccu caaaugaguu
gacuaugaac guagauuuuu 300aagugucgau guguuu
31649362DNALegionella pneumophila 49gtgggttgca
aaaccggaag tgcatgccga gaaggagatc tctcgtaaat aagactcaat 60taaatataaa
tgcaaacgat gaaaactttg ctggtgggga agctatcgct gcctaataag 120cactttagtt
aaaccatcac tgtgtactgg ccaataaacc cagtatcccg ttcgaccgag 180cccgcttatc
ggtatcgaat caacggtcat aagagataag ctagcgtcct aatctatccc 240gggttatggc
gcgaaactca gggaatcgct gtgtatcatc ctgcccgtcg gaggagccac 300agttaaattc
aaaagacaag gctatgcatg tagagctaaa ggcagaggac ttgcggacgc 360gg
36250362RNALegionella pneumophila 50guggguugca aaaccggaag ugcaugccga
gaaggagauc ucucguaaau aagacucaau 60uaaauauaaa ugcaaacgau gaaaacuuug
cuggugggga agcuaucgcu gccuaauaag 120cacuuuaguu aaaccaucac uguguacugg
ccaauaaacc caguaucccg uucgaccgag 180cccgcuuauc gguaucgaau caacggucau
aagagauaag cuagcguccu aaucuauccc 240ggguuauggc gcgaaacuca gggaaucgcu
guguaucauc cugcccgucg gaggagccac 300aguuaaauuc aaaagacaag gcuaugcaug
uagagcuaaa ggcagaggac uugcggacgc 360gg
36251322DNAListeria grayi 51acagggatag
gtcgagcttg agttgcgagc cggggggatc ggcccgtcat caacgtcaaa 60gccaataata
actggcaaac aaaacaacaa tttagctttc gctgcctaat agcagtctga 120atagctgatc
ctccgtgcat cacccatgtg ctacggtaag ggtctcactt ttaagtgggt 180tacgctggct
tatctccgtc tggggcaaac gagaagagca taatcagact agctagatag 240agccctgacg
ccgggcagac atctatgcga aatccaaata cggcaactac gctcgtagat 300gctcaagtgc
cgatatttct gg
32252322RNAListeria grayi 52acagggauag gucgagcuug aguugcgagc cggggggauc
ggcccgucau caacgucaaa 60gccaauaaua acuggcaaac aaaacaacaa uuuagcuuuc
gcugccuaau agcagucuga 120auagcugauc cuccgugcau cacccaugug cuacgguaag
ggucucacuu uuaagugggu 180uacgcuggcu uaucuccguc uggggcaaac gagaagagca
uaaucagacu agcuagauag 240agcccugacg ccgggcagac aucuaugcga aauccaaaua
cggcaacuac gcucguagau 300gcucaagugc cgauauuucu gg
32253322DNAListeria innocua 53acagggatag
ttcgagcttg agttgcgagt cggggggatc gtcctcgtta tcaacgtcaa 60agccaataat
aactggcaaa gaaaaacaaa acctagcttt cgctgcctaa taagcagtag 120catagctgat
cctccgtgca tcgcccatgt gctacggtaa gggtctcact ctaagtgggc 180tacactagtt
aatctccgtc tgaggttaaa tagaagagct taatcagact agctgaatgg 240aagcctgtta
ccgggctgat gtttatgcga aatgctaata cggtgactac gctcgtagat 300attcaagtgc
cgatatttct gg
32254322RNAListeria innocua 54acagggauag uucgagcuug aguugcgagu cggggggauc
guccucguua ucaacgucaa 60agccaauaau aacuggcaaa gaaaaacaaa accuagcuuu
cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca ucgcccaugu gcuacgguaa
gggucucacu cuaagugggc 180uacacuaguu aaucuccguc ugagguuaaa uagaagagcu
uaaucagacu agcugaaugg 240aagccuguua ccgggcugau guuuaugcga aaugcuaaua
cggugacuac gcucguagau 300auucaagugc cgauauuucu gg
32255322DNAListeria monocytogenes (NCTC 7973)
55acagggatag ttcgagcttg agttgcgagt cggggggatc gtcctcgtta tcaacgtcaa
60agccaataat aactggcaaa gaaaaacaaa acctagcttt cgctgcctaa taagcagtag
120catagctgat cctccgtgca tcgcccatgt gctacggtaa gggtctcact ctaagtgggc
180tacactagtt aatctccgtc tggggttaaa tagaagagct taatcagact agctgaatgg
240aagcctgtta ccgggccgat gtttatgcga aatgctaata cggtgactac gctcgtagat
300atttaagtgc cgatatttct gg
32256322RNAListeria monocytogenes (NCTC 7973) 56acagggauag uucgagcuug
aguugcgagu cggggggauc guccucguua ucaacgucaa 60agccaauaau aacuggcaaa
gaaaaacaaa accuagcuuu cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca
ucgcccaugu gcuacgguaa gggucucacu cuaagugggc 180uacacuaguu aaucuccguc
ugggguuaaa uagaagagcu uaaucagacu agcugaaugg 240aagccuguua ccgggccgau
guuuaugcga aaugcuaaua cggugacuac gcucguagau 300auuuaagugc cgauauuucu
gg 32257247DNAListeria
monocytogenes (NCTC 11994) 57caaagccaat aataactggc aaagaaaaac aaaacctagc
tttcgctgcc taataagcag 60tagcatagct gatcctccgt gcatcgccca tgtgctacgg
taagggtctc actctaagtg 120ggctacacta gttaatctcc gtctggggtt aaatagaaga
gcttaatcag actagctgaa 180tggaagcctg ttaccgggcc gatgtttatg cgaaatgcta
atacggtgac tacgctcgta 240gatattt
24758247RNAListeria monocytogenes (NCTC 11994)
58caaagccaau aauaacuggc aaagaaaaac aaaaccuagc uuucgcugcc uaauaagcag
60uagcauagcu gauccuccgu gcaucgccca ugugcuacgg uaagggucuc acucuaagug
120ggcuacacua guuaaucucc gucugggguu aaauagaaga gcuuaaucag acuagcugaa
180uggaagccug uuaccgggcc gauguuuaug cgaaaugcua auacggugac uacgcucgua
240gauauuu
24759322DNAListeria murrayi 59acagggatag ttcgagcttg agttgcgagt cggggggatc
gtcctcgtta tcaacgtcaa 60agccaataat aactggcaaa gaaaaacaaa acctagcttt
cgctgcctaa taagcagtag 120catagctgat cctccgtgca tcgcccatgt gctacggtaa
gggtctcact ctaagtgggc 180tacactagtt aatctccgtc tgaggttaaa tagaagagct
taatgagact agctgaatgg 240aagcctgtta ccgggctgat gtttatgcga aatgctaata
cggtgactac gctcgtagat 300attcaagtgc cgatatttct gg
32260322RNAListeria murrayi 60acagggauag
uucgagcuug aguugcgagu cggggggauc guccucguua ucaacgucaa 60agccaauaau
aacuggcaaa gaaaaacaaa accuagcuuu cgcugccuaa uaagcaguag 120cauagcugau
ccuccgugca ucgcccaugu gcuacgguaa gggucucacu cuaagugggc 180uacacuaguu
aaucuccguc ugagguuaaa uagaagagcu uaaugagacu agcugaaugg 240aagccuguua
ccgggcugau guuuaugcga aaugcuaaua cggugacuac gcucguagau 300auucaagugc
cgauauuucu gg
32261322DNAListeria welshimeri 61acagggatag ttcgagcttg agttgcgagt
cggggggatc gtcctcgtta tcaacgtcaa 60agccaataat aactggcaaa gaaaaacaaa
acctagcttt cgctgcctaa taagcagtag 120catagctgat cctccgtgca tcgcccatgt
gctacggtaa gggtctcact ctaagtgggc 180tacactggct aatctccgtc tgaggttagt
tggaagagct taatcagact agctgaatgg 240aagcctgtta ccgggccgat gtttatgcga
aatgctaata cggtgactac gctcgtagat 300atttaagtgc cgatatttct gg
32262322RNAListeria welshimeri
62acagggauag uucgagcuug aguugcgagu cggggggauc guccucguua ucaacgucaa
60agccaauaau aacuggcaaa gaaaaacaaa accuagcuuu cgcugccuaa uaagcaguag
120cauagcugau ccuccgugca ucgcccaugu gcuacgguaa gggucucacu cuaagugggc
180uacacuggcu aaucuccguc ugagguuagu uggaagagcu uaaucagacu agcugaaugg
240aagccuguua ccgggccgau guuuaugcga aaugcuaaua cggugacuac gcucguagau
300auuuaagugc cgauauuucu gg
32263322DNAMarinobacter hydrocarbonoclasticus 63gccggtgacg aacccttggg
tgcatgccga gatggcagcg aatctcgtaa atccaaagct 60gcaacgtaat agtcgcaaac
gacgaaaact acgcactggc ggcgtaagcc gttccagtcg 120tcctggctga ggcgcctata
actcagtagc aacatcccag gacgtcatcg cttataggct 180gctccgttca ccagagctca
ctggtgttcg gctaagatta aagagctcgc ctcttgcacc 240ctgaccttcg ggtcgcttga
ggttaaatca atagaaggac actaagcatg tagacctcaa 300ggcctagtgc tggcggacgc
gg 32264322RNAMarinobacter
hydrocarbonoclasticus 64gccggugacg aacccuuggg ugcaugccga gauggcagcg
aaucucguaa auccaaagcu 60gcaacguaau agucgcaaac gacgaaaacu acgcacuggc
ggcguaagcc guuccagucg 120uccuggcuga ggcgccuaua acucaguagc aacaucccag
gacgucaucg cuuauaggcu 180gcuccguuca ccagagcuca cugguguucg gcuaagauua
aagagcucgc cucuugcacc 240cugaccuucg ggucgcuuga gguuaaauca auagaaggac
acuaagcaug uagaccucaa 300ggccuagugc uggcggacgc gg
32265338DNAMycobacterium avium 65ttcgcgcatc
gaatcaaggg aagcgtgccg gtgcaggcaa ctgaccaccg taagcgtcgt 60tgcaaataga
taagcgccga ttcacatcag cgcgacttac ctctcgctgc ctaagcgaca 120gctagtccgt
cagcccggga acgccctcga cccggagcct ggcgtcagct agagggatcc 180accgatgagt
tcggtcgcgg gactcatcgg gacaccaaca gcgactggga tcgtcatcct 240ggcttgttcg
cgtgaccagg agatccgagt agaggcatag cgaactgcgc acggagaagc 300cttgagggaa
tgccgtagaa cccgggttcg attcccaa
33866338RNAMycobacterium avium 66uucgcgcauc gaaucaaggg aagcgugccg
gugcaggcaa cugaccaccg uaagcgucgu 60ugcaaauaga uaagcgccga uucacaucag
cgcgacuuac cucucgcugc cuaagcgaca 120gcuaguccgu cagcccggga acgcccucga
cccggagccu ggcgucagcu agagggaucc 180accgaugagu ucggucgcgg gacucaucgg
gacaccaaca gcgacuggga ucgucauccu 240ggcuuguucg cgugaccagg agauccgagu
agaggcauag cgaacugcgc acggagaagc 300cuugagggaa ugccguagaa cccggguucg
auucccaa 33867318DNAMycobacterium bovis
67ttcgcgcatc gaatcaaggg aagcgtgccg gtgcaggcaa gagaccaccg taagcgtcgt
60tgcgaccaaa taagcgccga ttcacatcag cgcgactacg tctcgctgcc taagcgacgg
120ctagtctgtc agaccgggaa cgccctcggc ccggaccctg gcatcagcta gagggatcca
180ccgatgagtc cggtcgcggg actcctcggg acaaccacag cgactgggat cgtcatctcg
240gctagttcgc gtgaccggga gatccgagca gaggcatagc gaactgcgca cggagaagcc
300ttgagggaat gccgtagg
31868318RNAMycobacterium bovis 68uucgcgcauc gaaucaaggg aagcgugccg
gugcaggcaa gagaccaccg uaagcgucgu 60ugcgaccaaa uaagcgccga uucacaucag
cgcgacuacg ucucgcugcc uaagcgacgg 120cuagucuguc agaccgggaa cgcccucggc
ccggacccug gcaucagcua gagggaucca 180ccgaugaguc cggucgcggg acuccucggg
acaaccacag cgacugggau cgucaucucg 240gcuaguucgc gugaccggga gauccgagca
gaggcauagc gaacugcgca cggagaagcc 300uugagggaau gccguagg
31869369DNAMycobacterium leprae
69ggggctgaaa ggtttcgact tcgcgcatcg aatcaaggga agcgtgccgg tgcaggcaag
60agaccaccgt aagcgtcgtt gcagcaatat aagcgccgat tcatatcagc gcgactatgc
120tctcgctgcc taagcgatgg ctagtctgtc agaccgggaa cgccctcgtc ccggagcctg
180gcatcagcta gagggatcta ccgatgggtt cggtcgcggg actcgtcggg acaccaaccg
240cgactgggat cgtcatcctg gctagttcgc gtgatcagga gatccgagta gaggcatagc
