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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