Table 1.

Sequences and relative fluorescence intensities of all probes used in this study

Probe nameE. coli positionaProbe sequence (5′→3′)Relative probe fluorescence (% Eco1482)bBright-ness classc
5′3′
Eco1119TGATCAAACTCTTCAATTT1VI
Eco131331CAATCTGAGCCATGATCAA35IV
Eco202037AGCGTTCAATCTGAGCCA44III
Eco323247GCCTGCCGCCAGCGTT42III
Eco383854GTGTTAGGCCTGCCGCC68II
Eco484865TCGACTTGCATGTGTTAG76II
Eco555572TTACCGTTCGACTTGCAT56III
Eco606077TCCTGTTACCGTTCGACT66II
Eco636380GCTTCCTGTTACCGTTCG67II
Eco666683GCTGCTTCCTGTTACCGT62II
Eco707088AGCAAGCTGCTTCCTGTTA48III
Eco737390GCAGCAAGCTGCTTCCTG27IV
Eco797996CAGCAAAGCAGCAAGCTG3VI
Eco8484101TCGTCAGCAAAGCAGCAA6V
Eco8787104CACTCGTCAGCAAAGCAG10V
Eco8989106GCCACTCGTCAGCAAAGC41III
Eco9191108CCGCCACTCGTCAGCAAA70II
Eco102102118ACTCACCCGTCCGCCAC46III
Eco109109126CAGACATTACTCACCCGT40IV
Eco119119136GGCAGTTTCCCAGACATT27IV
Eco127127144CTCCATCAGGCAGTTCC47III
Eco137137154AGTTATCCCCCTCCATCA35IV
Eco145145162TTTCCAGTAGTTATCCCC66II
Eco155155172TTAGCTACCGTTTCCAGT46III
Eco163163180ATGCGGTATTAGCTACCG30IV
Eco173173190TTGCGACGTTATGCGGTA39IV
Eco181181198CTTTGGTCTTGCGACGTT65II
Eco191191209AAGGTCCCCCTCTTTGGTC76II
Eco199199215GGCCCTAAGGTCCCCCT61II
Eco210210226CGATGGCAAGAGGCCCG5VI
Eco216216233GCACATCCGATGGCAAGA21IV
Eco227227243TCCCATCTGGGCACATC26IV
Eco234234251CTAGCTAATCCCATCTGG27IV
Eco244244261ACCCCACCTACTAGCTAA41III
Eco252252268AGCCGTTACCCCACCTA62II
Eco262262279TCGCCTAGGTGAGCCGTT19V
Eco269269285GGATCGTCGCCTAGGTG27IV
Eco280280297CAGACCAGCTAGGGATCG25IV
Eco285285302CCTCTCAGACCAGCTAGG53III
Eco298298315TGTGGCTGGTCATCCTCT56III
Eco303303320TCCAGTGTGGCTGGTCAT25IV
Eco316316333ACCGTGTCTCAGTTCCAG62II
Eco321321338TCTGGACCGTGTCTCAGT71II
Eco334334350CTCCCGTAGGAGTCTGG27IV
Eub338338353GCTGCCTCCCGTAGGAGT58III
Eco343343359CACTGCTGCCTCCCGTA64II
Eco351351369CAATATTCCCCACTGCTGC33IV
Eco360360377CCATTGTGCAATATTCCC35IV
Eco370370386GGCTTGCGCCCATTGTG52III
Eco378378394CTGCATCAGGCTTGCGC32IV
Eco387387403GCGGCATGGCTGCATCA39IV
Eco395395412TTCATACACGCGGCATGG35IV
Eco404404421AAGGCCTTCTTCATACAC37IV
Eco413413429TACAACCCGAAGGCCTTC62II
Eco422422439AAAGTACTTTACAACCCG37IV
Eco431431448TCCCCGCTGAAAGTACTT42III
Eco439439455CCCTTCCTCCCCGCTGA53III
Eco440440456TCCCTTCCTCCCCGCTG83I
Eco443443460TTACTCCCTTCCTCCCCG62II
Eco446446463ACTTTACTCCCTTCCTCC64II
Eco449449467ATTAACTTTACTCCCTTCC35IV
Eco455455473AAAGGTATTAACTTTACTC3VI
Eco468468486AACGTCAATGAGCAAAGGT3VI
Eco474474491CGGGTAACGTCAATGAGC3VI
Eco478478495TCTGCGGGTAACGTCAAT20V
Eco481481498TCTTCTGCGGGTAACGTC21IV
Eco484484501GCTTCTTCTGCGGGTAAC60III