300gaactacgca cggagaagcc ttgagggaaa tgccgtagga cccgggttcg attcccggca
360gctccacca
36970369RNAMycobacterium leprae 70ggggcugaaa gguuucgacu ucgcgcaucg
aaucaaggga agcgugccgg ugcaggcaag 60agaccaccgu aagcgucguu gcagcaauau
aagcgccgau ucauaucagc gcgacuaugc 120ucucgcugcc uaagcgaugg cuagucuguc
agaccgggaa cgcccucguc ccggagccug 180gcaucagcua gagggaucua ccgauggguu
cggucgcggg acucgucggg acaccaaccg 240cgacugggau cgucauccug gcuaguucgc
gugaucagga gauccgagua gaggcauagc 300gaacuacgca cggagaagcc uugagggaaa
ugccguagga cccggguucg auucccggca 360gcuccacca
36971338DNAMycobacterium
paratuberculosis 71ttcgcgcatc gaatcaaggg aagcgtgccg gtgcaggcaa ctgaccaccg
taagcgtcgt 60tgcaaataga taagcgccga ttcacatcag cgcgacttac ctctcgctgc
ctaagcgaca 120gctagtccgt cagcccggga acgccctcga cccggagcct ggcgtcagct
agagggatcc 180accgatgagt tcggtcgcgg gactcatcgg gacaccaaca gcgactggga
tcgtcatcct 240ggcttgttcg cgtgaccagg agatccgagt agaggcatag cgaactgcgc
acggagaagc 300cttgagggaa tgccgtagaa cccgggttcg attcccaa
33872338RNAMycobacterium paratuberculosis 72uucgcgcauc
gaaucaaggg aagcgugccg gugcaggcaa cugaccaccg uaagcgucgu 60ugcaaauaga
uaagcgccga uucacaucag cgcgacuuac cucucgcugc cuaagcgaca 120gcuaguccgu
cagcccggga acgcccucga cccggagccu ggcgucagcu agagggaucc 180accgaugagu
ucggucgcgg gacucaucgg gacaccaaca gcgacuggga ucgucauccu 240ggcuuguucg
cgugaccagg agauccgagu agaggcauag cgaacugcgc acggagaagc 300cuugagggaa
ugccguagaa cccggguucg auucccaa
33873368DNAMycobacterium tuberculosis 73ggggctgaac ggtttcgact tcgcgcatcg
aatcaaggga agcgtgccgg tgcaggcaag 60agaccaccgt aagcgtcgtt gcgaccaaat
aagcgccgat tcacatcagc gcgactacgc 120tctcgctgcc taagcgacgg ctagtctgtc
agaccgggaa cgccctcggc ccggaccctg 180gcatcagcta gagggatcca ccgatgagtc
cggtcgcggg actcctcggg acaaccacag 240cgactgggat cgtcatctcg gctagttcgc
gtgaccggga gatccgagca gaggcatagc 300gaactgcgca cggagaagcc ttgagggaat
gccgtaggac ccgggttcga ttcccggcag 360ctccacca
36874368RNAMycobacterium tuberculosis
74ggggcugaac gguuucgacu ucgcgcaucg aaucaaggga agcgugccgg ugcaggcaag
60agaccaccgu aagcgucguu gcgaccaaau aagcgccgau ucacaucagc gcgacuacgc
120ucucgcugcc uaagcgacgg cuagucuguc agaccgggaa cgcccucggc ccggacccug
180gcaucagcua gagggaucca ccgaugaguc cggucgcggg acuccucggg acaaccacag
240cgacugggau cgucaucucg gcuaguucgc gugaccggga gauccgagca gaggcauagc
300gaacugcgca cggagaagcc uugagggaau gccguaggac ccggguucga uucccggcag
360cuccacca
36875411DNAMycoplasma capricolum 75ggggatgtca tggatttgac aggatatctt
tagtacatat aagcagtagt gttgtagact 60ataaatacta ctaggtttaa aaaaacgcaa
ataaaaacga agaaactttt gaaatgccag 120catttatgat gaataatgca tcagctggag
caaactttat gtttgcttaa taactactag 180tttagttata gtatttcacg aattatagat
attttaagct ttatttataa ccgtattacc 240caagcttaat agaatatatg attgcaataa
atatatttga aatctaattg caaatgatat 300ttaaccttta gttaatttta gttaaatatt
ttaattagaa aattaactaa actgtagaaa 360gtatgtatta atatatcttg gacgcgagtt
cgattctcgc catctccacc a 41176411RNAMycoplasma capricolum
76ggggauguca uggauuugac aggauaucuu uaguacauau aagcaguagu guuguagacu
60auaaauacua cuagguuuaa aaaaacgcaa auaaaaacga agaaacuuuu gaaaugccag
120cauuuaugau gaauaaugca ucagcuggag caaacuuuau guuugcuuaa uaacuacuag
180uuuaguuaua guauuucacg aauuauagau auuuuaagcu uuauuuauaa ccguauuacc
240caagcuuaau agaauauaug auugcaauaa auauauuuga aaucuaauug caaaugauau
300uuaaccuuua guuaauuuua guuaaauauu uuaauuagaa aauuaacuaa acuguagaaa
360guauguauua auauaucuug gacgcgaguu cgauucucgc caucuccacc a
41177388DNAMycoplasma genitalium (ATTC 33530, #1) 77ggggatgttt tgggtttgac
ataatgctga tagacaaaca gtagcattgg ggtatgcccc 60ttacagcgct aggttcaata
accgacaaag aaaataacga agtgttggta gaaccaaatt 120tgatcattaa ccaacaagca
agtgttaact ttgcttttgc ataagtagat actaaagcta 180cagctggtga atagtcatag
tttgctagct gtcatagttt atgactcgag gttaaatcgt 240tcaatttaac ctttaaaaat
agaacttgtt gtttccatga ttgttttgtg atcaattgga 300aacaagacaa aaatccacaa
aactaaaatg tagaagctgt ttgttgtgtc ctttatggaa 360acgggttcga ttcccgtcat
ctccacca 38878388RNAMycoplasma
genitalium (ATTC 33530, #1) 78ggggauguuu uggguuugac auaaugcuga uagacaaaca
guagcauugg gguaugcccc 60uuacagcgcu agguucaaua accgacaaag aaaauaacga
aguguuggua gaaccaaauu 120ugaucauuaa ccaacaagca aguguuaacu uugcuuuugc
auaaguagau acuaaagcua 180cagcugguga auagucauag uuugcuagcu gucauaguuu
augacucgag guuaaaucgu 240ucaauuuaac cuuuaaaaau agaacuuguu guuuccauga
uuguuuugug aucaauugga 300aacaagacaa aaauccacaa aacuaaaaug uagaagcugu
uuguuguguc cuuuauggaa 360acggguucga uucccgucau cuccacca
38879243RNAMycoplasma genitalium (ATTC 33530, #2)
79acaaagcgaa gacaaacaga gcaggggagc cccacagcgc aggcaaaacc gacaaagaaa
60aaacgaaggg gagaccaaag acaaaccaac aagcaaggaa cgcgcaaaga gaacaaagca
120cagcgggaaa gcaaggcagc gcaagagacc gaggaaacgc aaaaccaaaa aagaacggcc
180agagggacaa ggaaacaaga caaaaaccac aaaacaaaag agaagcgggg ccaggaaacg
240ggc
24380350RNAMycoplasma genitalium (ATTC 33530, #2) 80acauaaugcu gauagacaaa
caguagcauu gggguaugcc ccuuacagcg cuagguucaa 60uaaccgacaa agaaaauaac
gaaguguugg uagauccaaa uuugaucauu aaccaacaag 120caaguguuaa cuuugcuuuu
gcauaaguag auacuaaagc uacagcuggu gaauagucau 180aguuugcuag cugucauagu
uuaugacucg agguuaaauc guucaauuua accuuuaaaa 240auagaacuug uuguuuccau
gauuguuuug ugaucaauug gaaacaagac aaaaauccac 300aaaacuaaaa uguagaagcu
guuuguugug uccuuuaugg aaacggguuc 35081387DNAMycoplasma
pneumophila 81ggggatgtag aggttttgac ataatgttga aaggaaaaca gttgcagtgg
ggtatgcccc 60ttacagctct aggtataata accgacaaaa ataacgacga agttttggta
gatccaatgt 120tgatcgctaa ccaacaagca agtatcaact acgctttcgc ttagaacata
ctaaagctac 180acgaattgaa tcgccatagt ttggttcgtg tcacagttta tggctcgggg
ttaactggtt 240caacttaatc cttaaattat gaacttatcg tttacttgtt tgtcttatga
tctaaagtaa 300gcgagacatt aaaacataag actaaactgt agaagctgtt ttaccaatcc
tttatggaaa 360cgggttcgat tcccgtcatc tccacca
38782387RNAMycoplasma pneumophila 82ggggauguag agguuuugac
auaauguuga aaggaaaaca guugcagugg gguaugcccc 60uuacagcucu agguauaaua
accgacaaaa auaacgacga aguuuuggua gauccaaugu 120ugaucgcuaa ccaacaagca
aguaucaacu acgcuuucgc uuagaacaua cuaaagcuac 180acgaauugaa ucgccauagu
uugguucgug ucacaguuua uggcucgggg uuaacugguu 240caacuuaauc cuuaaauuau
gaacuuaucg uuuacuuguu ugucuuauga ucuaaaguaa 300gcgagacauu aaaacauaag
acuaaacugu agaagcuguu uuaccaaucc uuuauggaaa 360cggguucgau ucccgucauc
uccacca 38783318DNANeisseria
gonorrhoeae (ATCC 19424) 83gggggttgcg aagcagatgc gggcataccg gggtctcaga
ttcccgtaaa acactgaatt 60caaatagtcg caaacgacga aacttacgct ttagccgctt
aaggctagcc gttgcagcag 120tcggtcaatg ggctgtgtgg cgaaagccac cgcaacgtca
tcttacattg actggtttcc 180agccgggtta cttggcagga aataagactt aaggtaactg
gtttccaaaa ggcctgttgg 240tcggcatgat ggaaataaga ttttcaaata gacacaacta
agtatgtaga acgctttgta 300gaggactttc ggacgggg
31884318RNANeisseria gonorrhoeae (ATCC 19424)
84ggggguugcg aagcagaugc gggcauaccg gggucucaga uucccguaaa acacugaauu
60caaauagucg caaacgacga aacuuacgcu uuagccgcuu aaggcuagcc guugcagcag
120ucggucaaug ggcugugugg cgaaagccac cgcaacguca ucuuacauug acugguuucc
180agccggguua cuuggcagga aauaagacuu aagguaacug guuuccaaaa ggccuguugg
240ucggcaugau ggaaauaaga uuuucaaaua gacacaacua aguauguaga acgcuuugua
300gaggacuuuc ggacgggg
31885363DNANeisseria gonorrhoeae (FA 1090) 85gggggcgacc ttggtttcga
cgggggttgc gaagcagatg cgggcatacc ggggtctcag 60attcccgtaa aacactgaat
tcaaatagtc gcaaacgacg aaacttacgc tttagccgct 120taaggctagc cgttgcagca
gtcggtcaat gggctgtgtg gtgaaagcca ccgcaacgtc 180atcttacatt gactggtttc
cagccgggtt acttggcagg aaataagact taaggtaact 240ggtttccaaa aggcctgttg
gtcggcatga tggaaataag attttcaaat agacacaact 300aagtatgtag aacgctttgt
agaggacttt cggacggggg ttcgattccc cccgcctcca 360cca
36386363RNANeisseria
gonorrhoeae (FA 1090) 86gggggcgacc uugguuucga cggggguugc gaagcagaug
cgggcauacc ggggucucag 60auucccguaa aacacugaau ucaaauaguc gcaaacgacg
aaacuuacgc uuuagccgcu 120uaaggcuagc cguugcagca gucggucaau gggcugugug
gugaaagcca ccgcaacguc 180aucuuacauu gacugguuuc cagccggguu acuuggcagg
aaauaagacu uaagguaacu 240gguuuccaaa aggccuguug gucggcauga uggaaauaag
auuuucaaau agacacaacu 300aaguauguag aacgcuuugu agaggacuuu cggacggggg
uucgauuccc cccgccucca 360cca
36387363DNANeisseria meningitidis 87gggggcgacc
ttggtttcga cgggggttgc gaagcagatg cgggcatacc ggggtctcag 60attcccgtaa
aacactgaat tcaaatagtc gcaaacgacg aaacttacgc tttagccgct 120taaggctagc
cgttgcagca gtcggtcaat gggctgtgtg gcgaaagcca ccgcaacgtc 180atcttacatt
gactggtttc ctgccgggtt atttggcagg aaatgagatt taaggtaact 240ggtttccaaa
aggcctgttg gtcggcatga tggaaataag attttcaaat agacacaact 300aagtatgtag
aacgctttgt agaggacttt cggacggggg ttcgattccc cccgcctcca 360cca
36388363RNANeisseria meningitidis 88gggggcgacc uugguuucga cggggguugc
gaagcagaug cgggcauacc ggggucucag 60auucccguaa aacacugaau ucaaauaguc
gcaaacgacg aaacuuacgc uuuagccgcu 120uaaggcuagc cguugcagca gucggucaau
gggcugugug gcgaaagcca ccgcaacguc 180aucuuacauu gacugguuuc cugccggguu
