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Database

Multiple Alignment

IDsAligned Sequences
Consensus structure

5'-.<<<<<<<<<<.<<<<.<<<...................<<<<<<<<.<<<.....................<<<.<<<<<.......<<<<<<<..

........<<....<<<<<..........................................>>>>>....>>........>>>>>>>...>>>>>...>>

>........................>>>.>>>>>.>>>..................>>>>>>>...>>>>>>>>>>..-3'

 
RS002261 (Aquifex aeolicus VF5)

5'-UAAGGUCUGCC-CUGUUCGUGGUGCGGGGGUU-------GUCAAUGGGGCCUACACCGUGGGUGUAA-----GGGAAGUCGACU----UCGGGAA--

--------------CU-------------------------------CCGGA------------AG-----------GA-UUCCCGA--GGGACU--UCC

CAC--CUUA---AAG---CUCUG-AGGC-CCA-C-GGCA-----CUUCCUGCACU-GCGGCAG---GGCGGACACUCU-3'

RS002262 (Synechococcus sp. WH 8102)

5'-CCUGAACUGCU-GUGUUGGUGACGGCCUUUUCUAG----UGCUCUGA--UCUGACUCUCUUUCGACUU----GGGGAGACUGUC----GUGACGGUG

C-C-----GU-AAACCGGC----------------------------CCUGU--------AGCCGGAA--AC---G--AAUCCCCAC-UUUGUUU--CCC

CUU--CUGG---UUC---UUCCA--GG--UC-GA-CCAC-----U--GGGGCUCGCACGGCAC---GGUGGUUCACCC-3'

RS002263 (Synechococcus elongatus PCC 7942)

5'-AUCUGGCUGCG-ACGU-UGGUGACUGCCAACAAUG----UUUUUUGA--UCUAUACCUUUCGAAGUU-----GGGCGCUCUCGCAG--AGCCGACGG

C-A-----GU-AGACCGAG----------------------------CUUGA---------CUCGGAA--AC---UUAAUGUUGGCC--GCAAGC--UCC

CCC--CUGG---UUC---UCCCA--GG--UCG---AAAU-------CUGAGGUAAAACGGCGU---CGCGGUUAGAUC-3'

RS002264 (Prochlorococcus marinus str. MIT 9313)

5'-CUUGAACUGCU-GUGU-UGGUGACGGCCUUUUUCUAG--UGCUCUGA-UCUGACUCUCUUUCGAUUU-----GGGGAGGCUGUC----GUGAAGGUG

A-C-----GU-AGACCGGA----------------------------CUUGC--------UUCCGGAA--AC---G--AAGCCCCAC-UUUGCUU--CCC

CUU--CUGG---UUC---UUCC---AGG-UCG-A-ACAC-----U--GGGGCUCGCACGGCAU---GGCGGUUCACCU-3'

RS002265 (Prochlorococcus marinus subsp. marinus str. CCMP1375)

5'-AGAGAACUGUU-UUGUUGGUGAUGACCUUUUAAGU----GC-UCUG--AUCUGACUCUUUUUCGACUU----GAGGAGACUGUU----GUUAUCGUG

AA------GU-AAACCAGU----------------------------CAUGC--------AACUGGAA--AU---GGAUC--AUUAC-UUUGACU--CCU

CUU--CUGG-CUUAU-----CCA--GGU--C-GAACGCU---------UAGGUCACACGGCAA---AAUGGUUCUAUA-3'

RS002266 (Prochlorococcus marinus subsp. pastoris str. CCMP1986)

5'-UACAUACUGGA-UCUUUGGUCAAGUUCUUCUUUAUG---UGCUCUGA-UCUGACUCUUUUUCGACUU-----GAGGAGACUGUC----GUGAUGUAG

A-C-----GU-AAACCAAU----------------------------CCUGU--------AAUUGGAA--AC---G-AAAGCC-CAC-UUUGACU--CCU

CUU--CUGG--CUUU----UCC---AGG-UCG-AUGCAU-------CAGAGAACUGGCGGGGA---UUCGGUGUUACC-3'

RS002267 (Bacillus subtilis subsp. subtilis str. 168)

5'-AAGAAGCUACU-UUGUGCGU--AUUGUUAAUU-------AAGUUUUA-ACCUUUAAGCUGUAAUA-------GGGAGUUUUAUAUC---GAAGCCGG

AAUG----UC-AUGCCUCC----------------------------AUUGC---------AGAGGAC--GA--CAGGAACGUUUC--UGCAAAC--ACC

CAC--UUUG---AGG----AGUGGUGGUUUAAAA-CUU------UCUUACUUGCAUACGGCAA-GACGUAGCGAAAGC-3'

RS002268 (Bacillus subtilis subsp. subtilis str. 168)

5'-AAAGUCCUGAU-GUGUUAGUUGUACACCUA---------GUUU-UGA--CCGAACAUUUUUUUGAUUU----GGGAGCCCGCAUU---UUUAAAUGG

CGU-----AC-AUGCCUCUUUUCA-----------------------UUCGG------UAAAGAGGAC--UU---ACAAGAUUUAAA-AGAGGGC--ACC

CAC--CUGC--UGAG----AGCG--GGU-UCA-A-AAC---AAAGGAAAGCUGCA-ACGGCAC--UAUUGGGACUUUA-3'

RS002269 (Bacillus phage phBC6A52)

5'-AAAUUCCUACG-GUGUACGUAGCUUAUGCAUG-------UCU--UAA-ACCAAUAAGUUUAAUAU-------GGAAGUUCAAUAUU--UAAAUGUAG

CUA-----AC-AUGCCAUC----------------------------UUUUU-------AAGAAGGAA--GU---UACAAACAUUUG-UGAGAGC--AUC

CAC--CUGU---GAG----AGCA--GGU-UUAU--GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAUA-3'