Eco487487504GGTGCTTCTTCTGCGGGT54III
Eco492492509TAGCCGGTGCTTCTTCTG46III
Eco499499516ACGGAGTTAGCCGGTGCT25IV
Eco505505522GCTGGCACGGAGTTAGCC56III
Eco510510527CGGCTGCTGGCACGGAGT37IV
Eco523523540CTCCGTATTACCGCGGCT54III
Eco528528545GCACCCTCCGTATTACCG42III
Eco541541558CCGATTAACGCTTGCACC96I
Eco548548566CAGTAATTCCGATTAACGC42III
Eco559559576GCTTTACGCCCAGTAATT46III
Eco567567584CTGCGTGCGCTTTACGCC44III
Eco577577594AACAAACCGCCTGCGTGC42III
Eco585585602TCTGACTTAACAAACCGC2VI
Eco595595613GGGATTTCACATCTGACTT2VI
Eco603603620GAGCCCGGGGATTTCACA4VI
Eco614614631GTTCCCAGGTTGAGCCCG25IV
Eco621621638AGATGCAGTTCCCAGGTT2VI
Eco627627644AGTATCAGATGCAGTTCC1VI
Eco632632649TTGCCAGTATCAGATGCA2VI
Eco639639656CTCAAGCTTGCCAGTATC4VI
Eco645645662ACGAGACTCAAGCTTGCC22IV
Eco650650667CCTCTACGAGACTCAAGC13V
Eco654654671CCCCCCTCTACGAGACTC17V
Eco657657674CTACCCCCCTCTACGAGA19V
Eco661661678AATTCTACCCCCCTCTAC22IV
Eco665665682CTGGAATTCTACCCCCCT21IV
Eco668668685CACCTGGAATTCTACCCC12V
Eco675675692ACCGCTACACCTGGAATT50III
Eco681681698CATTTCACCGCTACACCT55III
Eco686686703CTACGCATTTCACCGCTA40IV
Eco690690707ATCTCTACGCATTTCACC60III
Eco693693710CAGATCTCTACGCATTTC29IV
Eco704704721CGGTATTCCTCCAGATCT38IV
Eco711711728TCGCCACCGGTATTCCTC62II
Eco722722737GGGCCGCCTTCGCCTC21IV
Eco729729744GTCCAGGGGGCCGCCT37IV
Eco738738755CGTCAGTCTTCGTCCAGG19V
Eco745745762ACCTGAGCGTCAGTCTTC19V
Eco756756773CACGCTTTCGCACCTGAG15V
Eco763763780TGCTCCCCACGCTTTCGC77II
Eco774774791CTAATCCTGTTTGCTCCC52III
Eco781781799CAGGGTATCTAATCCTGTT4VI
Eco792792809CGTGGACTACCAGGGTAT2VI
Eco800800817GTTTACGGCGTGGACTAC31IV
Eco810810827AGTCGACATCGTTTACGG38IV
Eco818818835AACCTCCAAGTCGTCATC10V
Eco828828845TCAAGGGCACAACCTCCA6V
Eco836836852CCACGCCTCAAGGGCAC8V
Eco846846862GCTCCGGAAGCCACGCC42III
Eco853853870ACGCGTTAGCTCCGGAAG52III
Eco863863880GGTCGACTTAACGCGTTA42III
Eco871871888CCCCAGGCGGTCGACTTA87I
Eco881881897GGCCGTACTCCCCAGGC77II
Eco889889906TAACCTTGCGGCCGTACT85I
Eco898898916ATTTGAGTTTTAACCTTGC73II
Eco907907925CGTCAATTCATTTGAGTTT40IV
Eco917917933CGGGCCCCCGTCAATTC69II
Eco926926941CGCTTGTGCGGGCCCC38IV
Eco934934951CATGCTCCACCGCTTGTG50III
Eco942942959TTAAACCACATGCTCCAC46III
Eco952952969TTGCATCGAATTAAACCA4VI
Eco960960977TCTTCGCGTTGCATCGAA60III
Eco970970987CAGGTAAGGTTCTTCGCG33IV
Eco978978995GTCAAGACCAGGTAAGGT27IV
Eco9889881005TTCCGTGGATGTCAAGAC8V
Eco9969961013CTGAAAACTTCCGTGGAT10V
Eco100610061023ATTCTCATCTCTGAAAAC4VI
Eco101410141031GAAGGCACATTCTCATCT8V
Eco102410241041CACGGTTCCCGAAGGCAC31IV
Eco103210321049ACCTGTCTCACGGTTCCC52III
Eco104210421059GCCATGCAGCACCTGTCT48III
