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Table 1 The tRNA 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 ID
RD0260 GCGACCGGGGCUGGCUU-GGUA-AUGGUACUCCCCUGUCACGGGAGAG---------------AAUGUGGGUUCAAAUCCCAUCGGUCGCGCCA 77 RD0260
Phage T5 (Virus) (((((((..((((....-....-.)))).(((((.......)))))..---------------...(((((.......)))))))))))).... 21  
RD0500 GCCCGGGUGGUGCAGU--GGCCCAGCAUACGACCCUGUCACGGUCGUG---------------A-CGCGGGUUCAAAUCCCGCCUCGGGCGCCA 76 RD0500
Haloferax volcanii (Archæa) (((((((..((((...--......)))).(((((.......)))))..---------------.-.(((((.......)))))))))))).... 21  
RD1140 GGCCCCAUAGCGAAGUU-GGUU-AUCGCGCCUCCCUGUCACGGAGGAG---------------AUCACGGGUUCGAGUCCCGUUGGGGUCGCCA 77 RD1140
Mycoplasma capricolum (Eubacteria) (((((((..((((....-....-.)))).(((((.......)))))..---------------...(((((.......)))))))))))).... 21  
RD2640 GGGAUUGUAGUUCAAUU-GGUC-AGAGCACCGCCCUGUCAAGGCGGAA---------------GAUGCGGGUUCGAGCCCCGUCAGUCCCGCCA 77 RD2640
Hordeum vulgare (Plant chloroplast) (((((((..((((....-....-.)))).(((((.......)))))..---------------...(((((.......)))))))))))).... 21  
RD4800 AAAAAAUUAGUUUAAU--CA---AAAACCUUAGUAUGUCAAACUAAAA---------------A-AAUUAGAUCAU--CUAAUAUUUUUUACCA 71 RD4800
Aedes albopictus (Animal mitochondria) (((((((..((((...--..---.)))).(((((.......)))))..---------------.-.(((((.....--)))))))))))).... 21  
RE2140 GCCCCCAUCGUCUAGA--GGCCUAGGACACCUCCCUUUCACGGAGGCG---------------A-CAGGGAUUCGAAUUCCCUUGGGGGUACCA 76 RE2140
Synechocystis sp. (Eubacteria) (((((((..((((...--......)))).(((((.......)))))..---------------.-.(((((.......)))))))))))).... 21  
RE6781 UCCGUCGUAGUCUAGGUGGUUA--GGAUACUCGGCUCUCACCCGAGAG---------------A-CCCGGGUUCGAGUCCCGGCGACGGAACCA 76 RE6781
Hordeum vulgare (Plant chloroplast) (((((((..((((.........--)))).(((((.......)))))..---------------.-.(((((.......)))))))))))).... 21  
RF6320 GUCGCAAUGGUGUAGUUGGGA---GCAUGACAGACUGAAGAUCUGUUG---------------GUCAUCGGUUCGAUCCCGGUUUGUGACACCA 76 RF6320
Schizosaccharomyces pombe (Fungi cytoplasm) (((((((..((((........---)))).(((((.......)))))..---------------...(((((.......)))))))))))).... 21  
RL0503 GCGGGGGUGGCUGAGCCAGGCCAAAAGCGGCGGACUUAAGAUCCGCU-CCC--GUAG---GGGUUCGCGAGUUCGAAUCUCGUCCCCCGCACCA 88 RL0503
Haloferax volcanii (Archæa) (((((((..((('...........'))).(((((.......))))).-(((--....---)))...(((((.......)))))))))))).... 24  
RL1141 CCCCAAGUGGCGGAAUA-GGDA-GACGCAUUGGACUUAAAAUCCAAC-GGGC-UUAAU-AUCCUGUGCCGGUUCAAGUCCGGCCUUGGGGACCA 89 RL1141
Mycoplasma capricolum (Eubacteria) (((((((..(((..... -.... -..))).(((((.......))))).-.... -.....-.......(((((.......)))))))))))).... 20  
RS0380 GCCGAGGUAGCAUAGCUUGGCC-AAUGCGGUUGCUUCGAGAGCAACG-UUCC-ACAC--GGACU-CAGGAGUUCAAAUCUCCUCCUCGGCGCCA 88 RS0380
Halobacterium cutirubrum (Archæa) (((((((..((((.........-.)))).(((((.......))))).-'(((-....--)))'.-.(((((.......)))))))))))).... 25  
RS1141 GGAAGAUUACCCAAGUCCGGCUGAAGGGAUCGGUCUUGAAAACCGAGAGUCGGGGAAACCGAG--CGGGGGUUCGAAUCCCUCAUCUUCCGCCA 92 RS1141
Mycoplasma capricolum (Eubacteria) (((((((..((('...........'))).(((((.......)))))..'((((.....))))'--.(((((.......)))))))))))).... 26  
Consensus structure (((((((..(((.............))).(((((.......))))).................... (((((.......)))))))))))).... 20 Consensus