RS002270 (Bacillus thuringiensis serovar konkukian str. 97-27)

5'-CACAUCCUGCG-GUGUACGUAACUUAUUUA---------UGUCUAAA-ACCGAUGUUAGUUAUAC-------GGAAGCUCAAUAUUU-AGUGACCAU

C-A-----UC-AAGCCUUC----------------------------CUUGU---------GGAGGAA--GA---UGUACGGUAACUGUGAGGGC--AUC

CAC--CUGC--GAGU----AGCG--GGUUUUUGG-ACAU-----U---UACGAGGAGCGGCAC--GUGCGGGG-GUCU-3'

RS002271 (Bacillus cereus ATCC 10987)

5'-UACAUCCUGCG-GUGUACGUAACUUAUUUA---------UGUCUAAA-ACCGAUGUUAGUUAUAC-------GGAAGCUCAAUAUU--UAGCGACCA

UCA-----UC-AAGCCUUC----------------------------CUUGU---------GGAGGAA--GA--UGUACGGUAACUG-UGAGGGC--AUC

CAC--CUGC--GAGU----AGCG--GGUUUUUGG-ACAU-----U---UACGAGGAGCGGCAC--GUGCGGGG-GUCU-3'

RS002272 (Bacillus thuringiensis serovar konkukian str. 97-27)

5'-AAAUUCCUACG-GUGUACGUAGCUUAUGCAUG-------UCU--UAA-ACCAAUAAGUUUAAUAU-------GGAAGUUCAAUAUU--UAAAUGUAG

CUA-----AC-AUGCCAUC----------------------------UUUUU-------AAGAAGGAA--GU---UACAAACAUUUG-UGAGAGC--AUC

CAC--CUGU---GAG----AGCA--GGU-UUAU--GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAUA-3'

RS002273 (Bacillus cereus ATCC 10987)

5'-AAAUUCCUACG-GUGUACGUAGCUUAUGCAUG-------UCU--UAA-ACCAAUAAGUUUAAUAU-------GGAAGUUCAAUAUU--UAAAUGUAG

CUA-----AC-AUGCCAUC----------------------------UUUUU-------AAGAAGGAA--GU---UACAAACAUUUG-UGAGAGC--AUC

CAC--CUGU---GAG----AGCA--GGU-UUAU--GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAAA-3'

RS002274 (Bacillus anthracis str. 'Ames Ancestor')

5'-AAAUUCCUACG-GUGUACGUAGCAUAUGCAUG-------UCU--UAA-ACCAAUAAGUUUAAUAU-------GGAAGUUCAAUAUU--UAAAUGUAG

CUA-----AC-AUGCCAUC----------------------------UUUUU-------AAGAAGGAA--GU---UACAAACAUUUG-UGAGAGC--AUC

CAC--CUGU---GAG----AGCA--GGU-UUAU--GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAUA-3'

RS002275 (Listeria monocytogenes)

5'-GAAACCCUAAU-GUAUUCGAUAUAGUUCCUGAUA-----UUUU-UGA-ACCGAACAAUUUUUUAUACCUA--GGGAGCUUGGAGUU--CCGGCGCGG

CGC-----AC-AUGCCUU-----------------------------CACAC----------GAGGAA--GU---GCAAACCGUUAG-ACAGAGC--ACC

CAC--CUGCUUUAAUUGAGAGCG--GGU-UCA-A-AGG-----AAGGGAAUCCUAAACGGUAC--GAUUGGGGUUUCU-3'

RS002276 (Listeria monocytogenes str. 4b F2365)

5'-GAAACCCUAAU-GUAUUCGAUAUAGUUCCUAAUA-----UUUU-UGA-ACCGAACAAUUUUUUAUACCUA--GGGAGCUUGGAGUU--CCGGCGCGG

CGC-----AC-AUGCCUU-----------------------------CACAC----------GAGGAA--GU---GCAAACCGUUAG-ACAGAGC--ACC

CAC--CUGCUUUAAUUGAUAGCG--GGU-UCA-A-AGG-----AAGGGAAUCCUAAACGGUAC--GAUUGGGGUUUCU-3'

RS002277 (Listeria innocua)

5'-GAAACCCUAAU-GUAUUCGAUAUAGUUCCUGAUA-----UUUU-UGA-ACCGAACAAUUUUUUAUACCUA--GGGAGCUUGGAGUU--CCGGCGCGG

CGC-----AC-AUGCCUU-----------------------------CACAC----------GAGGAA--GU---GCAAACCGUUAG-ACAGAGC--ACC

CAC--CUGCUUUAAUUGAGAGCG--GGU-UCAAA-GGA------AGGGAAUCCUAAACGGUAC--GAUUGGGGUUUCU-3'

RS002278 (Sporosarcina pasteurii)

5'-UACAAGCUGCA-UUGUUCGU--AUCAUUAUUAAG-----UUU--UAA--CCUUUAAGCUGUAAAA-------GGGAGUUUUAUGAU--UGAAACUGA

AAU-----GGCAAGCCUCGUU--------------------------CUUUUAAUUAACAACGAGGACAGAC---AGGCAAGUUUCU--GCGAAC--ACC

CAC--UUUG---AGG----AGUGGUGGU-UUA---AGAC----UUUCUAGAGACGUACGGCAG--AGGCGGCUGAUAC-3'

RS002279 (Staphylococcus aureus subsp. aureus MSSA476)