Eco105010501067TGACGACAGCCATGCAGC6V
Eco106010601077CAACACGAGCTGACGACA2VI
Eco106810681085ACATTTCACAACACGAGC12V
Eco107810781095ACTTAACCCAACATTTCA6V
Eco108610861103GTTGCGGGACTTAACCCA10V
Eco109710971112GTTGCGCTCGTTGCGGG6V
Eco110411041121AGGATAAGGGTTGCGCTC8V
Eco111311131130TGGCAACAAAGGATAAGG2VI
Eco112211221139CCGGACCGCTGGCAACAA15V
Eco113111311146TTCCCGGCCGGACCGC40IV
Eco114011401157TCTCCTTTGAGTTCCCGG46III
Eco114711471165ACTGGCAGTCTCCTTTGAG13V
Eco115811581175CCAGTTTATCACTGGCAG2VI
Eco116611661183ACCTTCCTCCAGTTTATC10V
Eco117611761193CGTCATCCCCACCTTCCT50III
Eco118411841201TGACTTGACGTCATCCCC6V
Eco119411941211AGGGCCATGATGACTTGA10V
Eco120212021219TGGTCGTAAGGGCCATGA2VI
Eco121212121229TGTGTAGCCCTGGTCGTA25IV
Eco122012201237GTAGCACGTGTGTAGCCC58III
Eco123012301247ATGCGCCATTGTAGCACG35IV
Eco123812381255CTCTTTGTATGCGCCATT31IV
Eco124812481265GAGGTCGCTTCTCTTTGT58III
Eco125612561273GCTCTCGCGAGGTCGCTT62II
Eco126612661283AGGTCCGCTTGCTCTCGC58III
Eco127412741291ACTTTATGAGGTCCGCTT15V
Eco128412841301ACTACGACGCACTTTATG15V
Eco129212921309CAATCCGGACTACGACGC23IV
Eco130213021319TTGCAGACTCCAATCCGG33IV
Eco131013101327GAGTCGAGTTGCAGACTC2VI
Eco132013201337CGACTTCATGGAGTCGAG6V
Eco132813281345AGCGATTCCGACTTCATG65II
Eco133813381355CACGATTACTAGCGATTC15V
Eco134613461363TTCTGATCCACGATTACT12V
Eco135613561373CACCGTGGCATTCTGATC19V
Eco136413641382GAACGTATTCACCGTGGCA21IV
Eco137413741391AAGGCCCGGGAACGTATT52III
Eco138313831400GGTGTGTACAAGGCCCGG65II
Eco139213921409GTGACGGGCGGTGTGTAC67II
Eco140114011418TCCCATGGTGTGACGGGC67II
Eco141014101427GCAACCCACTCCCATGGT90I
Eco141914191436ACTTCTTTTGCAACCCAC23IV
Eco142814281445AAGCTACCTACTTCTTTT38IV
Eco143714371454CCGAAGGTTAAGCTACCT4VI
Eco144614461463AGCGCCCTCCCGAAGGTT44III
Eco145514551472AAAGTGGTAAGCGCCCTC31IV
Eco146414641481ATGAATCACAAAGTGGTA4VI
Eco147314731490ACCCCAGTCATGAATCAC65II
Eco148214821499TACGACTTCACCCCAGTC100I
Eco149114911508TTACCTTGTTACGACTTC31IV
Eco150015001517CCCCTACGGTTACCTTGT92I
Eco150915091525CGCAGGTTCCCCTACGG4VI
Eco151815181535GTGATCCAACCGCAGGTT17V
Eco152615261542TAAGGAGGTGATCCAAC25IV
  • a E. coli positions according to the numbering of Brosius et al. (7).

  • b Fluorescence intensities expressed as percentages of that for the brightest probe detected, Eco1482.

  • c Probes were grouped according to their relative fluorescences into six classes of brightness: class I (100 to 81% relative fluorescence compared to Eco1482), class II (80 to 61%), class II (60 to 41%), class IV (40 to 21%), class V (20 to 6%), and class VI (5 to 0%).