auuuggcagg aaaugagauu uaagguaacu 240gguuuccaaa aggccuguug gucggcauga
uggaaauaag auuuucaaau agacacaacu 300aaguauguag aacgcuuugu agaggacuuu
cggacggggg uucgauuccc cccgccucca 360cca
36389385DNANostoc muscorum PCC7120
89gggtccgtcg gtttcgacag gttggcgaac gctactctgt gattcaggtc gagagtgagt
60ctcctctgca aatcaaggct caaaacaaaa gtaaatgcga ataacatcgt taaatttgct
120cgtaaggacg ctctagtagc tgcctaaata gcctctttca ggttcgagcg tcttcggttt
180gactccgtta aggactgaag accaaccccc aacggatgct ctagcaatgt tctctggttg
240gcttgctagc taagatttaa tcagagcatc ctacgttcgg gataatgaac gattcccgcc
300ttgagggtca gaaaggctaa acctgtgaat gagcgggggg tcaataccca atttggacag
360cagttcgact ctgctcgatc cacca
38590385RNANostoc muscorum PCC7120 90ggguccgucg guuucgacag guuggcgaac
gcuacucugu gauucagguc gagagugagu 60cuccucugca aaucaaggcu caaaacaaaa
guaaaugcga auaacaucgu uaaauuugcu 120cguaaggacg cucuaguagc ugccuaaaua
gccucuuuca gguucgagcg ucuucgguuu 180gacuccguua aggacugaag accaaccccc
aacggaugcu cuagcaaugu ucucugguug 240gcuugcuagc uaagauuuaa ucagagcauc
cuacguucgg gauaaugaac gauucccgcc 300uugaggguca gaaaggcuaa accugugaau
gagcgggggg ucaauaccca auuuggacag 360caguucgacu cugcucgauc cacca
38591371DNAOdontella sinensis (diatom)
chloroplast 91ggggctgact tggtttcgac atttaaaaat tgttacagta tgatgcaggt
cgaagtttct 60aatcttcgta aaaaaagaga aatttataat aaatgctaat aatttaattt
cttctgtgtt 120taaaagttta tcaactaagc aaaatagttt aaatttaagt tttgctgttt
aagttttatg 180cacatttaat gatctagtaa ataactttgt tcgctataat ttatatttat
aactagactt 240ttgtcttttt tatagtttag aataacttta tcatttcaaa cctcgttcca
tctagttgaa 300ctaaacctgt gaacgaatac tataataaaa tttttagatg gacgtgggtt
cgactcccat 360cagctccacc a
37192371RNAOdontella sinensis (diatom) chloroplast
92ggggcugacu ugguuucgac auuuaaaaau uguuacagua ugaugcaggu cgaaguuucu
60aaucuucgua aaaaaagaga aauuuauaau aaaugcuaau aauuuaauuu cuucuguguu
120uaaaaguuua ucaacuaagc aaaauaguuu aaauuuaagu uuugcuguuu aaguuuuaug
180cacauuuaau gaucuaguaa auaacuuugu ucgcuauaau uuauauuuau aacuagacuu
240uugucuuuuu uauaguuuag aauaacuuua ucauuucaaa ccucguucca ucuaguugaa
300cuaaaccugu gaacgaauac uauaauaaaa uuuuuagaug gacguggguu cgacucccau
360cagcuccacc a
37193323DNAPorphyra purpureum (red alga) chloroplast 93ggggctgcaa
ggtttctaca ttgtgaaaaa acaaatatat gaaagtaaaa cgagctcatt 60attagagctt
ttagttaaat aaatgcagaa aataatatta ttgctttttc tcgaaaatta 120gctgttgcat
aaatagtctc aatttttgta attcgaagtg atagactctt atacactacg 180aatattctgt
tagagttgct cttaataaaa gaaaagtaaa aaaatacaaa ttcttatgtt 240ttttacctga
attgattcaa tttaaggtta gtattttttg atttttacaa tggacgtggg 300ttcaagtccc
accagctcca cca
32394323RNAPorphyra purpureum (red alga) chloroplast 94ggggcugcaa
gguuucuaca uugugaaaaa acaaauauau gaaaguaaaa cgagcucauu 60auuagagcuu
uuaguuaaau aaaugcagaa aauaauauua uugcuuuuuc ucgaaaauua 120gcuguugcau
aaauagucuc aauuuuugua auucgaagug auagacucuu auacacuacg 180aauauucugu
uagaguugcu cuuaauaaaa gaaaaguaaa aaaauacaaa uucuuauguu 240uuuuaccuga
auugauucaa uuuaagguua guauuuuuug auuuuuacaa uggacguggg 300uucaaguccc
accagcucca cca
32395407DNAPorphyromonas gingivalis 95ggggctgacc ggctttgaca gcgtgatgaa
gcggtatgta agcatgtagt gcgtgggtgg 60cttgcactat aatctcagac atcaaaagtt
taattggcga aaataactac gctctcgctg 120cgtaatcgaa gaatagtaga ttagacgctt
catcgccgcc aaagtggcag cgacgagaca 180tcgcccgagc agctttttcc cgaagtagct
cgatggtgcg gtgctgacaa atcgggaacc 240gctacaggat gcttcctgcc tgtggtcaga
tcgaacggaa gataaggatc gtgcattggg 300tcgtttcagc ctccgctcgc tcacgaaaat
tccaactgaa actaaacatg tagaaagcat 360attgattcca tgtttggacg agggttcaat
tccctccagc tccacca 40796407RNAPorphyromonas gingivalis
96ggggcugacc ggcuuugaca gcgugaugaa gcgguaugua agcauguagu gcgugggugg
60cuugcacuau aaucucagac aucaaaaguu uaauuggcga aaauaacuac gcucucgcug
120cguaaucgaa gaauaguaga uuagacgcuu caucgccgcc aaaguggcag cgacgagaca
180ucgcccgagc agcuuuuucc cgaaguagcu cgauggugcg gugcugacaa aucgggaacc
240gcuacaggau gcuuccugcc uguggucaga ucgaacggaa gauaaggauc gugcauuggg
300ucguuucagc cuccgcucgc ucacgaaaau uccaacugaa acuaaacaug uagaaagcau
360auugauucca uguuuggacg aggguucaau ucccuccagc uccacca
40797310DNAProteus rettgeri (NCTC 10975) 97gggatttgcg aaacccaagg
tgcatgccga ggggcggttg gcctcgtaaa aagccgcaaa 60aaaatagtcg caaacgacga
aaactacgct ttagcagctt aataacctgc ttagagccct 120ctctccctag cctccgctct
tggacgggga tcaagagagg tcaaacccaa aagagatcgc 180gtggatgcct tgcctggggt
tgaagcgtta aacttaatca ggatagtttg ttggtggcgt 240gtctgtccgc agctggcaaa
tgaattcaaa gactagacta agcatgtagt accgaggatg 300tagaaatttc
31098310RNAProteus rettgeri
(NCTC 10975) 98gggauuugcg aaacccaagg ugcaugccga ggggcgguug gccucguaaa
aagccgcaaa 60aaaauagucg caaacgacga aaacuacgcu uuagcagcuu aauaaccugc
uuagagcccu 120cucucccuag ccuccgcucu uggacgggga ucaagagagg ucaaacccaa
aagagaucgc 180guggaugccu ugccuggggu ugaagcguua aacuuaauca ggauaguuug
uugguggcgu 240gucuguccgc agcuggcaaa ugaauucaaa gacuagacua agcauguagu
accgaggaug 300uagaaauuuc
31099241DNAPseudoalteromonas haloplanktis 99gggagcgaaa
cccaagggca gccgaggggc ggggcccgaa aaagccgcaa aaaaaagcgc 60aaacgacgaa
aacacgcagc agcaaaaccg cagagccccc cccagccccg ccggacgggg 120acaagagagg
caaacccaaa agagacgcgg gagccgccgg gggaagcgaa acaacaggaa 180ggggggcggc
gccgcagcgg caaagaacaa agacagacaa gcagagaccg aggagagaaa 240c
241100313RNAPseudoalteromonas haloplanktis 100ggaauucaag aagcccgagg
ugcaugucga ggugcgguuu gccucguaaa aaagccgcaa 60uuuaaaguaa ucgcaaacga
cgauaacuac ucucuagcag cuuaggcugg cuagcgcucc 120uuccauguau ucuuguggac
uggauuuugg agugucaccc uaacaccuga ucgcgacgga 180aacccuggcc gggguugaag
cguuaaaacu aagcggccuc gccuuuaucu accguguuug 240uccgggauuu aaagguuaau
uaaaugacaa uacuaaacau guaguaccga cggucgaggc 300uuuucggacg ggg
313101353DNAPseudomonas
aeruginosa 101ggggccgatt aggattcgac gccggtaaca aaagttgagg ggcatgccga
gttggtagca 60gaactcgtaa attcgctgct gcaaacttat agttgccaac gacgacaact
acgctctagc 120tgcttaatgc ggctagcagt cgctagggga tgcctgtaaa cccgaaacga
ctgtcagata 180gaacaggatc gccgccaagt tcgctgtaga cgtaacggct aaaactcata
cagctcgctc 240caagcaccct gccactcggg cggcgcggag ttaactcagt agagctggct
aagcatgtaa 300aaccgatagc ggaaagctgg cggacggggg ttcaaatccc cccggatcca
cca 353102353RNAPseudomonas aeruginosa 102ggggccgauu aggauucgac
gccgguaaca aaaguugagg ggcaugccga guugguagca 60gaacucguaa auucgcugcu
gcaaacuuau aguugccaac gacgacaacu acgcucuagc 120ugcuuaaugc ggcuagcagu
cgcuagggga ugccuguaaa cccgaaacga cugucagaua 180gaacaggauc gccgccaagu
ucgcuguaga cguaacggcu aaaacucaua cagcucgcuc 240caagcacccu gccacucggg
cggcgcggag uuaacucagu agagcuggcu aagcauguaa 300aaccgauagc ggaaagcugg
cggacggggg uucaaauccc cccggcucca cca 353103363DNASalmonella
typhimurium 103ggggctgatt ctggattcga cgggatttgc gaaacccaag gtgcatgccg
aggggcggtt 60ggcctcgtaa aaagccgcaa aaaaatagtc gcaaacgacg aaacctacgc
tttagcagct 120taataacctg cttagagccc tctctcccta gcctccgctc ttaggacggg
gatcaagaga 180ggtcaaaccc aaaagagatc gcgcggatgc cctgcctggg gttgaagcgt
taaaacgaat 240caggctagtc tggtagtggc gtgtccgtcc gcaggtgcca ggcgaatgta
aagactgact 300aagcatgtag taccgaggat gtaggaattt cggacgcggg ttcaactccc
gccagctcca 360cca
363104363RNASalmonella typhimurium 104ggggcugauu cuggauucga
cgggauuugc gaaacccaag gugcaugccg aggggcgguu 60ggccucguaa aaagccgcaa
aaaaauaguc gcaaacgacg aaaccuacgc uuuagcagcu 120uaauaaccug cuuagagccc
ucucucccua gccuccgcuc uuaggacggg gaucaagaga 180ggucaaaccc aaaagagauc
gcgcggaugc ccugccuggg guugaagcgu uaaaacgaau 240caggcuaguc ugguaguggc
guguccgucc gcaggugcca ggcgaaugua aagacugacu 300aagcauguag uaccgaggau
guaggaauuu cggacgcggg uucaacuccc gccagcucca 360cca
363105355DNAShewanella
putrefaciens 105gggggcgatt ctggattcga caggattcac gaaaccctgg gagcatgccg
aggggcggtt 60ggcctcgtaa aaagccgcaa agttatagtt gcaaacgacg ataactacgc
tctagccgct 120taatgccgct agccatctac cacacgcttt gcacatgggc agtggatttg
atggtcatct 180cacatcgtgc tagcgaggga accctgtctg ggggtgaacc gcgaaacagt
accggactca 240ccgtgtggga tcctgtcttt cggagttcaa acggttaaac aatagaaaga
ctaagcatgt 300agcgccttgg atgtaggttt tctggacgcg ggttcaagtc ccgccgcctc
cacca 355106355RNAShewanella putrefaciens 106gggggcgauu
cuggauucga caggauucac gaaacccugg gagcaugccg aggggcgguu 60ggccucguaa
aaagccgcaa aguuauaguu gcaaacgacg auaacuacgc ucuagccgcu 120uaaugccgcu
agccaucuac cacacgcuuu gcacaugggc aguggauuug auggucaucu 180cacaucgugc
uagcgaggga acccugucug ggggugaacc gcgaaacagu accggacuca 240ccguguggga
uccugucuuu cggaguucaa acgguuaaac aauagaaaga cuaagcaugu 300agcgccuugg
auguagguuu ucuggacgcg gguucaaguc ccgccgccuc cacca
355107362DNAStaphylococcus aureus 107ggggacgttc atggattcga caggggtccc
ccgagctcat taagcgtgtc ggagggttgt 60cttcgtcatc aacacacaca gtttataata
actggcaaat caaacaataa tttcgcagta 120gctgcctaat cgcactctgc atcgcctaac
agcatttcct atgtgctgtt aacgcgattc 180aaccttaata ggatatgcta aacactgccg
tttgaagtct gtttagaaga aacttaatca 240aactagcatc atgttggttg tttatcactt