5'-AGUCAUCUGAG-UUGUUCGUAAGUUUGCUUUU-------UAAUUUGG-GCCUAACACUCUUUGAUCAA----GGGAGCCCAAUGGGUUUUCUUGCAG

CGU-----AC-ACGCCUU-----------------------------AUAUG----------AAGGAC--GU---ACAAAACAAGAA-ACAGGGC--ACC

CAC--CUGU--AUAU----AACA--GG--CCGAA-UGAU-CAAGCUAUUAUAACU-ACGGCAA---UACGGAC-UCUA-3'

RS002280 (Staphylococcus epidermidis ATCC 12228)

5'-AGUCAUCUGUG-GUGUUCGUAAGUUUGCUUU---------UUAUUUGGGCCUAACACUCUUUGAUCA-----GGGAGCCCAAUAGGUUUUCUCGCAG

CGC-----AC-ACGCCUC-----------------------------UAUAG----------GAGGAC--UU---GCAAAACGAGAA-ACAGGGC--ACC

CAC--CUGU--AUAU----AGCA--GGC-CGAAU-GAU-CAAGCUAUUUAUAACU-ACGGCAU--CAACGGACUCUAU-3'

RS002281 (Clostridium tetani E88)

5'-UAAUUUCUGAA-AUAUUUGAGGGUUCCAU----------AUUU-UGA-ACCUACAGAUCAUAAAC-------GGGAGUUCAAAAUU--UAGAUAUGA

AAU-----GA----CCUAUAAGA------------------------CCAGU---UUAAGGCAAGG----AC--AAUGCAGUAUCUG-UGAGAAC--ACC

CAC--CUAU-CAGAA----GAUA-GGGUGUCA-A-AAU----------UGGAGCAAACGGUAU---UUUGGAUUUCAG-3'

RS002282 (Clostridium acetobutylicum ATCC 824)

5'-GAUUUUCUGAA-GUAUUUGUGAAGCUCUUA---------UUU--UGA-ACCUACAGUUCAAACAA-------GGGAGUUCAAUAUU---UAGAUGAG

UAU-----AU-GUGC-UUCAUGUGAAUC-------------------CUUUU-ACGGUAUUGAAUGAG--AU---AGAUGCAUCUG--UGAGGAC--ACC

CAC--CUAU-CGUAG---AGAUA--GGUGUCA---AAAU---------UGGGGUA-ACGGUAU---UUUGGAUUUACA-3'

RS002283 (Clostridium acetobutylicum ATCC 824)

5'-UAUCUUCUAGA-GUAUACGCCAAGCUCUUA---------UC--UUGA-ACCUACAGUUUAAAAAC-------GGGAGUUCAAUAUA--UAAAUAUGG

A-U-----AU-GGAUUUCU----------------------------UAUGU-----UUUAAGAAAAG--AU---A-GAAGUAUUUU-UGCGAGC--ACC

CAC--CUAU--CAUU---AGAUA--GGUGUCAAU--GAA----------AGAGCA-GCGGUAU---UUUGGAUAUAUA-3'

RS002284 (Thermoanaerobacter tengcongensis MB4)

5'-AAAACCCUGUG-GUGUUCGUGUGACCCGGUGAA------AGGU-UGA-GCCAACACCAAAAAUAA-------GGGAGCCUGGGCUU--UGGCAGUGG

AUU-----GU-AGGCCGC-----------------------------CUCGU--------C-GCGGAA--AC---AUGAAGCUGCCA-AGAGGGC--ACC

CAC--UUUG--UGAG----GACG--GGU-UCAAAACCU------ACCGGUAGGC--ACGGCAC---UAUGGGGUUUUU-3'

RS002285 (Thermoanaerobacter tengcongensis MB4)

5'-AAGUUCCUGUG-GGGUUUGUAGCGGGCUAAUUU------GUUU-UCA-CCCAACGCAACCCAUAC-------GGGAAUCCGGGUU---CAUCAGUGG

AUG-----AA-AUGCCUGG-----------------------------GAAA---------CCAGGAC--UU---CAGAAGCUGGUG-ACAGGGU--ACC

CAC--CUGC---GAG----AGCA--GGGAUGA-A-AAC----------AUAGCCGUACGGCUC---CGUGGGUAAAGU-3'

RS002286 (Enterococcus faecalis V583)

5'-GUAAAUCUGUG-AUGUACGCGUUGUCCUUUCACU-----GUGU-UGA--CCGAACAUUUUUAUUGAUAUCUAGGGAUCCUGCUUGUA-UCAAAGUUG

GUA-----AC-AUGCCUU-----------------------------UUCUU----------UUGGUA--GU---UCAAUACUGCGA-UCGAGGA--ACC

CAC--CUGC--UUAU--CUUGCG--GGU-UCA-A-UAC-----UCUAGGACGAUUACCGGCAU--CGACGGAUUUUAC-3'

RS002287 (Lactobacillus plantarum WCFS1)

5'-AAAUUACUAAG-GUGUGCGCAUUGCUCUAAACAAA----GUGU--UG--CCGAACAAUUAAUACUACUUU--GGGAUGUCCGUUAG--CUAAUUCCA

U-A-----AC-AUGCCUU-----------------------------AUCCU----------UUGGUA--GU----UAGCGAAUUAGUCAGAACG--UCC

CAC--CUGC-CUUAA----AGCG--GG--UCA-A-UAC-----UGAAGGGCGAUUAACGGCAC--CACUAGUUUUUCC-3'

RS002288 (Lactococcus lactis subsp. lactis Il1403)

