Skip to main content

Table 2 The bacterial 5S rRNA sequences in the test data set. Reference alignment showing the reference structures and the ideal consensus structure (bottom). Quotes indicate non-canonical basepairs. The number of nucleotides and of basepairs is given for each sequence and structure.

From: Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?

ID & Species Sequence & Structure Length
AJ131594 -UGCC-UGAUGACCAUAGCAAGUUGGUACCACUCCUUCCCAUCCCGAACAGGACAGUGAAA-CGACUUUGCGCCGAUGAUAGUGCGG--GUU---CCCGUGUGAAAGUAGGUCAUCGUCAGGCNN--- 117
Comamonas acidovorans -'(((-((((((..... ((((((((....(((((((.............))))..)))...-)))))).)).(('((''..((((((--...---.))))))..''))'))...)))))))))'.--- 38
AJ251080 ---CC-UAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAG-CCCUCCAGCGCCGAUGGUAGUUGGGGCCAGC-GCCCCUGCAAGAGUAGGUCGCUGCUAGG----C- 117
Bacillus stearothermophilus ---((-((((((.....((((((((....'((((((.............))))..))'...-)))))).)).(('((''..(('(((((....-)))))'))..''))'))...))))))))----.- 38
K02682 -NGUC-UGGCGGCCAUAGCGUGGGGGAAACGCCCGGUCCCAUCCCGAACCCGGAAGCUAAG-CCCCAUAGCGCCGAUGGUACUGCAACCGGGA-GGUUGUGGGAGAGUAGGUCGCCGCCGGAC---A- 120
Micrococcus luteus -.(((-((((((.....((((((((....'((((((.............))))..))'...-)))))).)).(('((''.. ((((((((....-))))))))..''))'))...)))))))))---.- 39
M10816 -NNCC-UAGUGACAAUAGCGGAGAGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAG-CUCUCCAGCGCCGAUGGUAGUUGGGGCCAGC-GCCCCUGCAAGAGUAGGUCGUUGCUAGG----C- 119
Bacillus stearothermophilus -..((-((((((..... ((((((((....'((((((.............))))..))'...-)))))).)).(('((''.. (('(((((....-)))))'))..''))'))...))))))))----.- 38
M16532 -NCUC-GGACCACCAUACCGGGGGGGAAACACCCGGUCCCAUUCCGAACCCGGAAGUUAAG-CCCCCCAGGGCCGAUGAUAGCCUCGC-CCCGA-GCGAGGUGAAAGUAGGUCGUGGUCCGGGCAC-- 121
Thermus sp. -'(((-((((((.....((((((((....'((((((.............))))..))'...-)))))).)).(('((''..(((((((-.....-)))))))..''))'))...)))))))))'..-- 39
M25591 ---CC-UAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAG-CCCUCCAGCGCCGAUGGUAGUUGGGGCCAGC-GCCCCUGCAAGAGUAGGCCGCUGCUAGG----C- 117
Bacillus stearothermophilus ---((-((((((.....((((((((....'((((((.............))))..))'...-)))))).)).(('((''..(('(((((....-)))))'))..''))'))...))))))))----.- 38
V00336 -UGCC-UGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAA-CGCCGUAGCGCCGAUGGUAGUGUGGGGUCU--CCCCAUGCGAGAGUAGGGAACUGCCAGGCA--U- 120
Escherichia coli -((((-((((((.....((((((((....(((((((.............))))..)))...-)))))).)).(('((''..((((((((...--))))))))..''))'))...))))))))))--.- 40
X02024 -NNUU-UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAG-CUCUUCAGCGCCGAUGGUAGUUGGGGUGUUA-GCCCCUGCAAGAGUAGGACGUUGCCAGG----C- 119
Bacillus pasteurii -..((-((((((.....((((((((....'((((((.............))))..))'...-)))))).)).(('((''..(('(((((....-)))))'))..''))'))...))))))))----.- 38
X02627 CGACC-UGGUGGUCAUCGCGGGGCGGCUGCACCCGUUCCCUUUCCGAACACGGCCGUGAAA-CGCCCCAGCGCCAAUGGUACUUCGUC-UCAA--GACGCGGGAGAGUAGGUCGCUGCCAGGUC---U 120
Agrobacterium tumefaciens .((((-((((((.....((((((((....(((((((.............))))..)))...-)))))).)).(('((''..(('((((-....--))))'))..'')) '))...))))))))))---. 39
X04585 -CGUU-UGGUGGUCAUAGCGUUGGCUAAACACCCGAUCCCAUCCCGAACUCGGCCGUUAAGGGCCAACA-CGCCGAUGGUACUGCGUC-UCAA--GACGUGGGAGAGUAGGUCACCGCCAAACCN--- 119
Rhodobacter capsulatus -'(((-((((((.....(.((((((....'((((((.............))))..))'....)))))).-).(('((''..(((((((-....--)))))))..''))'))...)))))))))'.--- 38
X08000 -NAUUACGGCGGUCAUAGCGUGGGGGAAACGCCCGGUCCCAUUCCGAACCCGGAAGCUAAG-ACCCACAGCGCCGAUGGUACUGCACCCGGGA-GGGUGUGGGAGAGUAGGUCACCGCCGGACAC--- 122
Arthrobacter oxidans -.'((.((((((.....((((((('....'((((((.............))))..))'...-'))))).)).(('((''..((((((((....-))))))))..''))'))...))))))))'..--- 39
X08002 -NAUUACGGCGGUCAUAGCGUGGGGGAAACGCCCGGUCCCAUUCCGAACCCGGAAGCUAAG-ACCCACAGCGCCGAUGGUACUGCACCCGGGA-GGGUGUGGGAGAGUAGGUCACCGCCGGACAC--- 122
Arthrobacter globiformis -.'((.((((((.....((((((('....'((((((.............))))..))'...-'))))).)).(('((''..((((((((....-))))))))..''))'))...))))))))'..--- 39
Consensus Structure ...((.((((((.....(.(((((......((((((.............))))..))......)))))..).((.((....((.(((.........))).))....)).))...))))))))...... 29