ttcatgatgc gaaacctatc gataaactac 300acacgtagaa agatgtgtat caggaccttt
ggacgcgggt tcaaatcccg ccgtctccac 360ca
362108362RNAStaphylococcus aureus
108ggggacguuc auggauucga cagggguccc ccgagcucau uaagcguguc ggaggguugu
60cuucgucauc aacacacaca guuuauaaua acuggcaaau caaacaauaa uuucgcagua
120gcugccuaau cgcacucugc aucgccuaac agcauuuccu augugcuguu aacgcgauuc
180aaccuuaaua ggauaugcua aacacugccg uuugaagucu guuuagaaga aacuuaauca
240aacuagcauc auguugguug uuuaucacuu uucaugaugc gaaaccuauc gauaaacuac
300acacguagaa agauguguau caggaccuuu ggacgcgggu ucaaaucccg ccgucuccac
360ca
362109349DNAStreptococcus gordonii 109ggggtcgtta cggattcgac aggcattatg
aggcatattt tgcgactcat ctagcggatg 60taaaacgcca gttaaatata actgcaaaaa
ataatacttc ttacgcttta gctgcctaaa 120aaccagcggg cgtgacccga ttcggattgc
ttgtgtctga tgacaggtct tattattagc 180aagctacggt agaatcttgt ctagtgattt
tacaagagat tgatagactc gcttgatttg 240ggcttgagtt atgtgtcaaa atcaagttaa
aacaatacat agcctatggt tgtagacaaa 300tgtgttggca gatgtttgga cgtgggttcg
actcccaccg gctccacca 349110349RNAStreptococcus gordonii
110ggggucguua cggauucgac aggcauuaug aggcauauuu ugcgacucau cuagcggaug
60uaaaacgcca guuaaauaua acugcaaaaa auaauacuuc uuacgcuuua gcugccuaaa
120aaccagcggg cgugacccga uucggauugc uugugucuga ugacaggucu uauuauuagc
180aagcuacggu agaaucuugu cuagugauuu uacaagagau ugauagacuc gcuugauuug
240ggcuugaguu augugucaaa aucaaguuaa aacaauacau agccuauggu uguagacaaa
300uguguuggca gauguuugga cguggguucg acucccaccg gcuccacca
349111349DNAStreptococcus mutans 111ggggtcgtta cggattcgac aggcattatg
agacctattt tgcgactcat ctagcggatg 60taaaacgcca gttaaatata actgcaaaaa
atacaaattc ttacgcagta gctgcctaaa 120aaccagcctg tgtgatcaat aacaaattgc
ttgtgtttgt tgattggtct tattgttaac 180aagctacgtt agaactgagt caggctgttc
taaaagagtt ctactgactc gcatcgttag 240agtttgagtt atgtattgta acggtgttaa
ataaacacat aacctatagt tgtagacaaa 300tgggttagca gatgtttgga cgtgggttcg
actcccaccg gctccacca 349112349RNAStreptococcus mutans
112ggggucguua cggauucgac aggcauuaug agaccuauuu ugcgacucau cuagcggaug
60uaaaacgcca guuaaauaua acugcaaaaa auacaaauuc uuacgcagua gcugccuaaa
120aaccagccug ugugaucaau aacaaauugc uuguguuugu ugauuggucu uauuguuaac
180aagcuacguu agaacugagu caggcuguuc uaaaagaguu cuacugacuc gcaucguuag
240aguuugaguu auguauugua acgguguuaa auaaacacau aaccuauagu uguagacaaa
300uggguuagca gauguuugga cguggguucg acucccaccg gcuccacca
349113348DNAStreptococcus pneumoniae 113ggggtcgtta cggattcgac aggcattatg
aggcatattt tgcgactcgt gtggcgacgt 60aaacgctcag ttaaatataa ctgcaaaaaa
taacacttct tacgctctag ctgcctaaaa 120accagcaggc gtgacccgat ttggattgct
cgtgttcaat gacaggtctt attattagcg 180agatacgatt aagccttgtc tagcggtttg
ataagagatt gatagactcg cagtttctag 240acttgagtta tgtgtcgagg ggctgttaaa
ataatacata acctatggtt gtagacaaat 300atgttggcag gtgtttggac gtgggttcga
ctcccaccgg ctccacca 348114348RNAStreptococcus pneumoniae
114ggggucguua cggauucgac aggcauuaug aggcauauuu ugcgacucgu guggcgacgu
60aaacgcucag uuaaauauaa cugcaaaaaa uaacacuucu uacgcucuag cugccuaaaa
120accagcaggc gugacccgau uuggauugcu cguguucaau gacaggucuu auuauuagcg
180agauacgauu aagccuuguc uagcgguuug auaagagauu gauagacucg caguuucuag
240acuugaguua ugugucgagg ggcuguuaaa auaauacaua accuaugguu guagacaaau
300auguuggcag guguuuggac guggguucga cucccaccgg cuccacca
348115348DNAStreptococcus pyogenes 115ggggttgtta cggattcgac aggcattatg
aggcatgttt tgcgtcccat cggcagatgt 60aaattgccag ttaaatataa ctgcaaaaaa
tacaaactct tacgctttag ctgcctaaaa 120accagctagc gtgacttcta caagattgct
tgtgtcctgt tagaagtctc aaaatagcaa 180gctacggtta cgaaattgtc tagtttcgtg
acaagagatt gatagactcg caaactaatg 240gcttgagtta tgtgtcttta gtttgttaaa
tgaagacata acctatggac gtagacaaat 300atgttggcag gtgtttggac gtgggttcga
ctcccaccag ctccacca 348116348RNAStreptococcus pyogenes
116gggguuguua cggauucgac aggcauuaug aggcauguuu ugcgucccau cggcagaugu
60aaauugccag uuaaauauaa cugcaaaaaa uacaaacucu uacgcuuuag cugccuaaaa
120accagcuagc gugacuucua caagauugcu uguguccugu uagaagucuc aaaauagcaa
180gcuacgguua cgaaauuguc uaguuucgug acaagagauu gauagacucg caaacuaaug
240gcuugaguua ugugucuuua guuuguuaaa ugaagacaua accuauggac guagacaaau
300auguuggcag guguuuggac guggguucga cucccaccag cuccacca
348117394DNASynechococcus sp. PCC6301 117ggggctgtaa tggtttcgac gtgttggtga
atccttcacc gtgattcagg ccgagaggga 60gtccactctc gtaaatccag gctcaaccaa
aagtaactgc gaacaacatc gttcctttcg 120ctcgtaaggc tgctcctgta gctgcttaaa
cgccacaaac tttctggctc gagcgtctag 180tcgtagactc cgttaatacg cctagactta
aacccccaac ggatgctcga gtggcggcct 240caggtccgtc ctctcgctaa gcaaaaacct
gagcatcccg ccaacgggga taatcgttgg 300ctcccgcaca gtgggtcaac cgtgctaagc
ctgtgaacga gcggaaagtt actagtcaat 360gcggacagcg gttcgattcc gctcagctcc
acca 394118394RNASynechococcus sp. PCC6301
118ggggcuguaa ugguuucgac guguugguga auccuucacc gugauucagg ccgagaggga
60guccacucuc guaaauccag gcucaaccaa aaguaacugc gaacaacauc guuccuuucg
120cucguaaggc ugcuccugua gcugcuuaaa cgccacaaac uuucuggcuc gagcgucuag
180ucguagacuc cguuaauacg ccuagacuua aacccccaac ggaugcucga guggcggccu
240cagguccguc cucucgcuaa gcaaaaaccu gagcaucccg ccaacgggga uaaucguugg
300cucccgcaca gugggucaac cgugcuaagc cugugaacga gcggaaaguu acuagucaau
360gcggacagcg guucgauucc gcucagcucc acca
394119399DNASynechocystis PCC6803 119ggggccgcaa tggtttcgac aggttggcga
aagcttgccc gtgatacagg tcgagagtga 60gtctcctctc gcaaatcaaa ggctcaaaaa
aaagtaactg cgaataacat cgtcagcttc 120aaacgggtag ccatagcagc ctagtctgta
aaagctacat tttcttgtca aagaccgttt 180acttcttttc tgactccgtt aaggattaga
ggttaacccc aacggatgct ttgtttggct 240cttctctagt tagctaaaca atcaagactc
agactagagc atcccaccat cagggataat 300cgatggtccc cgtcctaggg ctagaaggac
taaacctgtg aatgagcgga aagttaatac 360ccagtttgga cagcagttca attctgctcg
gctccacca 399120399RNASynechocystis PCC6803
120ggggccgcaa ugguuucgac agguuggcga aagcuugccc gugauacagg ucgagaguga
60gucuccucuc gcaaaucaaa ggcucaaaaa aaaguaacug cgaauaacau cgucagcuuc
120aaacggguag ccauagcagc cuagucugua aaagcuacau uuucuuguca aagaccguuu
180acuucuuuuc ugacuccguu aaggauuaga gguuaacccc aacggaugcu uuguuuggcu
240cuucucuagu uagcuaaaca aucaagacuc agacuagagc aucccaccau cagggauaau
300cgaugguccc cguccuaggg cuagaaggac uaaaccugug aaugagcgga aaguuaauac
360ccaguuugga cagcaguuca auucugcucg gcuccacca
399121356DNAThermotoga maritima 121gggggcgaac gggttcgacg gggatggagt
cccctgggaa gcgagccgag gtccccacct 60cctcgtaaaa aaggtgggac aaagaataag
tgccaacgaa cctgttgctg ttgccgctta 120atagataagc ggccgtcctc tccgaagttg
gctgggcttc ggaagagggc gtgagagatc 180cagcctaccg attcagcttc gccttccggc
ctgaatcggg aaaactcagg aaggctgtgg 240gagaggacac cctgcccgtg ggaggtccct
cccgagagcg aaaacacggg ctgcgctcgg 300agaagcccag gggcctccat cttcggacgg
gggttcgaat ccccccgcct ccacca 356122356RNAThermotoga maritima
122gggggcgaac ggguucgacg gggauggagu ccccugggaa gcgagccgag guccccaccu
60ccucguaaaa aaggugggac aaagaauaag ugccaacgaa ccuguugcug uugccgcuua
120auagauaagc ggccguccuc uccgaaguug gcugggcuuc ggaagagggc gugagagauc
180cagccuaccg auucagcuuc gccuuccggc cugaaucggg aaaacucagg aaggcugugg
240gagaggacac ccugcccgug ggaggucccu cccgagagcg aaaacacggg cugcgcucgg
300agaagcccag gggccuccau cuucggacgg ggguucgaau ccccccgccu ccacca
356123349DNAThermus thermophilus 123gggggtgaaa cggtctcgac gggggtcgcc
gagggcgtgg ctgcgcgccg aggtgcgggt 60ggcctcgtaa aaacccgcaa cggcataact
gccaacacca actacgctct cgcggcttaa 120tgaccgcgac ctcgcccggt agccctgccg
ggggctcacc ggaagcgggg acacaaaccc 180ggctagcccg gggccacgcc ctctaacccc
gggcgaagct tgaagggggc tcgctcctgg 240ccgcccgtcc gcgggccaag ccaggaggac
acgcgaaacg cggactacgc gcgtagaggc 300ccgccgtaga gaccttcgga cgggggttcg
actcccccca cctccacca 349124349RNAThermus thermophilus
124gggggugaaa cggucucgac gggggucgcc gagggcgugg cugcgcgccg aggugcgggu
60ggccucguaa aaacccgcaa cggcauaacu gccaacacca acuacgcucu cgcggcuuaa
120ugaccgcgac cucgcccggu agcccugccg ggggcucacc ggaagcgggg acacaaaccc
180ggcuagcccg gggccacgcc cucuaacccc gggcgaagcu ugaagggggc ucgcuccugg
240ccgcccgucc gcgggccaag ccaggaggac acgcgaaacg cggacuacgc gcguagaggc
300ccgccguaga gaccuucgga cggggguucg acucccccca ccuccacca
349125354DNATreponema pallidum 125ggggatgact aggtttcgac tagggatgtg
gggtgttgcg ctgcaggtgg agtgtcgatc 60tcctgattcg gcgcctttat aactgccaat
tctgacagtt tcgactacgc gctcgccgcg 120taatcgcggg cctgtgtttg cgctgctctg
agcgaacata tcggcccgac gccaaacgga 180gcttgctctt acgttgtgca cggcggacgt
agggggactt ttgtctgtgc taagactctg 240gcgcgtgcgg tgcaggccta gcagagtccg
acaaacgcag tacgcaccgc taaacctgta 300ggcgcgcagc actcgctctt taggacgggg
gttcgattcc ccccatctcc acca 354126354RNATreponema pallidum
126ggggaugacu agguuucgac uagggaugug ggguguugcg cugcaggugg agugucgauc
60uccugauucg gcgccuuuau aacugccaau ucugacaguu ucgacuacgc gcucgccgcg
120uaaucgcggg ccuguguuug cgcugcucug agcgaacaua ucggcccgac gccaaacgga
180gcuugcucuu acguugugca cggcggacgu agggggacuu uugucugugc uaagacucug