5'-AAAGCACUGG-AAUGUGCGAGCUCUUUCAUUUUU---------UUGA--CCGACUAUAUUUGUAUUGCAUA-GGG-GUUCAUGAGAC-AUUCGGUAG

CGUA-------AUACCUCG----------------------------AACGA-----AAGUAGGGGAA-G-----CUGAUGC-GAAG-CGAGAAC--ACC

CAC--CUGG-CGUUU---UAGCG--GGU-UCAA--UAC------ACGGAAGAGCAUACGGCAUUCAAUCAGUGUUUUU-3'

RS002289 (Streptococcus pyogenes MGAS8232)

5'-ACAUUGCUGUG-GCAUACGA-AUCCACAUCUAA------GUGU-UGA--CCGACUAUUUCUUUGUAUUUUC-GGGAAACAAAGAC---UCUUUCUAG

UCU-----GC-AAGCCGU-----------------------------UUCAC----------GCGGAC--GCAACUUCCAAGAAAGA-GCGCGUU--ACC

CAC--CUGCUUAUAC----UGCGCGGGC-UCA-A-UAC----AAAAACGUGGAUCACCGGUGCCAAUACAGCAUUCUU-3'

RS002290 (Streptococcus agalactiae NEM316)

5'-ACAUUGCUGUG-GCAUACGA-AUCCACAUCUAA------GUGU-UGA--CCGACUAUUUCUUUGUAUUUC--GGGAAACGAAGU----CAUCUCUAG

UGC-----GC-AAGCCGU-----------------------------UAACA--------C-GCGGAA--GC-CACUUAAAGAGGUG--CGAGUU--ACC

CAC--CUGC--UUAUUUUGUGCG--GGA-UCA-A-UAC-----AAAAAGUGGAUCAUCGGUGCCAAUACAGCUUCCUA-3'

RS002291 (Streptococcus pneumoniae TIGR4)

5'-GAAACGCUGUG-GUGUACGACUUCACACUUAA-G-----UGU--UGA--CCGACUAUUUUUUGUAUUAUUA-GGGAAACAAAAGUC--UUCUAACAG

CAU-----GU-AGGCCGU-----------------------------CUCAC----------ACGGAA--AC-AGCUUCAGUUAGAG--CGAGUU--GCC

CAC--CUGC-UUAAU----UGCGCGGGU-UCA---AUAC----AAACCGUGAAGUUUCGGCACCAAUACAGCUUUUUU-3'

RS002292 (Caulobacter crescentus CB15)

5'-GUCUUGCUGUG-GCUCUCGUCGAAGAUUUCUAU------UCCCAGGG-ACCUUAAUCUCUCUAUC-------GGGACCUGUUCCCU-----------

--C-----------CCGUGGC--------------------------CGUGG--------CUGCGG-----------GAA---------CACGGG--GCC

CAC--CUGU---AAC---UAACA--GGU-UCGAGUGGAU-----UGAAACGUCUUCACGGUUC-UUCGCGGCGCCGCC-3'

RS002293 (Bartonella henselae)

5'-GGUGUUCUGCG-CCUCUCGACAGGAAAUAACAUA-----UUCCUGAG-ACCUUAGUGAUUUCCAA-------GGGAGCUGUCCC----UGA------

--------------UUAAG----------------------------CUCGU------GGGCUUUU------------------UCA--UAUGGC--GCC

CAC--CUAU--UUAU-----AUA--GGUUCCCAG-GGAU-----CAACUUUUUCCAUCGGUUG--UUGUGGAUCACCA-3'

RS002294 (Bartonella quintana str. Toulouse)

5'-GGUGUUCUGCG-CUUCUCGACAGGAAAUAACAUA-----UCCUGAGA--CCUUAGUGAUCUCCAA-------GGGAGCUGUCCCU---GAUCAAG--

--------------CC-------------------------------CGUG-------------GG--------------CUUUUUC-AUAUGGC--GCC

CAC--CUAU---UUU-----GUA--GGU-UCCCG-GGAU-----CAACUUUUUCCAUCGGUCG--UUGUGGAUCACCA-3'

RS002295 (Rhodopseudomonas palustris CGA009)

5'-GCGAAGCUGCG-GGACGCGUCAGGAGCCAUAUA------UCCCCGGG-GCCUUAUCGAUCCUUUC-------GGGAACUGUCCC-------------

-----------UGGCCGGGUC--------------------------CGUGG--------ACCCGGUC-A-------------------UAUGGU--GCC

CAC--CUAC---UUU----CGUA-GGGAACUCCG-GGAU-----CGAGUGCUUCA-ACGGUCA--CCGUGGCCUCGCA-3'

RS002296 (Brucella melitensis 16M)

5'-GGCGAACUGCG-CUUCCCGACAGGUGUAACAGCA-----UCCCCGGG-GCCUUAUUGAUCUCUAA-------GGGAGCUGUCCCU---GUGAAGG--

--------------CU-------------------------------UGCGG-------------G--------------CUUUCGC-AUAUGGC--GCC

CAC--CUAC---UUU-----GUA--GGU-UCCCG-GGAU-----CAAUCACUACCAUCGGCCG--UCGUGGU-CGCCG-3'

RS002297 (Agrobacterium tumefaciens str. C58)

5'-UGCGUUCUGCG-CUUCCCGACAGGAACCACA--------AUCCCUGGGGCCAUACUCGAUCCAAA-------GGGAGCUGUCCC-------------

--------UG---GCCAGU----------------------------CCUGU------GGGACUGGA---CA-----------------CACGGC--GCC

CAC--CUAC---UUU----UGUA--GGCACCCAG-GAUC-----GUAAAUCUCCA-UCGGUCG--CCGCGGAUCGCAC-3'

