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Database

Multiple Alignment

IDsAligned Sequences
Consensus structure

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

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

 
RS013932 (Bacillus subtilis)

5'-AAUCACAAGCAGAAGC-ACCC--GCUUCUCACCUGAUU-GAC-AC--AUGCA-UGU-AGUUGGCAGGU---------UGACCGUACAUUUUUAUUGA

UACAGAUGUUCGUAGUGUGGGUGUU---UUAU---AAUGCCCACACUUUUUGUUUGCC-3'

RS013933 (Bacillus subtilis subsp. subtilis str. 168)

5'-AAUCACAAGCAGAAGC-ACCC--GCUUCUCACCUGAUU-GAC-AC--AUGCA-UGU-AGUUGGCAGGU---------UGACCGUACAUUUUUAUUGA

UACAGAUGUUCGUAGUGUGGGUGUU---UUAU---AAUGCCCACACUUUUUGUUUGCC-3'

RS013934 (Bacillus licheniformis ATCC 14580)

5'-AUCAACAAGCAGAAGC-ACCC--GCUUCUCACCUGAUU-GAC-AC--AUUCU-UGU-AGUUGGCAGGU-----UAAACGUACAUUUCUUAUUUUUCU

AUGCAAUGUUCGCAGUGUGGGUGU----UUCG----AUGCCCGCACUUUUUGUUUGCC-3'

RS013935 (Bacillus halodurans C-125)

5'-CAAAGCAAGAAGGAGC-GCCC--GCUUCUCACCUGAUC-GAC-GC--ACAGC--GC-AGUUGACAGGU--------CUACAUGUAAUAAUGUCUCAU

GAUGACAAACAUGAGUGUGGGCGU----CGU-----AUGCCCACACUCUUUUGUGUUG-3'

RS013936 (Bacillus clausii KSM-K16)

5'-UAGAGCAAGAAGAAGC-GCCC--GCUUCUCACCUGU---ACG-AC--AUUG---GU--UGC--CAGGU----------UAGAAACCGUCAGUUUGUU

AAAAUGCUGAUUAAGUGUGGGUGC----CGU-----GCGUCCACACUUUUUUCACGUU-3'

RS013937 (Bacillus licheniformis ATCC 14580)

5'-AUCAACAAGCAGAAGC-ACCC--GCUUCUCACCUGAUU-GAC-AC--AUUCU-UGU-AGUUGGCAGGU-----UAAACGUACAUUUCUUAUUUUUCU

AUGCAAUGUUCGCAGUGUGGGUGU----UUCG----AUGCCCGCACUUUUUGUUUGCC-3'

RS013938 (Bacillus cereus group.Viruses.Viruses.Viruses.Viruses)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013939 (Bacillus phage phBC6A52)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUAACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUUCG-3'

RS013940 (Bacillus anthracis str. Sterne)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013941 (Bacillus anthracis str. 'Ames Ancestor')

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013942 (Bacillus cereus E33L)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013943 (Bacillus thuringiensis serovar konkukian str. 97-27)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013944 (Bacillus cereus ATCC 10987)

5'-UGGAACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUAC

UUAAGAUUUUACAAGUGUGGGUGU----CGU-----AUGCCCGCACUUUUUUUGUCGG-3'

RS013945 (Geobacillus kaustophilus HTA426)

5'-UAACAAAAGCAGAAGCACCCC--GCUUCUCACCUGACC-GAC-GCC-A-AGACGGC-UGUUGGCAGGU-------UGUUACGGUUCGUCAAUGCGAG

UGUAAGGACGUACUGCGCGGGUGCU---UUG----UGCAUCUGCGCUUUUUUUUGGGC-3'

RS013946 (Geobacillus stearothermophilus)

5'-UAACGAAAGCAGAAGC-GCCC--GCUUCUCACCUGACC-GAC-GCU-AAGAA-GGC-UGUUGGCAGGU--------UGUUACGGUUCGCCAACUUUU

UGUCCGAACGUCGUGCGCGGGUGCU---UUG----UGCAUCCGCGCUUUUUCGUUGAG-3'

RS013947 (Oceanobacillus iheyensis HTE831)

5'-UAAGACAAGUAGAAGC-ACCC--GCUUCUCACCUGAUU-GAC-ACCGAUUAU-GGU-AGUUGACUGGU------------UCCAACCUUUUAUUUAA

AUGUAUUUGGAGAUGUGUGGGUGCG---UGUA---UGUACCGACACUUUUUUAAUUGC-3'

RS013948 (Listeria innocua)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAGCUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013949 (Listeria monocytogenes)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUACGUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013950 (Listeria ivanovii)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCG---UUA-AC--AUGGA-UGU--UUU--CAGGCAAAAAAUUCAAACUUUCGUCGCGUUACUU

GCGCGACUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013951 (Listeria innocua)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013952 (Listeria monocytogenes)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAGCUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013953 (Listeria welshimeri)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUU

ACGCGAUUUUGAAUGUGCGGGAUUGCUGGAAA--GCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013954 (Listeria monocytogenes str. 4b F2365)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013955 (Listeria monocytogenes)

5'-ACAAGAAAGAAGAAGCAACCC--GCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAGCUU

ACGCGAUUUUGAAUGUGCGGGAUUGC--UGAAAAGCAG-CCCGUUUUUUUAUGGCCUC-3'

RS013956 (Staphylococcus aureus subsp. aureus N315)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013957 (Staphylococcus aureus subsp. aureus MW2)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013958 (Staphylococcus epidermidis ATCC 12228)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUGGCGAC-GC---UGAA--GC-AGUUGGCAGGU-----------CAAUCAUGUUACACAUUU

AUUGUGUCUAAGAAGAGCGGGUA-----GUUA-----UACUCGCUCUUCUUUUUGCUU-3'

RS013959 (Staphylococcus aureus subsp. aureus MSSA476)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013960 (Staphylococcus aureus subsp. aureus COL)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013961 (Staphylococcus aureus subsp. aureus MRSA252)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUUAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013962 (Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305)

5'-CGAACCAAGUAGAAGC-UCCC--GCUUCUCACCUGUUGCGAC-GCU-AUAG---GC-AGUUGGCAGGU---------CUUAUAUAUACAUGUUAAUU

UCAUGUGUAGAGAAGAGCGGGUAUA---UUA----UAUACUCGCUCUUUUUGCUUGGG-3'

RS013963 (Staphylococcus aureus subsp. aureus Mu50)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013964 (Staphylococcus haemolyticus JCSC1435)

5'-CGUACCAAGUAGAAAC-ACCC--GUUUCUCACCUGUAGCGAC-GC--AUCAA--GC-AGUUGGCAGGU---------UAAUCAUGUCACACAUUAUA

UGUGUAUGAGAGAAGAGCGGGCAU----UCU-----AUGCUCGCUCUUUUUGCUUGGA-3'

RS013965 (Staphylococcus aureus)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAA

CUGUGUAUAAGGAAGAGCGGGUAU----UUU-----AUACCUGCUCUUCCUUUUUGCU-3'

RS013966 (unclassified Lambda-like viruses)

5'-CGAACCAAGUAGAAGC-ACCC--GCUUCUCACCUGUGGCGAC-GC---UGAA--GC-AGUUGGCAGGU-----------CAAUCAUGUUACACAUUU

AUUGUGUCUAAGAAGAGCGGGUA-----GUUA-----UACUCGCUCUUCUUUUUGCUU-3'

RS013967 (Clostridium acetobutylicum ATCC 824)

5'-GUAUUGAAGAAGAAACUUGCC--GUUUCUCACCUU-----AC-AG--CAAAG--CU-AGU---AAGGU--------UAAAGAUAUGCAGCUUAUUUU

GCUAUGUAUAUUUGAGACGGUG------AAUA-------ACCGUCUUUUUUUAUUAUA-3'

RS013968 (Clostridium perfringens str. 13)

5'-GAUGUCAAGAAGAAAC-AGCC--GUUUCUCACCUU-----ACAGCU-AUUAA-UGCUAGU---UUGGU---------CAUGAAUUUUAUUACAUUUG

AUUUUGGUAAUAGAGGACGGCU------UAA-------AACCGUCCUUUUUUAUUUAU-3'

RS013969 (Clostridium tetani E88)

5'-AACGUUAAGAAGAAACUAGCC--GUUUCUCACCUU-----ACAGC--AUA----GCUAGU---AAGGU---------------UAUGAAAUCAGUUU

AUUAUUUUGAUUAGAGGACGGC------AUUU------GCCGUCUUUUUUUAUUUUAA-3'

RS013970 (Thermoanaerobacter tengcongensis MB4)

5'-GCGAAUAAGUAGAAGC-GCCC--GCUUCUCACCUU-----UC-GCC-AUAG--GGC-AGA---AAGGU---------UUCUUCUUGAAAGUCAAAAG

UAAUAUGGGCGAAGAAGCGGGUG-----GAU------UAUCCGCUUUUAUUUUUUGAU-3'

RS013971 (Enterococcus faecalis V583)

5'-AAAUGAAAGCAGAAGC-ACCC--GCUUCUCGCCUUA----GUUGA--GUAUA--UC--GC---UGGGC--UAGAUAAAGUAUUCCUUAUUUUUUUAA

GUAAGGCAGACUGUUGGCGGGUUCUG--GAUA---GGAACCUGUUUUUUUAUUGCAUU-3'

RS013972 (Siphoviridae)

5'-GAGAACAAGAAGAAGC-UCCC--GCUUCUCGCCUA-----AGUUA--AUAU---UA-CCU--CUGGGC-------------------UGAUCGAUAA

UAUCUGUUGAUUAAAAGCGGGCGUU---AAC----UUUGCCCGCUUUUUUCUUGUCCU-3'