240gcgcgugcgg ugcaggccua gcagaguccg acaaacgcag uacgcaccgc uaaaccugua
300ggcgcgcagc acucgcucuu uaggacgggg guucgauucc ccccaucucc acca
354127367DNAVibrio cholerae 127ggggctgatt caggattcga cgggaatttt
gcagtctgag gtgcatgccg aggtgcggta 60ggcctcgtta acaaaccgca aaaaaatagt
cgcaaacgac gaaaactacg cactagcagc 120ttaataccct gctcagagcc cttcctccct
agcttccgct tgtaagacgg ggaaatcagg 180aaggtcaaac caaatcaagc tggcgtggat
tcccccacct gagggatgaa gcgcgagatc 240taattcaggt tagccattcg ttagcgtgtc
ggttcgcagg cggtggtgaa attaaagatc 300gactaagcat gtagtaccaa agatgaatgg
ttttcggacg ggggttcaac tccccccagc 360tccacca
367128367RNAVibrio cholerae
128ggggcugauu caggauucga cgggaauuuu gcagucugag gugcaugccg aggugcggua
60ggccucguua acaaaccgca aaaaaauagu cgcaaacgac gaaaacuacg cacuagcagc
120uuaauacccu gcucagagcc cuuccucccu agcuuccgcu uguaagacgg ggaaaucagg
180aaggucaaac caaaucaagc uggcguggau ucccccaccu gagggaugaa gcgcgagauc
240uaauucaggu uagccauucg uuagcguguc gguucgcagg cgguggugaa auuaaagauc
300gacuaagcau guaguaccaa agaugaaugg uuuucggacg gggguucaac uccccccagc
360uccacca
367129364DNAYersinia pestis 129ggggctgatt ctggattcga cgggattcgc
gaaacccaag gtgcatgccg aggtgcggtg 60gcctcgtaaa aaaccgcaaa aaaaatagtt
gcaaacgacg aaaactacgc actagcagct 120taataacctg cttagagccc tctctgccta
gcctccgctc ttaggacggg gatcaagaga 180ggtcaaacct aaaagagctc gtgtggaaac
cttgcctggg gtggaagcat taaaactaat 240caggatagtt tgtcagtagc gtgtccatcc
gcagctggcc ggcgaatgta atgattggac 300taagcatgta gtgccgacgg tgtagtaatt
tcggacgggg gttcaaatcc ccccagctcc 360acca
364130364RNAYersinia pestis
130ggggcugauu cuggauucga cgggauucgc gaaacccaag gugcaugccg aggugcggug
60gccucguaaa aaaccgcaaa aaaaauaguu gcaaacgacg aaaacuacgc acuagcagcu
120uaauaaccug cuuagagccc ucucugccua gccuccgcuc uuaggacggg gaucaagaga
180ggucaaaccu aaaagagcuc guguggaaac cuugccuggg guggaagcau uaaaacuaau
240caggauaguu ugucaguagc guguccaucc gcagcuggcc ggcgaaugua augauuggac
300uaagcaugua gugccgacgg uguaguaauu ucggacgggg guucaaaucc ccccagcucc
360acca
364131309DNACampylobacter fetus 131aggagtaagt ctgcttagat ggcatgtcgc
tttgggcaaa gcgtaaaaag cccaaataaa 60attaaacgca aacaacgtta aattcgctcc
tgcttacgct aaagctgcgt aagttcagtt 120gagcctgaaa tttaagtcat actatctagc
ttaattttcg gtcatctttg atagtgtagc 180cttgcgtttg acaagcgttg aggtgaaata
aagtcttagc cttgcttttg agttttggaa 240gatgagcgaa gtagggtgaa gtagtcatct
ttgctaagca tgtagaggtc tttgtgggat 300tatttttgg
309132309RNACampylobacter fetus
132aggaguaagu cugcuuagau ggcaugucgc uuugggcaaa gcguaaaaag cccaaauaaa
60auuaaacgca aacaacguua aauucgcucc ugcuuacgcu aaagcugcgu aaguucaguu
120gagccugaaa uuuaagucau acuaucuagc uuaauuuucg gucaucuuug auaguguagc
180cuugcguuug acaagcguug aggugaaaua aagucuuagc cuugcuuuug aguuuuggaa
240gaugagcgaa guagggugaa guagucaucu uugcuaagca uguagagguc uuugugggau
300uauuuuugg
309133309DNACampylobacter coli (BM2509) 133aggagtaagt ctgcttagat
ggcatgtcgc tttggacaaa gcgtaaaaag tccaaattaa 60aattaaacgc aaataacgtt
aaatttgctc ctgcttacgc taaagctgcg taagttcagt 120tgagcccgaa actcaagtga
tgctatctag cttgaatttt ggtcatcttt gatagtgtag 180attgaaaatt gacaactttt
aatcgaagtt aaagtcttag tctagcttga aattttggaa 240ggtgagttta gccagatgaa
gttttcacct ttgctaaaca tgtagaagtc tttgtggggt 300tatttttgg
309134309RNACampylobacter
coli (BM2509) 134aggaguaagu cugcuuagau ggcaugucgc uuuggacaaa gcguaaaaag
uccaaauuaa 60aauuaaacgc aaauaacguu aaauuugcuc cugcuuacgc uaaagcugcg
uaaguucagu 120ugagcccgaa acucaaguga ugcuaucuag cuugaauuuu ggucaucuuu
gauaguguag 180auugaaaauu gacaacuuuu aaucgaaguu aaagucuuag ucuagcuuga
aauuuuggaa 240ggugaguuua gccagaugaa guuuucaccu uugcuaaaca uguagaaguc
uuuguggggu 300uauuuuugg
309135311DNAUnknownDescription of Unknown
OrganismCampylobacter chicken isolate 135acaggagtaa gtctgcttag
atggcatgtc gctttgggca aagcgtaaaa agcccaaata 60aaattaaacg caaacaacgt
taaattcgct cctgcttacg ctaaagctgc gtaagttcag 120ttgagcctga aatttaagtc
atactatcta gcttaatttt cggtcatttt tgatagtgta 180gccttgcgtt tgacaagcgt
tgaggtgaaa taaggtctta gccttgcttt tgagttttgg 240aagatgagcg aagtagggtg
aagtagtcat ctttgctaag catgtagagg tctttgtggg 300attatttttg g
311136311RNAUnknownDescription of Unknown OrganismCampylobacter
chicken isolate 136acaggaguaa gucugcuuag auggcauguc gcuuugggca aagcguaaaa
agcccaaaua 60aaauuaaacg caaacaacgu uaaauucgcu ccugcuuacg cuaaagcugc
guaaguucag 120uugagccuga aauuuaaguc auacuaucua gcuuaauuuu cggucauuuu
ugauagugua 180gccuugcguu ugacaagcgu ugaggugaaa uaaggucuua gccuugcuuu
ugaguuuugg 240aagaugagcg aaguagggug aaguagucau cuuugcuaag cauguagagg
ucuuuguggg 300auuauuuuug g
311137313DNAClostridium perfringens 137acgggggtag gatgggtttg
ataagcgagt cgagggaagc atggtgcctc gataataaag 60tatgcattaa agataaacgc
acgagataat tttgcattag cagcttaagt tagcgctgct 120catccttcct caattgccca
cggttgagag taagggtgtc atttaaaagt ggggaaccga 180gcctagcaaa gctttgagct
aggaacggaa tttatgaagc ttaccaaaga ggaagtttgt 240ctgtggacgt tctctgaggg
aattttaaaa cacaagacta cactcgtaga aagtcttact 300ggtctgcttt cgg
313138313RNAClostridium
perfringens 138acggggguag gauggguuug auaagcgagu cgagggaagc auggugccuc
gauaauaaag 60uaugcauuaa agauaaacgc acgagauaau uuugcauuag cagcuuaagu
uagcgcugcu 120cauccuuccu caauugccca cgguugagag uaaggguguc auuuaaaagu
ggggaaccga 180gccuagcaaa gcuuugagcu aggaacggaa uuuaugaagc uuaccaaaga
ggaaguuugu 240cuguggacgu ucucugaggg aauuuuaaaa cacaagacua cacucguaga
aagucuuacu 300ggucugcuuu cgg
313139331DNAHaemophilus ducreyi (NCTC 10945) 139acgggattag
cgaagtccaa ggtgcacgtc gaggtgcggt aggcctcgta acaaaccgca 60aaaaaatagt
cgcaaacgac gaacaatacg ctttagcagc ttaataacct gcatttagcc 120ttcgcgccct
agctttcgct cgtaagacgg ggagcacgcg gagtcaaacc aaaacgagat 180cgtgtggacg
cttccgcttg tagatgaaac actaaattga atcaagctag tttatttctt 240gcgtgtctgt
ccgctggaga taagcgaaat taaagaccag actaaacgtg tagtactgaa 300gatagagtaa
tttcggaccc gggttcgact c
331140331RNAHaemophilus ducreyi (NCTC 10945) 140acgggauuag cgaaguccaa
ggugcacguc gaggugcggu aggccucgua acaaaccgca 60aaaaaauagu cgcaaacgac
gaacaauacg cuuuagcagc uuaauaaccu gcauuuagcc 120uucgcgcccu agcuuucgcu
cguaagacgg ggagcacgcg gagucaaacc aaaacgagau 180cguguggacg cuuccgcuug
uagaugaaac acuaaauuga aucaagcuag uuuauuucuu 240gcgugucugu ccgcuggaga
uaagcgaaau uaaagaccag acuaaacgug uaguacugaa 300gauagaguaa uuucggaccc
ggguucgacu c 331141232DNAListeria
innocua (food isolate #1) 141ggcaaagaaa aacaaaacct agctttcgct gcctaataac
cagtagcata gctgatcctc 60cgtgcatcgc ccatgtgcta cggtaagggt ctcactctaa
gtgggctaca ctagttaatc 120tccgtctgag gttaaataga agagcttaat cagactagct
gaatggaagc ctgttaccgg 180gctgatgttt atgcgaaatg ctaatacggt gactacgctc
gtagatattc aa 232142232RNAListeria innocua (food isolate #1)
142ggcaaagaaa aacaaaaccu agcuuucgcu gccuaauaac caguagcaua gcugauccuc
60cgugcaucgc ccaugugcua cgguaagggu cucacucuaa gugggcuaca cuaguuaauc
120uccgucugag guuaaauaga agagcuuaau cagacuagcu gaauggaagc cuguuaccgg
180gcugauguuu augcgaaaug cuaauacggu gacuacgcuc guagauauuc aa
232143232DNAListeria innocua (food isolate #2) 143ggcaaagaaa aacaaaacct
agctttcgct gcctaataag cagtagcata gctgatcctc 60cgtgcatcgc ccatgtgcta
cggtaagggt ctcactctaa gtgggctaca ctagttaatc 120tccgtctgag gttaaataga
agagcttaat cagactagct gaatggaagc ctgttaccgg 180gccgatgttt atgcgaaatg
ctaatacggt gactacgctc gtagatattt aa 232144232RNAListeria
innocua (food isolate #2) 144ggcaaagaaa aacaaaaccu agcuuucgcu gccuaauaag
caguagcaua gcugauccuc 60cgugcaucgc ccaugugcua cgguaagggu cucacucuaa
gugggcuaca cuaguuaauc 120uccgucugag guuaaauaga agagcuuaau cagacuagcu
gaauggaagc cuguuaccgg 180gccgauguuu augcgaaaug cuaauacggu gacuacgcuc
guagauauuu aa 232145232DNAListeria innocua (food isolate #3)
145ggcaaagaaa aacaaaacct agctttcgct gcctaataag cagtagaata gctgatcctc
60cgtgcatcgc ccatgtgcta cggtaagggt ctcactctaa gtgggctaca ctagttaatc
120tccgtctgag gttaaataga agagcttaat cggactagct gaatggaagc ctgttaccgg
180gccgatgttt atgcgaaatg ctaatacggt gactacgctc gtagatattt aa
232146232RNAListeria innocua (food isolate #3) 146ggcaaagaaa aacaaaaccu
agcuuucgcu gccuaauaag caguagaaua gcugauccuc 60cgugcaucgc ccaugugcua
cgguaagggu cucacucuaa gugggcuaca cuaguuaauc 120uccgucugag guuaaauaga
agagcuuaau cggacuagcu gaauggaagc cuguuaccgg 180gccgauguuu augcgaaaug
cuaauacggu gacuacgcuc guagauauuu aa 232147232DNAListeria
innocua (ATCC 12210) 147ggcaaagaaa aacaaaacct agctttcgct gcctaataag
cagtagcata gctgatcctc 60cgtgcatcgc ccatgtgcta cggtaagggt ctcactctaa
gtgggctaca ctagttaatc 120tccgtctggg gttaaataga agagcttaat cagactagct
gaatggaagc ctgttactgg 180gccgatgttt atgcgaaatg ctaatacggt gactacgctc
gtagatattt aa 232148232RNAListeria innocua (ATCC 12210)
148ggcaaagaaa aacaaaaccu agcuuucgcu gccuaauaag caguagcaua gcugauccuc
60cgugcaucgc ccaugugcua cgguaagggu cucacucuaa gugggcuaca cuaguuaauc
120uccgucuggg guuaaauaga agagcuuaau cagacuagcu gaauggaagc cuguuacugg