RS002298 (Sinorhizobium meliloti)

5'-GGCGAUCUGCG-CUUCCCGACAGGAACCACAA-------UCCCCGGG-GCCAUACACGAUCUCAA-------GGGGACUGUCCCUG-----------

--G-----------CCGGA----------------------------CCCGU------GGGUCCGG-----------GCA---------UACGGU--GCC

CAC--CUAC---CUA-----GUA--GGU-ACCCG-GGAU----CGUAAAUCAUCCAUCGGUCG--UCGUGGAUCGCAC-3'

RS002299 (Anaplasma phagocytophilum)

5'-GGGGGUCUGCG-UUGUUCGU--GUAGGUUGAAAG-----UGCCUCGA-GCCCGAUUUUGUUCUUAUA-----GGGAGCCGUCAC----UGGUAAC--

--------------CU-------------------------------CGAGU------------AG--------------GUUAUUA--CACGGC--GCC

CAC--CUUA---GCU-----UUA--GUC-UC-AG-G-AC--ACUAAGCAAAGCGUUACGGCAA--AUGCGGAUCUCCU-3'

RS002300 (Rickettsia conorii)

5'-A-UUAGCUGCU-UGGUUCGUGAGCUUAAUAUUAA-----CCU--AGG-ACUACCACUAACUUUUA-------GGACAUCGUCCC----UGUCUAAUA

--------------CU-------------------------------AAUUC------------AG---------U----UUAGAUA--UAUGAA--GUC

CAC--CUUU---ACA----UAAA--GGU-CUUUGAAGG--------AUUUUAAGUAACGGCCA--AAGCGGUCAUGUA-3'

RS002301 (Rickettsia conorii str. Malish 7)

5'-UAUUAGCUGCU-UGGUUCGUGAGCUUAAUAUUAA-----CCU--AGG-ACUACCACUAACUUUUA-------GGACAUCGUCCC----UGUCUAAUA

--------------CU-------------------------------AAUUC------------AG---------U----UUAGAUA--UAUGAA--GUC

CAC--CUUU---ACA----UAAA--GGU-CUUUGAAGG--------AUUUUAAGUAACGGCCA--AAGCGGUCAUGUA-3'

RS002302 (Rickettsia typhi str. Wilmington)

5'-UCUUGGCUGCU-UGGUGCGUGAGCUUAAUAUUAA-----CCUAGGACUACCACUAACUUUUA----------GGACAUCAUCUC----UGUCUAACA

--------------CU-------------------------------AAUUC------------AG---------U----UUAGAUA--UAUGAA--GUC

CAC--CUUU---ACA----UCAA--GGUCUUUGA-AGGAUU--------UUAAGUAACGGCCA--AAGCGGUCAUGUA-3'

RS002303 (Rickettsia prowazekii)

5'-UCUUGGCUGCU-UGGUGCGUGAGCUUAAUAUUAA-----CCU--AGG-ACUACCACUAACUUUUA-------GGACAUCGUCUC----UGUCUAAUA

C-------------UC-------------------------------AUUCA------------GU--------------UUAGAUA--UAUGAA--GUC

CAC--CUUU---ACA----UCAA--GGU-CUUUGAAGG--------AUUUUAAGUAACGGCCA--AAGCGGUCAUGUA-3'

RS002304 (Wolbachia endosymbiont of Drosophila melanogaster)

5'-AAGGGUCUGU-UCUAUGCGUUAUGAGUUAAGUUAAA---UUUCCCGA--GCGAUAAUUUCUAGUCAA-----GGGAAUUGCCUC----UGUUAAU--

--------------UU-------------------------------CGUUG------------AA--------------AUUGAUA--CGCGAU--GCC

CAC--CUUA---ACU-----UUA--GUC-UC-AG-GAAU-----CUACUAAGGCUGACGGUAG--AUACGGAUCCUAU-3'

RS002305 (Bordetella pertussis)

5'-UUGUCCCUGCC-GUGCUCGUGACUUGGCCAUACAU----UCUCU-GA-ACCUAUGUCUUACGGCAUAUG---GGUUGCGGGAGU----GUAGAGUUG

GAG--------UGAUCGUCUA--------------------------CUCGU--------AGACGAACCC-------GAUGCUCUUC-GGAUCGC--GAC

CAC--CUUG---AAC----CUCA-GGGU-UC--G-AGAU-----GCCGGCC--UUGACGGCAC--AGGCGGGG-CAUC-3'

RS002306 (Bordetella parapertussis)

5'-UUGUCCCUGCC-GUGCUCGUGACUUGGCCAUACAU----UCUCU-GA-ACCUAUGUCUUACGGCAUAUG---GGUUGCGGGAGU----GUAGAGCUG

GAG--------UGAUCGUCUA--------------------------CUCGU--------AGACGAACCC-------GAUGCUCUUC-GGAUCGC--GAC

CAC--CUUG---AAC----CUCA-GGGU-UC--G-AGAU-----GCCGGCC--UUGACGGCAC--AGGCGGGG-CAUC-3'

RS002307 (Ralstonia solanacearum)

5'-GUUUCCCUGCC-UGGUUCGCCA--AGGCCAUUAA-----UUCCUUGA-ACCGAUAAGCAUUGCUU-------GG-UGCGGGAUAUG--CCGUGUGGG

CGAGCGCGUC-UUCCAGCGCACAGCAGGCGACGAAAGUCGUGUGCUCCCUGU-------GCCGGUGAU--GU--ACCCAAAAUGCGG-CUUCCGC--AGC

CAC-UCUGAACCAUA----CUUG--GGU-UCA-G-GAGG-----C----GGGUCUAGCGGCCG--AGGUGGGGACCCA-3'

