NUCLEIC ACID PROBE-BASED DIAGNOSTIC ASSAYS TARGETING SSRA GENES OF PROKARYOTIC AND EUKARYOTIC ORGANISMS

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.

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 microrganisms. 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 is 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 GTAGAGGACTTTCGGACGGGG 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 TB01 SEQ ID NO: 219 5'-ACTCCTCGGACA (A/G) CCACAGCGA-3'

3) Oligonucleotide probes for detection of M. avium and M. paratuberculosis sequences

TABLE-US-00004 Probe 1: SEQ ID NO: 220 PAV1-5'-GTTGCAAATAGATAAGCGCC-3' Probe 2: SEQ ID NO: 221 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: SEQ ID NO: 222 5'-TTTTGTTTTTCTTTGCCA-3'

Escherichia coli: 5) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells:

TABLE-US-00006 Evtm: SEQ ID NO: 223 5'-AGTTTTCGTCGTTTGCGA-3'

[0054] Further representative primers identified in accordance with the invention are as follows:

Mycobacteria:

[0055] 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 5' Primer: SEQ ID NO: 226 AP1for-5'-TGCCGGTGCAGGCAACTG-3' 3' Primer: SEQ ID NO: 227 AP2rev-5'-CACGCGAACAAGCCAGGA-3'

BRIEF DESCRIPTION OF THE DRAWINGS

[0056] In the accompanying drawings:

[0057] FIG. 1 is a clustal alignment of E. coli and V. cholerae ssrA gene sequences;

[0058] FIG. 2 is a photograph of an agarose gel of total cellular RNA prepared from E. coli and V. cholerae cells;

[0059] 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;

[0060] FIG. 4 is a photograph of an agarose gel of the amplified products of universal ssrA gene amplification primers from a panel of organisms;

[0061] FIG. 5 is a clustal alignment of the ssrA gene sequences from the Listeria species;

[0062] FIG. 6 is a clustal alignment of the L. monocytogenes and B. subtilus ssrA/tmRNA gene sequences;

[0063] 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;

[0064] 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;

[0065] 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;

[0066] 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.

[0067] FIG. 11 is a clustal alignment of ssrA gene sequences from C. trachomatis strains;

[0068] FIG. 12 is a clustal alignment of ssrA gene sequences from H. pylori strains;

[0069] FIG. 13 is a clustal alignment of ssrA gene sequences from M. genitalium strains;

[0070] FIG. 14 is a clustal alignment of ssrA gene sequences from N. gonorrhoeae strains;

[0071] FIG. 15 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains;

[0072] FIG. 16 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains and the L. innocua strain;

[0073] 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;

[0074] 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;

[0075] 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;

[0076] 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

[0077] FIG. 21 is a photograph of an agarose gel of RT-PCR generated tmRNA products at various time points post heat treatment.

[0078] 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

[0079] 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. Bacillus subtilus vs. Escherichia coli vs. Mycobacterium Vibrio cholerae tuberculosis rRNA % homology 88 66 tmRNA % homology 68 25

[0080] 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.

[0081] 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.

[0082] 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

[0083] 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.

[0084] The sequence of the V. cholerae tmRNA specific probe is

TABLE-US-00010 5'-AACGAATGGCTAACCTGAA-3' SEQ ID NO. 169

[0085] 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

[0086] 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

[0087] 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.

[0088] Degenerate oligonucleotide primers were synthesised to PCR amplify ssrA gene sequences from total genomic DNA preparations from a broad range of bacteria.

[0089] The sequences of the synthesised degenerate oligonucleotides are as follows:

TABLE-US-00011 (a) tmU5': 5' in vitro PCR amplification primer SEQ ID NO: 170 5'-GGG(A/C)(C/T)TACGG(A/T)TTCGAC-3' (b) tmU3': 3' in vitro PCR amplification primer SEQ ID NO: 171 5'-GGGA(A/G)TCGAACC(A/G)(C/G)GTCC-3'

[0090] Degenerate base positions are in parentheses.

[0091] 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.

[0092] 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

[0093] The universal primers amplified the ssrA gene from both Gram positive and Gram negative bacteria, as shown in Table 2.

TABLE-US-00012 TABLE 2 Bacterial species tested with universal amplification primers. PCR Product Gram negative bacteria Escherichia coli + Salmonella poona + Klebsiella aerogenes + Proteus mirabilis + Proteus rettgeri + Aeromonas hydrophilia + Gram positive bacteria Staphyloccus aureus + 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

[0094] 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.

[0095] The nucleotide sequence determined for the M. bovis ssrA gene shared 100% homology with the Mycobacterium tuberculosis ssrA gene sequence.

[0096] 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.

[0097] 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.

[0098] 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

[0099] 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.

[0100] The sequences of the synthesised oligonucleotides are as follows:

TABLE-US-00013 (a) Ltm1: 5' Listeria genus specific amplification primer SEQ ID NO: 172 5'-AAAGCCAATAATAACTGG-3' (b) Ltm2: 3' Listeria genus specific amplification primer SEQ ID NO: 173 5'-CCAGAAATATCGGCACTT-3' (c) LGtm: Listeria genus specific hybridisation probe SEQ ID NO: 174 5'-GTGAGACCCTTACCGTAG-3' (d) LStm: L. monocytogenes species specific hybridisation probe SEQ ID NO: 175 5'-TCTATTTAACCCCAGACG-3'

[0101] 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.

[0102] 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-00014 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 -

[0103] 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.

[0104] 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

[0105] 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.

[0106] 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-00015 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 - -

[0107] 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

[0108] 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

[0109] 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

[0110] 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 [0111] tested for viability at 0 h, 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

[0112] 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 [0113] +ve is a positive control total RNA sample.

Example 9

Use of the tmRNA Transcript in Distinguishing Between Viable and Non-Viable Bacteria

[0114] 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.

[0115] 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.

[0116] 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.

[0117] 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) [0118] -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), [0119] -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), [0120] -RT, +TP; Lane 6: RT-PCR of RNA (at 1 h time after heat treatment), [0121] +RT, +TP; Lane 7: PCR amplification of RNA (at 2 h time after heat treatment), [0122] -RT, +TP; Lane 8: RT-PCR of RNA (at 2 h time after heat treatment), +RT, +TP; Lane 9: PCR amplification of RNA (at 6 h time after heat treatment), -RT, +TP; Lane 10: RT-PCR of RNA (at 6 h time after heat treatment), +RT, +TP; Lane 11: PCR amplification of RNA (at 24 h time after heat treatment), [0123] -RT, +TP; Lane 12: RT-PCR of RNA (at 24 h time after heat treatment), [0124] +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

Claims

1-29. (canceled)

30. An isolated nucleic acid sequence selected from the group consisting of the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20, 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:19.

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 Chlamydia trachomatis set forth in SEQ ID NO:20, 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:19.

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 Chlamydia trachomatis set forth in SEQ ID NO:20.

36. The method of claim 32, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20.

37. The method of claim 34, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20.

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