180gccgauguuu augcgaaaug cuaauacggu gacuacgcuc guagauauuu aa
232149322DNAListeria ivanovii (NCTC 11846) 149acagggatag ttcgagcttg
agttgcgagt cggggggatc gtcctcgtta ttaacgtcaa 60agccaataat aactggcaaa
gaaaaacaaa acctagcttt cgctgcctaa taagcagtag 120catagctgat cctccgtgca
tcgcccatgt gctacggtaa gggtctcact ttaagtgggc 180tacactaaat aatctccgtc
tggggttagt tagaagagct taatcagact agctgaatgg 240aagcctgtta ccgggctgat
gtttatgcga aatgctaata cggtgactac gctcgtagat 300atttaagtgc cgatatttct
gg 322150321RNAListeria
ivanovii (NCTC 11846) 150acagggauag uucgagcuug aguugcgagu cggggggauc
guccucguua uuaacgucaa 60agccaauaau aacuggcaaa gaaaaacaaa accuagcuuu
cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca ucgcccaugu gcuacgguaa
gggucucacu uuaagugggc 180uacacuaaau aaucuccguc ugggguuagu uagaagagcu
uaaucagacu agcugaaugg 240aagccuguua ccgggcugau guuuaugcga aaugcuaaua
cggugacucg cucguagaua 300uuuaagugcc gauauuucug g
321151322DNAListeria seeligeri (NCTC 11856)
151acagggatag ttcgagcttg agttgcgagt cggggggatc gtcctcgtta tcaacgtcaa
60agccaataat aactggcaaa gaaaaacaaa acctagcttt cgctgcctaa taagcagtag
120catagctgat cctccgtgca tcgcccatgt gctacggaaa gggtctcact ttaagtgggc
180tacactaaat aatctccgtc tggggttagt tagaagagct taatcagact agctgaatgg
240aagcctgtta ccgggctgat gtttatgcga aatactaata cggtgactac gctcgtagat
300atttaagtgc ccatatttct gg
322152322RNAListeria seeligeri (NCTC 11856) 152acagggauag uucgagcuug
aguugcgagu cggggggauc guccucguua ucaacgucaa 60agccaauaau aacuggcaaa
gaaaaacaaa accuagcuuu cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca
ucgcccaugu gcuacggaaa gggucucacu uuaagugggc 180uacacuaaau aaucuccguc
ugggguuagu uagaagagcu uaaucagacu agcugaaugg 240aagccuguua ccgggcugau
guuuaugcga aauacuaaua cggugacuac gcucguagau 300auuuaagugc ccauauuucu
gg 322153314DNASalmonella
enteritidis 153acgggatttg cgaaacccaa ggtgcatgcc gaggggcggt tggcctcgta
aaaagccgca 60aaaaaatagt cgcaaacgac gaaacctacg ctttagcagc ttaataacct
gcttagagcc 120ctctctccct agcctccgct cttaggacgg ggatcaagag aggtcaaacc
caaaagagat 180cgcgtggatg ccctgcctgg ggttgaagcg ttaaaacgaa tcaggctagt
ctggtagtgg 240cgtgtccgtc cgcaggtgcc aggcgaatgt aaagactgac taagcatgta
gtaccgagga 300tgtaggaatt tcgg
314154314RNASalmonella enteritidis 154acgggauuug cgaaacccaa
ggugcaugcc gaggggcggu uggccucgua aaaagccgca 60aaaaaauagu cgcaaacgac
gaaaccuacg cuuuagcagc uuaauaaccu gcuuagagcc 120cucucucccu agccuccgcu
cuuaggacgg ggaucaagag aggucaaacc caaaagagau 180cgcguggaug cccugccugg
gguugaagcg uuaaaacgaa ucaggcuagu cugguagugg 240cguguccguc cgcaggugcc
aggcgaaugu aaagacugac uaagcaugua guaccgagga 300uguaggaauu ucgg
314155313DNAStaphylococcus
epidermidis (NCTC 11047) 155acaggggtcc cccgagctta ttaagcgtgt cggagggttg
gctccgtcat caacacattt 60cggttaaata taactgacaa atcaaacaat aatttcgcag
tagctgcgta atagccactg 120catcgcctaa cagcatctcc tacgtgctgt taacgcgatt
caaccctagt aggatatgct 180aaacactgcc gcttgaagtc tgtttagatg aaatataatc
aagctagtat catgttggtt 240gtttattgct tagcatgatg cgaaaattat caataaacta
cacacgtaga aagatttgta 300tcaggacctc tgg
313156313RNAStaphylococcus epidermidis (NCTC
11047) 156acaggggucc cccgagcuua uuaagcgugu cggaggguug gcuccgucau
caacacauuu 60cgguuaaaua uaacugacaa aucaaacaau aauuucgcag uagcugcgua
auagccacug 120caucgccuaa cagcaucucc uacgugcugu uaacgcgauu caacccuagu
aggauaugcu 180aaacacugcc gcuugaaguc uguuuagaug aaauauaauc aagcuaguau
cauguugguu 240guuuauugcu uagcaugaug cgaaaauuau caauaaacua cacacguaga
aagauuugua 300ucaggaccuc ugg
313157302DNAStreptococcus agalactiae (NCTC 8181)
157acaggcatta tgaggtatat tttgcgactc atcggcagat gtaaaatgcc agttaaatat
60aactgcaaaa aatacaaatt cttacgcatt agctgcctaa aaaacagcct gcgtgatctt
120cacaagattg tttgcgtttt gctagaaggt cttatttatc agcaaactac gtttggctac
180tgtctagtta gttaaaaaga gatttataga ctcgctatgt gagggcttga gttatgtgtc
240atcacctagt taaatcaata cataacctat agttgtagac aaatatatta gcagatgttt
300gg
302158302RNAStreptococcus agalactiae (NCTC 8181) 158acaggcauua ugagguauau
uuugcgacuc aucggcagau guaaaaugcc aguuaaauau 60aacugcaaaa aauacaaauu
cuuacgcauu agcugccuaa aaaacagccu gcgugaucuu 120cacaagauug uuugcguuuu
gcuagaaggu cuuauuuauc agcaaacuac guuuggcuac 180ugucuaguua guuaaaaaga
gauuuauaga cucgcuaugu gagggcuuga guuauguguc 240aucaccuagu uaaaucaaua
cauaaccuau aguuguagac aaauauauua gcagauguuu 300gg
302159168DNABordetella
bronchiseptica 159ggggccgatc cggattcgac gtgggtcatg aaacagctca aggcatgccg
agcaccagta 60agctcgttaa tccactggaa cactacaaac gccaacgacg agcgtttcgc
tctcgccgct 120taagcggtga gccgctgcac tgatctgtcc ttgggtcacg cgggggaa
168160168RNABordetella bronchiseptica 160ggggccgauc
cggauucgac gugggucaug aaacagcuca aggcaugccg agcaccagua 60agcucguuaa
uccacuggaa cacuacaaac gccaacgacg agcguuucgc ucucgccgcu 120uaagcgguga
gccgcugcac ugaucugucc uugggucacg cgggggaa
168161426DNAChlamydia pneumoniae (CWL029) 161gggggtgtat aggtttcgac
ttgaaaatga agtgttaatt gcatgcggag ggcgttggct 60ggcctcctaa aaagccaaca
aaacaataaa tgccgaacct aaggctgaat gcgaaattat 120tagcttgttt gactcagtag
aggaaagact agctgcttaa ttagcaaaag ttgttagcta 180gataatctct aggtaacccg
gtatctgcga gctccaccag aggcttgcaa aataccgtca 240tttatctggt tggaacttac
tttctctaat tctcaaggaa gttcgttcga gatttttgag 300agtcattggc tgctatagag
gcttctagct aagggagtcc aatgtaaaca attctagaag 360ataagcatgt agaggttagc
agggagtttg tcaaggacga gagttcgagt ctctccacct 420ccacca
426162426RNAChlamydia
pneumoniae (CWL029) 162ggggguguau agguuucgac uugaaaauga aguguuaauu
gcaugcggag ggcguuggcu 60ggccuccuaa aaagccaaca aaacaauaaa ugccgaaccu
aaggcugaau gcgaaauuau 120uagcuuguuu gacucaguag aggaaagacu agcugcuuaa
uuagcaaaag uuguuagcua 180gauaaucucu agguaacccg guaucugcga gcuccaccag
aggcuugcaa aauaccguca 240uuuaucuggu uggaacuuac uuucucuaau ucucaaggaa
guucguucga gauuuuugag 300agucauuggc ugcuauagag gcuucuagcu aagggagucc
aauguaaaca auucuagaag 360auaagcaugu agagguuagc agggaguuug ucaaggacga
gaguucgagu cucuccaccu 420ccacca
426163421DNAFrancisella tularensis 163gggggcgaat
atggtttcga catgaatgtc aaaatctaag gtgcatgccg aggaagtacc 60gtaacctcgt
taataacagt acaaatgcca ataataactg gcaacaaaaa agcaaaccgc 120gtagcggcta
acgacagcaa ctttgctgct gttgctaaag ctgcctagtc tagcttaata 180atctagatgc
gcacggatat gatagtcttt cttatgacac tatctataca tccgttcata 240ttccgcataa
gacggtcttt gctttttgtc tgggagttaa ggctgtattt aacagactcg 300ctaactatta
ccctggctaa ttggggaata gtcaagctaa actcaaatag attagcctaa 360gcatgtagat
ccaaagatct agagtttgtg gacgcgggtt caaatcccgc cgcctccacc 420a
421164421RNAFrancisella tularensis 164gggggcgaau augguuucga caugaauguc
aaaaucuaag gugcaugccg aggaaguacc 60guaaccucgu uaauaacagu acaaaugcca
auaauaacug gcaacaaaaa agcaaaccgc 120guagcggcua acgacagcaa cuuugcugcu
guugcuaaag cugccuaguc uagcuuaaua 180aucuagaugc gcacggauau gauagucuuu
cuuaugacac uaucuauaca uccguucaua 240uuccgcauaa gacggucuuu gcuuuuuguc
ugggaguuaa ggcuguauuu aacagacucg 300cuaacuauua cccuggcuaa uuggggaaua
gucaagcuaa acucaaauag auuagccuaa 360gcauguagau ccaaagaucu agaguuugug
gacgcggguu caaaucccgc cgccuccacc 420a
421165330DNAGuillardia theta (plastid)
165ggggctgatt tggattcgac atataaattt gcgtgtttca ttatgaagca agtcaagttt
60aatgatcttg taaaaaacat taaagtacaa ataaatgcaa gcaatatagt ttcatttagt
120tcaaaacgtt tagtctcttt tgcataagca aaatgtgtta ataactttct tagtagaaat
180tggagaagtt tactaagatt tatatttact ccataattat tttaaagatg gtaaaaaggt
240gattcatcat ttgtatgttt ctaaactttg tgaaagaata gtgggctcca tttataatga
300acgtgggttc aaatcccacc agctccacca
330166330RNAGuillardia theta (plastid) 166ggggcugauu uggauucgac
auauaaauuu gcguguuuca uuaugaagca agucaaguuu 60aaugaucuug uaaaaaacau
uaaaguacaa auaaaugcaa gcaauauagu uucauuuagu 120ucaaaacguu uagucucuuu
ugcauaagca aaauguguua auaacuuucu uaguagaaau 180uggagaaguu uacuaagauu
uauauuuacu ccauaauuau uuuaaagaug guaaaaaggu 240gauucaucau uuguauguuu
cuaaacuuug ugaaagaaua gugggcucca uuuauaauga 300acguggguuc aaaucccacc
agcuccacca 330167348DNAThalassiosira
Weissflogii (plastid) 167ggggctgatt tggtttcgac atttaaaact tctttctatg
tgtcaggtca aagtttgtat 60tctttgtaaa aaaatactaa aatactaata aatgctaata
atataatacc gtttattttt 120aaagcagtaa aaacaaaaaa agaagcaatg gctttaaatt
ttgctgtata gttcattaac 180ttaggttatt aaatattttt tcattataac tggacttttc
tctagtttat agtttagaat 240aaatttaaat tttgcaaaac tcgttcgaaa attttcgggc
taaacctgta aacgcaaata 300ctaagaaatt ttagatggac atgggttcaa ttcccatcag
ttccacca 348168348RNAThalassiosira Weissflogii (plastid)
168ggggcugauu ugguuucgac auuuaaaacu ucuuucuaug ugucagguca aaguuuguau
60ucuuuguaaa aaaauacuaa aauacuaaua aaugcuaaua auauaauacc guuuauuuuu
120aaagcaguaa aaacaaaaaa agaagcaaug gcuuuaaauu uugcuguaua guucauuaac
180uuagguuauu aaauauuuuu ucauuauaac uggacuuuuc ucuaguuuau aguuuagaau
240aaauuuaaau uuugcaaaac ucguucgaaa auuuucgggc uaaaccugua aacgcaaaua
300cuaagaaauu uuagauggac auggguucaa uucccaucag uuccacca
34816919DNAArtificial SequenceDescription of Artificial SequenceV.