RS002308 (Chromobacterium violaceum ATCC 12472)

5'-UAUCCCCUGCG-GUGUUCGUGAAGGCACACAA-------UUCCUUUGUACCAAUGCGUUCGCUUUU------GGCUGCCAGCGUG----AGACAUGG

GCGU----GCC---GCGUU----------------------------CUCUG------GUGAACGC----GC---CCGAAAUGUCU--GGCAGGC--GGC

CCCUCCUGG---AAA-----CAG--GGUACAAG-CGAA--------UUUAGCCCGAACGGCAC--UCGCGGGGGUUCC-3'

RS002309 (Neisseria meningitidis Z2491)

5'-UUUUCCCUGCG-GUGUCCGCGA--AGGCAUAUAU-----UCCUUUGA-ACCAAUAAGUUCGCUUAA------GGUUGCCGGGAGC----AGUAGUGG

G-C-----GC-GAGCGUC-----------------------------CUUUU----------GCGGAC--GC-ACCCGAAACUACC---CGAGGC--AGC

CGC--CUUG---UCA-----GCA-AGGU-UCAAG-CGGA-----UUCGGCCG--AAACGGCUC--UCGCGGGGAUUCC-3'

RS002310 (Nitrosomonas europaea ATCC 19718)

5'-UAAUCCCUGCG-GUGUUUGUCAAGGUUUGUAU-------UCUU-UGA-ACCAAUUCGUUGUAUCU-------GGCUGCCAGUCAA---UGGUCGCUG

UUGU----GC-GUA-CUCU----------------------------CUCGU---------GGAGCAU--GC---CUGAUGCGGCCG--ACAGGC--GGC

CAC-UCUUG---AAC-----CUG-UGGU-UCA---AGA------UAACAACCUG--ACGGCAU--UCGCGGGGACCCC-3'

RS002311 (Bdellovibrio bacteriovorus)

5'-AGAAGGGUUCG-ACGG-CGUAAAGCUCUAUC-------GAAAA-UAA-ACCUUACAAGCAUAUUUUU-----GGGGACUGUCCC----UGACAAUGG

UGA-----GC-AAGCUCAG----------------------------CUCGU--------ACUGAGAA--GC---CUAAAGUUGUUA-UCAUGGU-UACC

CAC--CUUA-GCUAA----AACA--GGU-UUACUUUUU-------------CAGAGUGGUCUU---CGAGCCUUUUUU-3'

RS002312 (Desulfotalea psychrophila LSv54)

5'-AUUCCCCUGUG-CUGUUGGUGAUUGCUAAAGUGU------GU--UGA-GCCAACUCUCAAUAAAA-------GGGCGUUGUCUCU---UGUCAGU--

--------AA-AGGUGAA-----------------------------UCGGU----------GACGAA--UU--GGCUGAGCUGAUA-AUAUGAU--GCC

CAC--CUAU--UAAU-----UUA--GGU-UUA---AC-------UAUCUUAGCGACACGGCAG---UGUGGGGGAUUU-3'

RS002313 (Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough)

5'-GUACCCCUGGA-GUGUGCGUGAUAGAUAUGCCAUC----GC---UGA--CCUCACAAGCUUGAAAUA-----GGGCAUCGGUACG---GUGGACCGG

UGU-----GC-ACGCCCGG----------------------------CAUGA---------CCGGGUA--GC---CUGAAGGCCCGC---CCGAGAAGCC

CCC--CUGG-UCAAC----ACCA--GG--UCC---UGCU-----UUGGUAUGUCACACGGCUC---UCCGGGGCCACU-3'

RS002314 (Geobacter sulfurreducens PCA)

5'-UUCUCUCUACC-AUGCGCGUGAGGCUGACAC--G-----CC-C-C-A-GCGGAACAUUUACUAUCAUUU---GG-GGGCUCUUU----AAGCCGUGG

UGU-----GC-UGCCCCA-----------------------------GUACG----------UGGGAUUUGC---CUGAAGCGGCAC--AGAGCC--UGC

CAC--CUGU---AAG-----GAACUCGC-U-GUG-AGGC-----CCUUACAAGCCAACGGCAU---GGUGGAGAGACU-3'

RS002315 (Shewanella oneidensis MR-1)

5'-UGCUCCCUGGG-AUGCAGGCCAACUGGUAAU--------GUCCCUGU-GCCGAUAAUUUUGAUCUCA-----GGGUGAAUGCUU----UACUGACAU

UGA-----GC-AGGCUCGG----------------------------CUCGU--------ACCGAGAA--GC---C-UUAGGAGGUA-AUCAUUU--ACC

CGC--CUUG---AAC-----CUA-CGGU-UCAAG-GGCU-------ACACCGGUA-GCGGCAU---UCUGGGGAGCAU-3'

RS002316 (Escherichia coli)

5'-AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUCAUACCACAA----GAAUGUGGCGCUC---CGCGGUUGG

UGA-----GC-AUGCUCGG----------------------------UCCGU---------CCGAGAA--GC---CUUAAAACUGCG-ACGACAC--AUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC-3'

RS002317 (Escherichia coli CFT073)

5'-AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUCAUACCACAA----GAAUGUGGCGCUC---CGCGGUUGG

UGA-----GC-AUGCUCGG----------------------------UCCGU---------CCGAGAA--GC---CUUAAAACUGCG-ACGACAC--AUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC-3'

RS002318 (Escherichia coli)