RS013973 (Lactobacillus plantarum WCFS1)

5'-GAAAAAAAGCAGAAGC-ACCC--GCUUCUCGCCUUG---GUG-AC--C-AGA--GU--CAU--CGGGC--------AGAUGAACGAUGAAUUGAUUC

CCAUUAACGGGGUUGAGCGGGCGUA---CUA----UGCGCCCGCUCUUUUUGUGAAUU-3'

RS013974 (Lactobacillus acidophilus NCFM)

5'-GAGAACAAGAAGAAGC-ACCC--GCUUCUCGCCUA-----AG-UU--AAGUA--AA-CCU--CUAGGC-------------------UGAUCGAUAA

UUUCUGUUGAUUAAAGGCGGGGUGA---UAC----UUAUCCCGCCUUUUUCUUGUCCU-3'

RS013975 (Lactococcus lactis subsp. lactis Il1403)

5'-GUUGAAAAGCAGAAGC-ACCC--GCUUCUCGCCUUA----GA-GG--UUAUA--GC--CC---UGGGC-------AAACGAAUGGAAUUAUUCAAAA

ACGAAUGUUUUCAUGAGCGGGGCGAG--AUUG---UCGUUCCGCUUUUGUUUUUCUUU-3'

RS013976 (Streptococcus.Viruses.Viruses.Viruses)

5'-UGAGAAAAGUAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013977 (Streptococcus.Viruses.Viruses.Viruses.Viruses.Viruses.Viruses)

5'-UGAGAAAAGCAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUAUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013978 (Streptococcus pyogenes MGAS8232)

5'-UGAGAAAAGUAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013979 (Streptococcus agalactiae 2603V/R)

5'-UGAGAAAAGCAGAAGUGAGA---ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC--------CCAACAUGUCAAGAUUCCAUC

UAGGAAGAUUAUAUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013980 (Streptococcus pyogenes SSI-1)

5'-UGAGAAAAGCAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUAUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013981 (Streptococcus agalactiae NEM316)

5'-UGAGAAAAGCAGAAGUGAGA---ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC--------CCAACAUGUCAAGAUUCCAUC

UAGGAAGAUUAUAUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013982 (Streptococcus pneumoniae TIGR4)

5'-UGAGAAAAGCAGAAGUGAGA---GCUUCUCGCCUU----GUG-AC--AUUAA--GU--UGC--CUGGC-----CCUACGGAUGAAAAGUUUCGAAGA

AACGCUAUCAUAACGUGCGGGCUUGUA-UAUU-UACAAGUCCGCUAUUGUUUUUCUCU-3'

RS013983 (Streptococcus.Viruses.Viruses.Viruses.Viruses)

5'-UGAGAAAAGUAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013984 (Streptococcus thermophilus LMG 18311)

5'-UGAGAAAAGCAGAAGUGAGA---ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCAACAUGUCAAAUCCUUA

AAGGGAUAUUAUGUGUGCGGGCUUGU--AUAU---CAAGUCCGCUUUGUUUUUCUCUA-3'

RS013985 (Streptococcus pyogenes MGAS10394)

5'-UGAGAAAAGUAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGU----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013986 (Streptococcus thermophilus CNRZ1066)

5'-UGAGAAAAGCAGAAGUGAGA---ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCAACAUGUCAAAUCCUUA

AAGGGAUAUUAUGUGUGCGGGCUUGU--AUAU---CAAGUCCGCUUUGUUUUUCUCUA-3'

RS013987 (Streptococcus mutans UA159)

5'-UGAGAAAAGCAGAAGUGAGA---ACUUCUCGCCUU----GCG-AC--UUAAA--GU--UGU--CUGGC--------CCAACAUGUUAAAGUUCCUGU

GGAAUAUUAUGUGUAUACGGGCUUGA--UUUG--UCAGGUCCGUUUUUGUUUUUCUCA-3'

RS013988 (Streptococcus pneumoniae R6)

5'-UGAGAAAAGCAGAAGUGAGA---GCUUCUCGCCUU----GUG-AC--AUUAA--GU--UGC--CUGGC-----CCUACGGAUGAAAAGUUUCGAAGA

AACGCUAUCAUAACGUGCGGGCUUGUA-UAUU-UACGAGUCCGCUAUUGUUUUUCUCU-3'

RS013989 (Caudovirales.Viruses.Viruses.Viruses)

5'-UGAGAAAAGUAGAAGUGAGA---GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCU

AUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA--UCAAGUCCGCUUUCGUUUUUCUCU-3'

RS013990 (Thermotoga maritima MSB8)

5'-AAAAGCAAGUGGAGGCCAGCCCGGCUUCCCACCCUG----GG-GC--AAGAG--GCUACC---AGGGU------------AAAUAUCCCUGAAAGAU

UCAGCUUCAAGGGGAAGCGGGC---U--UUUU------GCCCGCUAUUUUUUAUGACU-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.