cholerae tmRNA specific probe 169aacgaatggc taacctgaa
1917017DNAArtificial
SequenceDescription of Artificial SequenceUniversal ssrA/tmRNA 5'
in vitro amplification primer 170gggmytacgg wttcgac
1717118DNAArtificial SequenceDescription of
Artificial SequenceUniversal ssrA/tmRNA 3' in vitro amplification
primer 171gggartcgaa ccrsgtcc
1817218DNAArtificial SequenceDescription of Artificial Sequence5'
Listeria genus specific PCR amplification primer 172aaagccaata
ataactgg
1817318DNAArtificial SequenceDescription of Artificial Sequence3'
Listeria genus specific amplification primer 173ccagaaatat cggcactt
1817418DNAArtificial
SequenceDescription of Artificial SequenceListeria genus specific
hybridisation probe 174gtgagaccct taccgtag
1817518DNAArtificial SequenceDescription of Artificial
SequenceListeria monocytogenes species specific hybridisation probe
175tctatttaac cccagacg
18176348DNAHelicobacter pylori 176tggggatgtt acggtttcga caggggtagt
tcgagcttag gtggcgagtc gaggggatcg 60gcctcgttaa aacgtcaaag cctataactg
gcaaacaaca aaacaacttc gctttagcag 120cttaataagc tcttagcggt tcctccctcc
atcgcccatg tggtagggta agggactcaa 180attaagtggg ctacgctgga ttccaccgtc
tgaggatgaa agaagagaac aaccagacta 240gctacccgga cgcccgtcga taggcagatg
gagtagcgaa tcgcgaatat atcgactaca 300ctcgtagaag cttaagtgcc gatattcttg
gacgtgggtt cgactccc 348177348RNAHelicobacter pylori
177uggggauguu acgguuucga cagggguagu ucgagcuuag guggcgaguc gaggggaucg
60gccucguuaa aacgucaaag ccuauaacug gcaaacaaca aaacaacuuc gcuuuagcag
120cuuaauaagc ucuuagcggu uccucccucc aucgcccaug ugguagggua agggacucaa
180auuaaguggg cuacgcugga uuccaccguc ugaggaugaa agaagagaac aaccagacua
240gcuacccgga cgcccgucga uaggcagaug gaguagcgaa ucgcgaauau aucgacuaca
300cucguagaag cuuaagugcc gauauucuug gacguggguu cgacuccc
348178344DNAHelicobacter pylori 178tggggacgtt acggtttcga cagggatagt
tcgagcttag gttgcgagtc gaggggatcg 60gcctcgttaa aacgtcaaag cctataattg
gcaaacaaaa caatctttct ttagctgctt 120aattgcacta aaggttcctc cctccatcgt
ccatgtggta gggtaaggga ctcaaactaa 180gtggactacg ccggagttcg ccgtctgagg
acaaaggaag agaacaacca gactagcaac 240ttggaagcct gtcgataggc cgaagagttc
gcgaaatgct aatatatcga ctacactcgt 300agaagcttaa gtgccgatat ttttggacgt
gggttcgatt ccct 344179344RNAHelicobacter pylori
179uggggacguu acgguuucga cagggauagu ucgagcuuag guugcgaguc gaggggaucg
60gccucguuaa aacgucaaag ccuauaauug gcaaacaaaa caaucuuucu uuagcugcuu
120aauugcacua aagguuccuc ccuccaucgu ccauguggua ggguaaggga cucaaacuaa
180guggacuacg ccggaguucg ccgucugagg acaaaggaag agaacaacca gacuagcaac
240uuggaagccu gucgauaggc cgaagaguuc gcgaaaugcu aauauaucga cuacacucgu
300agaagcuuaa gugccgauau uuuuggacgu ggguucgauu cccu
344180322DNAListeria seeligeri (NCTC 11856) 180acagggatag ttcgagcttg
agttgcgagt cggggggatc gtcctcgtta tcaacgtcaa 60agccaataat aactggcaaa
gaaaaacaaa acctagcttt cgctgcctaa taagcagtag 120catagctgat cctccgtgca
tcgcccatgt gctacggaaa gggtctcact ttaagtgggc 180tacactaaat aatctccgtc
tggggttagt tagaagagct taatcagact agctgaatgg 240aagcctgtta ccgggctgat
gtttatgcga aatactaata cggtgactac gctcgtagat 300atttaagtgc ccatatttct
gg 322181322RNAListeria
seeligeri (NCTC 11856) 181acagggauag uucgagcuug aguugcgagu cggggggauc
guccucguua ucaacgucaa 60agccaauaau aacuggcaaa gaaaaacaaa accuagcuuu
cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca ucgcccaugu gcuacggaaa
gggucucacu uuaagugggc 180uacacuaaau aaucuccguc ugggguuagu uagaagagcu
uaaucagacu agcugaaugg 240aagccuguua ccgggcugau guuuaugcga aauacuaaua
cggugacuac gcucguagau 300auuuaagugc ccauauuucu gg
322182322DNAListeria ivanovii (NCTC 11846)
182acagggatag ttcgagcttg agttgcgagt cggggggatc gtcctcgtta ttaacgtcaa
60agccaataat aactggcaaa gaaaaacaaa acctagcttt cgctgcctaa taagcagtag
120catagctgat cctccgtgca tcgcccatgt gctacggtaa gggtctcact ttaagtgggc
180tacactaaat aatctccgtc tggggttagt tagaagagct taatcagact agctgaatgg
240aagcctgtta ccgggctgat gtttatgcga aatgctaata cggtgactac gctcgtagat
300atttaagtgc cgatatttct gg
322183321RNAListeria ivanovii (NCTC 11846) 183acagggauag uucgagcuug
aguugcgagu cggggggauc guccucguua uuaacgucaa 60agccaauaau aacuggcaaa
gaaaaacaaa accuagcuuu cgcugccuaa uaagcaguag 120cauagcugau ccuccgugca
ucgcccaugu gcuacgguaa gggucucacu uuaagugggc 180uacacuaaau aaucuccguc
ugggguuagu uagaagagcu uaaucagacu agcugaaugg 240aagccuguua ccgggcugau
guuuaugcga aaugcuaaua cggugacucg cucguagaua 300uuuaagugcc gauauuucug g
321184319DNAMycobacterium
africanum 184acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcgacca aataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cggctagtct gtcagaccgg gaacgccctc ggcccggacc ctggcatcag
ctagagggat 180ccaccgatga gtccggtcgc gggactcctc gggacaacca cagcgactgg
gatcgtcatc 240tcggctagtt cgcgtgaccg ggagatccga gcagaggcat agcgaactgc
gcacggagaa 300gccttgaggg aatgccgta
319185319RNAMycobacterium africanum 185acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcgacca aauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cggcuagucu gucagaccgg
gaacgcccuc ggcccggacc cuggcaucag cuagagggau 180ccaccgauga guccggucgc
gggacuccuc gggacaacca cagcgacugg gaucgucauc 240ucggcuaguu cgcgugaccg
ggagauccga gcagaggcau agcgaacugc gcacggagaa 300gccuugaggg aaugccgua
319186319DNAMycobacterium
gordonae 186acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca tataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cggctagtct gtcggaccgg gaacgccctc gccccggacc ccggcatcag
ctagagggat 180caaccgatga gttcggtcgc gggactcatc gggacaccaa cagcgactgg
gatcgtcatc 240ctggctagtc cgtgtgacca ggagatccga gcagagacat agcggactgc
gcacggagaa 300gccttgaggg aatgccgta
319187319RNAMycobacterium gordonae 187acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca uauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cggcuagucu gucggaccgg
gaacgcccuc gccccggacc ccggcaucag cuagagggau 180caaccgauga guucggucgc
gggacucauc gggacaccaa cagcgacugg gaucgucauc 240cuggcuaguc cgugugacca
ggagauccga gcagagacau agcggacugc gcacggagaa 300gccuugaggg aaugccgua
319188319DNAMycobacterium
kansasii 188acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca aataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cggctagtct gtcagaccgg gaccgccctc gacccggact ctggcatcag
ctagagggat 180caaccgatga gttcggtcgc gggactcgtc gggacaccaa cagcgactgg
gatcgtcatc 240ctggctagtt cgcgtgacca ggagatccga gcagaggcat agcgaactgc
gcacggagaa 300gccttgaggg aatgccgta
319189319RNAMycobacterium kansasii 189acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca aauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cggcuagucu gucagaccgg
gaccgcccuc gacccggacu cuggcaucag cuagagggau 180caaccgauga guucggucgc
gggacucguc gggacaccaa cagcgacugg gaucgucauc 240cuggcuaguu cgcgugacca
ggagauccga gcagaggcau agcgaacugc gcacggagaa 300gccuugaggg aaugccgua
319190320DNAMycobacterium
chelonae 190acagcgagtc tcgacttaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60attgcaacca attaagcgcc gattctcatc agcgcgacta cgcactcgct
gcctaagcga 120ctgcgtgtct gtcagaccgg gagcgccctc agcccggacc ctggcatcag
ctagagggac 180aaactacggg ttcggtcgcg ggacccgtag ggacatcaaa cagcgactgg
gatcgtcatc 240tcggcttgtt cgcgggaccg agagatccaa gtagaggcat agcgaactgc
gcacggagaa 300gccttaatga acggccgttg
320191320RNAMycobacterium chelonae 191acagcgaguc ucgacuuaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60auugcaacca auuaagcgcc
gauucucauc agcgcgacua cgcacucgcu gccuaagcga 120cugcgugucu gucagaccgg
gagcgcccuc agcccggacc cuggcaucag cuagagggac 180aaacuacggg uucggucgcg
ggacccguag ggacaucaaa cagcgacugg gaucgucauc 240ucggcuuguu cgcgggaccg
agagauccaa guagaggcau agcgaacugc gcacggagaa 300gccuuaauga acggccguug
320192320DNAMycobacterium
szulgai 192acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca attaagcgcc gagaacactc agcgcgactt cgctctcgct
gcctaagcga 120cagcaagtcc gtcagaccgg gaaagccctc gacccggacc ctggcgtcat
ctagagggat 180ccaccggtga gttcggtcgc gggactcatc gggacaccaa cagcgactgg
gatcgtcatc 240ctggctagtt cgcgtgacca ggagatccga gtagagacat agcgaactgc
gcacggagaa 300gccttgaggg aatgccgtag
320193320RNAMycobacterium szulgai 193acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca auuaagcgcc
gagaacacuc agcgcgacuu cgcucucgcu gccuaagcga 120cagcaagucc gucagaccgg
gaaagcccuc gacccggacc cuggcgucau cuagagggau 180ccaccgguga guucggucgc
gggacucauc gggacaccaa cagcgacugg gaucgucauc 240cuggcuaguu cgcgugacca
ggagauccga guagagacau agcgaacugc gcacggagaa 300gccuugaggg aaugccguag
320194320DNAMycobacterium
malmoense 194acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca tataagcgcc gtttcaacac agcgcgacta cgctctcgct
gcctaagcga 120cagctagtcc gtcagaccgg gaacgccctc gacccggagc ctggcgtcag
ctggagggat 180ccaccggtga gtccggtcgc gggactcatc gggacataca cagcgactgg
gatcgtcatc 240ctggctggtt cgcgtgaccg ggagatccga gcagaggcat agcgaactgc
gcacggagaa 300gccttgaggg aatgccgtag
320195320RNAMycobacterium malmoense 195acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca uauaagcgcc
guuucaacac agcgcgacua cgcucucgcu gccuaagcga 120cagcuagucc gucagaccgg
gaacgcccuc gacccggagc cuggcgucag cuggagggau 180ccaccgguga guccggucgc
gggacucauc gggacauaca cagcgacugg gaucgucauc 240cuggcugguu cgcgugaccg
ggagauccga gcagaggcau agcgaacugc gcacggagaa 300gccuugaggg aaugccguag
320196321DNAMycobacterium
flavescens 196acttcgagcg tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca attaagcgcc gattccaatc agcgcgacta cgcactcgct
gcctaagcga 120ctgcgtgtct gtcagcccgg gagagccctc gacccggtgt ctggcatcag
ctagagggat 180aaaccggtgg gtccggtcgc gggactcatc gggacatcaa acagcgactg
ggatcgtcat 240cctgacttgt tcgcgtgatc aggagatccg agtagagaca tagcgaactg
cgcacggaga 300agccttgagg gaacgccgta g
321197321RNAMycobacterium flavescens 197acuucgagcg ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca auuaagcgcc
gauuccaauc agcgcgacua cgcacucgcu gccuaagcga 120cugcgugucu gucagcccgg
gagagcccuc gacccggugu cuggcaucag cuagagggau 180aaaccggugg guccggucgc
gggacucauc gggacaucaa acagcgacug ggaucgucau 240ccugacuugu ucgcgugauc
aggagauccg aguagagaca uagcgaacug cgcacggaga 300agccuugagg gaacgccgua g
321198320DNAMycobacterium
marinum 198acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gatgcaacta gataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cggctagtct gtcggaccgg gaacgccctc gccccggacc ccggcatcag
ctagagggat 180caaccgatga gttcggtcgc ggggctcatc gggacatcaa cagcgactgg
gatcgtcatc 240ctggctagtt cgcgtgacca ggagatccga gcagagacct agcggactgc
gcacggagaa 300gccttgaggg aatgccgtag
320199320RNAMycobacterium marinum 199acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60gaugcaacua gauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cggcuagucu gucggaccgg
gaacgcccuc gccccggacc ccggcaucag cuagagggau 180caaccgauga guucggucgc
ggggcucauc gggacaucaa cagcgacugg gaucgucauc 240cuggcuaguu cgcgugacca
ggagauccga gcagagaccu agcggacugc gcacggagaa 300gccuugaggg aaugccguag
320200319DNAMycobacterium