5'-AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU-------CCCC-UGA-GCCGAUAUUUCAUACCACAA----GAAUGUGGCGCUC---CGCGGUUGG

UGA-----GC-AUGCUCGG----------------------------UCCGU---------CCGAGAA--GC---CUUAAAACUGCG-ACGACAC--AUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC-3'

RS002319 (Erwinia carotovora subsp. atroseptica SCRI1043)

5'-AUUUCUCUGAG-AUGUUUGUCAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUUAUACCAAACA---GAAUGUAAUGCUC---UGCGGUUGG

UGC-----GC-AAGCUCGG----------------------------UUCGU---------CCGAGAA--GC---CUUAAGACUGCG-ACGUUAU--GUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUCCC-3'

RS002320 (Photorhabdus luminescens subsp. laumondii TTO1)

5'-AUUUCUCUGAG-AUGUUCGUUAACGGGGAAAGU-------CCCCUGA-GCCGAUAUUUCAUACAUUAUA---GAAUGUGGUGCUCC--GUAGUCUGG

UGU-----GC-AUGCUCGG----------------------------UCCAG---------CCGAGAA--GC---CUUAAAG-CUGCGACGCUGC--GUU

CAC--CUUG---AAC----CGAG--GGU-UCAAG-GG-------UUACUACCUGUAACGGCAU---CUUGGAGAAUCU-3'

RS002321 (Salmonella enterica subsp. enterica serovar Typhi Ty2)

5'-AUUUCUCUGAG-AUGUUUGCAAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUCAUACCACAA----GAAUGUGGCGCUC---CGCGGUUGG

UGA-----GC-AUGCUCGG----------------------------UUCGU---------CCGAGAA--GC---CUUAAAACUGUG-ACGACAC--AUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC-3'

RS002322 (Shigella flexneri 2a str. 2457T)

5'-AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUCAUACCACAA----GAAUGUGGCGCUC---CGCGGUUGG

UGA-----GC-AUGCUCGG----------------------------UUCGU---------CCGAGAA--GC---CUUAAAACUGCG-ACGACAC--AUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC-3'

RS002323 (Yersinia pestis KIM)

5'-AUUUCUCUGAG-GUGUUUGCCAGCGGGCCAGU--------CCCCUGA-GCCGAUAUUUAAUACCAACA----GAAUGUAGUGCUC---CGUAACCGG

UGA-----GC-AUGCUCGG-----------------------------UCCG---------CCGAGAA--GC---CUUAAGGUUGCG-ACGCUGC--GUU

CAC--CUUG---AAC-----CAA-GGGU-UCAAG-GG------UUACAGCCUGCG-ACGGCAC---CUCGGAGAUCCC-3'

RS002324 (Haemophilus influenzae Rd KW20)

5'-AAUUACCUGGA-GUGUUCGUCAGUAGGCUAU--------GUCCCUGA-GCCGAUACUUUAAAUCUUAU----AAAUUGGUUUCC----UAUCGUUGG

UGU-----GU-AGGCUUAACCUUUGA---------------------CUCGU-UCAUUGGGCUAAGAA--AC---CUGAAAACGGUA-UCAACUG--AUU

U-C--CUUG---AAC---CGUCG--GGU-UCAAG-GACU------ACUGCCCGCA-GCGGCAC---UCUGGGGUCUUC-3'

RS002325 (Haemophilus ducreyi 35000HP)

5'-CACUACCGGGG-GUGUUCGUUAUUAGUUAC---------GUCCCUGA-GCCGAUAAUUGAAAACUUU-----GAGUUGAACAUCU---AAUCGCUGG

UGA-----GC-AAGCUUAC----------------------------CUUGA---------GUAAGAA--GC---CUAAAAGCUAUU-AAGCUUA--ACU

C-C--CUUG---AAC----CAUU-UGGU-UCAAG-GGCC------UUCACUGAUA-ACGGCAC---UCCGGGUAUCUU-3'

RS002326 (Pasteurella multocida subsp. multocida str. Pm70)

5'-GAUUACCUGAG-GUGUUUGCCAGUGGGUUAU--------GUCCCUGA-GCCGAUACUUUUAUUUUAU-----GAAUCGGUUUCU----AAUUGUUGG

UGU-----GC-AUGCUUAG----------------------------CUUGA---------CUAAGAA--GC---CUAAAAAUAGUU-AUAACUG--AUU

C-C--CUUG---AAC----CGUU-GGGU-UCAAG-GACU-----G--AGACUUGCAGCGGCAU---CUCGGGUUCUUC-3'

RS002327 (Acinetobacter sp. ADP1)

5'-UUGUCUCUGGG-AUGCUCGCCAGCGAGUCAGAAU-----CCCC-UGA-GCCGAUACUAUCACUUUA------GGAUAGCGUUCUG---CAUAUUUAG

AGU-----GU-AUGCCUAC----------------------------CCAGA---------GUAGGAA--AC---CCAGCAAGUAUG-CGUCGCU---UC

CAC--CUUG---AAC----UUAA-GGGU-UCAAG-GG-------UAAUGACAGGCAGCGGCAU--CUUCGGAGGCAUU-3'

RS002328 (Pseudomonas aeruginosa PAO1)

5'-CGCUCCCUGGU-GUGUUGGCCAGUCGGUGAU--------GUCCCUGA-GCCGAUAACUGCAACAAC------GGAGGUUGCCAGU----UGGACCGG

UGU-----GC-AUGUCCG-----------------------------CACGA----------CGGAAA--GC---CUUAAGGUCUA--CUGCAAC--CGC

CAC--CUUG---AAC---UUUCG--GGU-UCAAG-GGCU-------AACCCGACA-GCGGCAC--GACCGGGGAGCUA-3'

RS002329 (Pseudomonas putida KT2440)

5'-CACUCCCUGGG-GGAUGCGCCAGUCGGUUAU--------GUCCCUGA-GCCGAUACGCACAACCAC------GGGGGUUGCACGCU---GGGGCCGG

UGU-----GC-AUGUCCG-----------------------------CCCGA----------CGGAAA--GC---CUUAACGCCCC--CUGCAAU--CUC

CAC--CUUG---AAC---UUUCG--GGU-UCAAG-GGCU-------ACACCGAUA-GCGGUCU--UAUCGGGGAGCCU-3'

RS002330 (Photobacterium profundum)

5'-UUGACCCUAGG-GUGUACGUCAGUGUGUCAAC-------GUCCCCGA-GCCGAUAAGCAAAUAACCC-----GGAUCAGCUUUU----AUUAGCUAU

UGU-----GC-AAGCUCAG----------------------------CUCGA---------CUGAGAA--GC---C-UGCGGCUAAU-GUUGCUG--AAC

CAC--CUUG---AAC----AUCU--GGU-UCAAG-GGCC------UAGAUGCGCA-ACGGCAC---CUUGGGG-CAUA-3'

RS002331 (Vibrio cholerae O1 biovar eltor str. N16961)

5'-UUUACCCUGGG-GUGUUCGUCAGCGGAUUUAU-------GUCCCUGA-GCCGAUAAGCAACAUAACA-----GGGUUGGUAUUG----GGUAGCUAU

UGA-----GC-AAGCUCGG----------------------------CUUGU--------ACCGAGAA--GC---C-UGCGGUUACC-AUUACUG--AUC

CGC--CUUG---AAC-----CUGAUGGU-UCAAG-GGCU------ACGAUCCUCA-ACGGCAU---CCCGGGGUUCUC-3'

RS002332 (Xanthomonas axonopodis pv. citri str. 306)

5'-CGUUCUCUGCG-GUAAACGACAGCGUGCAAAACAUU---CGCCUUGU--CCCUUAAUUACGACCAC------GGGGGCGCGAC-----GAAGCCGGG

UGU-----GC-AAGUCCGC----------------------------CUUGU--------AGCGGGAA--GC---C-CGAUGGCCUC-ACAACGU--CCC

CA---CUUG---AAC----CCCG--GGU-UCAAG-GUCG-----UUUCGCCCGC-AUCGUCAC---GGCGGAGAAUGC-3'

RS002333 (Xanthomonas campestris pv. campestris str. ATCC 33913)

5'-CGUUCUCUGCU-GUGAACGACGGUGUGCAAAACAUU---CGCCUUGU--CCCUUAAUUACGACCAC------GGGGGCGCGACG-----AAGCCGGG

AGU-----GC-AAGUCCGC----------------------------CUUGU--------AGCGGGAA--GC---C-CGACGGCCU-AACAACGU--CCC

CA---CUUG---AAC----CCCG--GGU-UCAAG-GUCG-----UUUCGCACAC-AUCGUCAU---GGCGGAGAAUGC-3'

RS002334 (Xylella fastidiosa 9a5c)

5'-CGUUCUCUGCU-GUGAACGACGGCGCGUGCAAACAUUUA-GCCUUGU--CCCUUAAUCACGACCAA------GGG-GCGCGAC-----GAUACCGGG

AGU-----GC-AAGUCUGC----------------------------CUUAG-------CAGCGGAAA--GC---C-CAAUGGUAUU-UCAACGC--CUC

CA---CUUG---AAC----CACA--GGU-UCAAG-GU------CGUUUCGCGAGCAUCGUCAU---AGCGGAGAAUGC-3'

RS002335 (Xylella fastidiosa Temecula1)

5'-CGUUCUCUGCU-GUGAACGACGGCGCGUGCAAACAUUUA-GCCUUGU--CCCUUAAUCACGACCAA------GGAGGCGCGAC-----GAUACCGGG

AGU-----GC-AAGUCUGC----------------------------CUUAG-------GAGCGGAAA--GC---C-CAAUGGUAUU-UCAACGC--CGC

CA---CUUG---AAC----CACU--GGU-UCAAG-GU------CGUUUCGCGAGCAUCGUCAU---AGCGGAGAAUGC-3'

RS002336 (Borrelia burgdorferi B31)

5'-AAGCUCCUGGG-AGGUUUAAUUUUAAGAAUUAGAGUUA-UUUU-UUU-GCGACAUCUCAUAAAAUUUA----GGAAUUUGAAUAUU--UUUAGUCAA

UG---------AUAGC-------------------------------CAAAA------------GCAA-U-----UCAGAGGUUAAGAAUAAAAA--UUC

CGC--CUUG---AAA-----AAUAGCGCUAAAUA-AAA-------AUGUUCUUAUGUUGGCUU---UUUGGGAGUUUA-3'

RS002337 (Chlorella vulgaris)

5'-GAGAUUAUGUA-CUCCACUCCGAUUACCUA---------GUUU-UGA--CCGAACAUUUUUUUAUAC-----GGGAGCUUGCCCUU--UCCUUUCUG

CAU-----AA-AUGCCCUC-----------------------------AUUA---------GAGGCAC--UU---AUAAAGUCAGGA-AGAAAGC--ACC

CAC--CUGC--CAUG---GUGCG-GGGU-UCA-A-AAC------GAAGGAAAGGA-GGGGAAGAAAUAAGAAAGAUAU-3'


References:

  1. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R., RFam: an RNA family database, Nucleic Acids Research, 2003, 31, 1, 439-441.