microti 200acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcgacca aataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cggctagtct gtcagaccgg gaacgccctc ggcccggacc ctggcatcag
ctagagggat 180ccaccgatga gtccggtcgc gggactcctc gggacagcca cagcgactgg
gatcgtcatc 240tcggctagtt cgcgtgaccg ggagatccga gcagaggcat agcgaactgc
gcacggagaa 300gccttgaggg aatgccgta
319201319RNAMycobacterium microti 201acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcgacca aauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cggcuagucu gucagaccgg
gaacgcccuc ggcccggacc cuggcaucag cuagagggau 180ccaccgauga guccggucgc
gggacuccuc gggacagcca cagcgacugg gaucgucauc 240ucggcuaguu cgcgugaccg
ggagauccga gcagaggcau agcgaacugc gcacggagaa 300gccuugaggg aaugccgua
319202321DNAMycobacterium
smegmatis 202acttcgagca tcgaatccag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacca attaagcgcc gattccaatc agcgcgacta cgccctcgct
gcctaagcga 120cggctggtct gtcagaccgg gagtgccctc ggcccggatc ctggcatcag
ctagagggac 180ccacccacgg gttcggtcgc gggacctgtg gggacatcaa acagcgactg
ggatcgtcat 240ctcggcttgt tcgtgtgacc gggagatccg agtagagaca tagcgaactg
cgcacggaga 300agcctcgagg acatgccgta g
321203321RNAMycobacterium smegmatis 203acuucgagca ucgaauccag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacca auuaagcgcc
gauuccaauc agcgcgacua cgcccucgcu gccuaagcga 120cggcuggucu gucagaccgg
gagugcccuc ggcccggauc cuggcaucag cuagagggac 180ccacccacgg guucggucgc
gggaccugug gggacaucaa acagcgacug ggaucgucau 240cucggcuugu ucgugugacc
gggagauccg aguagagaca uagcgaacug cgcacggaga 300agccucgagg acaugccgua g
321204320DNAMycobacterium
xenopi 204acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aagagaccac
cgtaagcgtc 60gttgcaacta aataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cagctagtcc gtcaggccgg gagttccctc gacccggatc ctggcgtcag
ctagagggat 180ccaccgatgg gttcggtcgc gggacccatc gggacaccac acagcgactg
ggatcgccgt 240cccggctagt tcgcgagacc gggagatccg agtaagggca aagcgaactg
cgcacggaga 300agccttgagg gtatgccgta
320205320RNAMycobacterium xenopi 205acuucgcgca ucgaaucaag
ggaagcgugc cggugcaggc aagagaccac cguaagcguc 60guugcaacua aauaagcgcc
gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cagcuagucc gucaggccgg
gaguucccuc gacccggauc cuggcgucag cuagagggau 180ccaccgaugg guucggucgc
gggacccauc gggacaccac acagcgacug ggaucgccgu 240cccggcuagu ucgcgagacc
gggagauccg aguaagggca aagcgaacug cgcacggaga 300agccuugagg guaugccgua
320206320DNAMycobacterium
intracellulare 206acttcgcgca tcgaatcaag ggaagcgtgc cggtgcaggc aaccgaccac
cgtaagcgtc 60gttgcaaaca gataagcgcc gattcacatc agcgcgacta cgctctcgct
gcctaagcga 120cagctagtcc gtcagaccgg gaacgccctc gacccggagc ctggcgtcag
ctagagggat 180ccaccgatga gtccggtcgc gggacttatc gggacaccaa cagcgactgg
gatcgtcatc 240tcggcttgtt cgcgtgaccg ggagatccga gtagaggcat agcgaactgc
gcacggagaa 300gtcttgaggg aatgccgtag
320207320RNAMycobacterium intracellulare 207acuucgcgca
ucgaaucaag ggaagcgugc cggugcaggc aaccgaccac cguaagcguc 60guugcaaaca
gauaagcgcc gauucacauc agcgcgacua cgcucucgcu gccuaagcga 120cagcuagucc
gucagaccgg gaacgcccuc gacccggagc cuggcgucag cuagagggau 180ccaccgauga
guccggucgc gggacuuauc gggacaccaa cagcgacugg gaucgucauc 240ucggcuuguu
cgcgugaccg ggagauccga guagaggcau agcgaacugc gcacggagaa 300gucuugaggg
aaugccguag
320208320DNAMycobacterium scrofulaceum 208acatcgcgca tcgaatcaag
ggaagcgtgc cggtgcaggc aagagaccac cgtaagcgtc 60gttgcaacca attaagcgcc
gattcacatc agcgcgacta cgctctcgct gcctaagcga 120cagctagtcc gtcagaccgg
gaaagccctc gacccggagc ctggcgtcag ctagagggat 180caaccgatga gttcggtcgc
gggactcatc gggacaccaa cagcgactgg gatcgtcatc 240ctggctagtc cgcgtgacca
ggagatccga gcagaggcat agcggactgc gcacggagaa 300gtcttgaggg aatgccgttg
320209320RNAMycobacterium
scrofulaceum 209acaucgcgca ucgaaucaag ggaagcgugc cggugcaggc aagagaccac
cguaagcguc 60guugcaacca auuaagcgcc gauucacauc agcgcgacua cgcucucgcu
gccuaagcga 120cagcuagucc gucagaccgg gaaagcccuc gacccggagc cuggcgucag
cuagagggau 180caaccgauga guucggucgc gggacucauc gggacaccaa cagcgacugg
gaucgucauc 240cuggcuaguc cgcgugacca ggagauccga gcagaggcau agcggacugc
gcacggagaa 300gucuugaggg aaugccguug
320210326DNANocardia asteroides 210actgtgtgcg ccgaggtagg
ggaagcgtgt cggtgcaggc tggagaccac cgttaagcgt 60cgcggcaacc aattaagcgc
cgattccaat cagcgcgact acgccctcgc tgcctgatca 120gcgacggcta gctgtcggcc
cgggttgtgt tcccgaaccc ggatgccggc atcatctcag 180ggaactcacc gtgttcgccg
gtcgcggacg gacacgggac agcaaacagc gactgggatc 240gtcatctcgg cttgttcgcg
tgaccgggag atccaagtag agacatagcg gactgcacac 300ggagaagccc tactgactcg
acacag 326211325RNANocardia
asteroides 211acugugugcg ccgagguagg ggaagcgugu cggugcaggc uggagaccac
cguuaagcgu 60cgcggcaacc aauuaagcgc cgauuccaau cagcgcgacu acgcccucgc
ugccugauca 120gcgacggcua gcugucggcc cggguugugu ucccgaaccc ggaugccggc
aucaucucag 180ggaacucacc guguucgccg gucgcggacg gacacgggac agcaaacagc
gacugggauc 240gucaucucgg cuuguucgcg ugaccgggag auccaaguag agacauagcg
gcugcacacg 300gagaagcccu acugacucga cacag
325212314DNASalmonella enteritidis 212acgggatttg cgaaacccaa
ggtgcatgcc gaggggcggt tggcctcgta aaaagccgca 60aaaaaatagt cgcaaacgac
gaaacctacg ctttagcagc ttaataacct gcttagagcc 120ctctctccct agcctccgct
cttaggacgg ggatcaagag aggtcaaacc caaaagagat 180cgcgtggatg ccctgcctgg
ggttgaagcg ttaaaacgaa tcaggctagt ctggtagtgg 240cgtgtccgtc cgcaggtgcc
aggcgaatgt aaagactgac taagcatgta gtaccgagga 300tgtaggaatt tcgg
314213314RNASalmonella
enteritidis 213acgggauuug cgaaacccaa ggugcaugcc gaggggcggu uggccucgua
aaaagccgca 60aaaaaauagu cgcaaacgac gaaaccuacg cuuuagcagc uuaauaaccu
gcuuagagcc 120cucucucccu agccuccgcu cuuaggacgg ggaucaagag aggucaaacc
caaaagagau 180cgcguggaug cccugccugg gguugaagcg uuaaaacgaa ucaggcuagu
cugguagugg 240cguguccguc cgcaggugcc aggcgaaugu aaagacugac uaagcaugua
guaccgagga 300uguaggaauu ucgg
314214313DNAStaphylococcus epidermidis (NCTC 11047)
214acaggggtcc cccgagctta ttaagcgtgt cggagggttg gctccgtcat caacacattt
60cggttaaata taactgacaa atcaaacaat aatttcgcag tagctgcgta atagccactg
120catcgcctaa cagcatctcc tacgtgctgt taacgcgatt caaccctagt aggatatgct
180aaacactgcc gcttgaagtc tgtttagatg aaatataatc aagctagtat catgttggtt
240gtttattgct tagcatgatg cgaaaattat caataaacta cacacgtaga aagatttgta
300tcaggacctc tgg
313215313RNAStaphylococcus epidermidis (NCTC 11047) 215acaggggucc
cccgagcuua uuaagcgugu cggaggguug gcuccgucau caacacauuu 60cgguuaaaua
uaacugacaa aucaaacaau aauuucgcag uagcugcgua auagccacug 120caucgccuaa
cagcaucucc uacgugcugu uaacgcgauu caacccuagu aggauaugcu 180aaacacugcc
gcuugaaguc uguuuagaug aaauauaauc aagcuaguau cauguugguu 240guuuauugcu
uagcaugaug cgaaaauuau caauaaacua cacacguaga aagauuugua 300ucaggaccuc
ugg
313216302DNAStreptococcus agalactiae (NCTC 8181) 216acaggcatta tgaggtatat
tttgcgactc atcggcagat gtaaaatgcc agttaaatat 60aactgcaaaa aatacaaatt
cttacgcatt agctgcctaa aaaacagcct gcgtgatctt 120cacaagattg tttgcgtttt
gctagaaggt cttatttatc agcaaactac gtttggctac 180tgtctagtta gttaaaaaga
gatttataga ctcgctatgt gagggcttga gttatgtgtc 240atcacctagt taaatcaata
cataacctat agttgtagac aaatatatta gcagatgttt 300gg
302217302RNAStreptococcus
agalactiae (NCTC 8181) 217acaggcauua ugagguauau uuugcgacuc aucggcagau
guaaaaugcc aguuaaauau 60aacugcaaaa aauacaaauu cuuacgcauu agcugccuaa
aaaacagccu gcgugaucuu 120cacaagauug uuugcguuuu gcuagaaggu cuuauuuauc
agcaaacuac guuuggcuac 180ugucuaguua guuaaaaaga gauuuauaga cucgcuaugu
gagggcuuga guuauguguc 240aucaccuagu uaaaucaaua cauaaccuau aguuguagac
aaauauauua gcagauguuu 300gg
30221821DNAArtificial SequenceDescription of
Artificial Sequence Salmonella genus specificic probe 218cgaatcaggc
tagtctggta g
2121923DNAArtificial SequenceDescription of Artificial Sequence
Oligonucleotide probe for detection of tuberculosis complex
219actcctcggg acarccacag cga
2322020DNAArtificial SequenceDescription of Artificial Sequence
Oligonucleotide probes for detection of M.avium and M.
paratuberculosis sequences 220gttgcaaata gataagcgcc
2022120DNAArtificial SequenceDescription of
Artificial Sequence Oligonucleotide probe for detection of M. avium
and M. paratuberculosis sequences 221tccgtcagcc cgggaacgcc
2022218DNAArtificial
SequenceDescription of Artificial Sequence Oligonucleotide probe
used in determination of tmRNA integrity after heat killing
treatment of Listeria cells 222ttttgttttt ctttgcca
1822318DNAArtificial SequenceDescription
of Artificial Sequence Oligonucleotide probe used in determination
of tmRNA integrity after heat killing treatment of Escherichia
coli cells 223agttttcgtc gtttgcga
1822420DNAArtificial SequenceDescription of Artificial Sequence
Degenerative oligonucleotide primer for amplification of all
mycobacterial sequences 224caggcaashg accaccgtaa
2022523DNAArtificial SequenceDescription of
Artificial Sequence Degenerative oligonucleotide primers for
amplification of all mycobacterial sequences 225ggatctccyg
rtcwcrcgra cwa
2322618DNAArtificial SequenceDescription of Artificial Sequence
Oligonucleotide primer for amplification of M. avium and M.
paratuberculosis sequences 226tgccggtgca ggcaactg
1822718DNAArtificial SequenceDescription of
Artificial Sequence Oligonucleotide primer for amplification of M.
avium and M. paratuberculosis sequences 227cacgcgaaca agccagga
1822823DNAArtificial
SequenceDescription of Artificial Sequence Oligonucleotide probe for
the detection of Listeria ssrA gene sequences 228cattaaactt
tagcaaggaa gtg
23229228DNAListeria monocytogenes 229caaagaaaaa caaaacctag ctttcgctgc
ctaataagca gtagcatagc tgatcctccg 60tgcatcgccc atgtgctacg gtaagggtct
cactctaagt gggctacact agttaatctc 120cgtctgaggt taaatagaag agcttaatca
gactagctga atggaagcct gttaccgggc 180cgatgtttat gcgaaatgct aatacggtga
ctacgctcgt agatattt 22823017DNAArtificial
SequenceDescription of Artificial Sequence Synthetic oligonucleotide
primer 230gggnntacgg nttcgac
1723118DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide primer 231gggantcgaa ccnngtcc
1823221DNAArtificial
SequenceDescription of Artificial Sequence Synthetic oligonucleotide
primer 232ggggctgatt ctggattcga c
2123319DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide primer 233ggagttgaac ccccgtccg
1923415DNAArtificial
SequenceDescription of Artificial Sequence Synthetic oligonucleotide
primer 234tggtggagcc ggggg
1523514DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide primer 235agcgacttgg cttc
1423620DNAArtificial
SequenceDescription of Artificial Sequence Synthetic oligonucleotide
primer 236tacatgctta gcaaagatga
2023718DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide primer 237ggagatggng ggaatnga
1823817DNAArtificial
SequenceDescription of Artificial Sequence Synthetic oligonucleotide
primer 238tggtggagat gacggga
1723918DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide primer 239ggggatgtag aggttttg
18
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