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Table 3 Accuracies for the BRAlibaseII multiple alignment dataset. SPS and MCC values (%) for the BRAlibaseII multiple alignment dataset are presented. Each family has 5 RNA sequences. Family: Rfam family name. %id: average sequence identity. length: average sequence length (bases) in each family. Average(all): the results of the average value of the SPS or MCC for all families. Average(sub): the average SPS or MCC for the subset of families with an average sequence length of less than or equal to 100 bases. Because PMmulti and Stemloc were unable to align all data, the proportion of data that was aligned is given in parentheses as no. of sequences aligned/total no. of sequences. FoldalignM consists of two modes: FoldalgnM_FoldalignM and FoldalignM_McCaskill, which are separately evaluated and indicated as FoldalignM(1) and FoldalignM(2) respectively.

From: A fast structural multiple alignment method for long RNA sequences

SPS:Family %id length MXSCARNA Murlet ProbCons MAFFT ClustalW StrAl RNASampler  
tRNA 69 76 91 91 91 89 85 89 92  
Intron_gpII 64 80 79 80 80 77 75 79 74  
5S_rRNA 70 117 89 90 90 89 88 89 90  
U5 72 118 74 75 76 72 72 73 78  
SRP 67 300 88 88 88 87 87 86 82  
Average(all)    84 85 85 83 81 83 83  
Average(sub)    83 84 84 82 80 82 83  
SPS:Family RNAlara Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc    
tRNA 95 93 (98/98) 94 (97/98) 90 (91/98) 79 (98/98) 90 (89/98) 88 (98/98)    
Intron_gpII 75 71 (89/92) 70 (92/92) 67 (89/92) 76 (92/92) 77 (61/92) 77 (92/92)    
5S_rRNA 93 92 (89/89) 92 (88/89) 89 (89/89) 58 (78/89) 85 (89/89) 72 (89/89)    
U5 80 77 (109/109) 72 (108/109) 69 (107/109) 85 (74/109) 56 (105/109) 64 (109/109)    
SRP 82 83 (84/93)         
Average(all) 85 83         
Average(sub) 86 83 82 79 74 77 75    
MCC:Family %id length MXSCARNA Murlet ProbCons MAFFT ClustalW StrAl RNASampler RNAlara
tRNA 69 76 94 92 91 90 83 88 94 93
Intron_gpII 64 80 82 80 77 76 74 74 80 79
5S_rRNA 70 117 71 69 67 68 67 69 69 70
U5 72 118 80 75 70 66 66 69 77 72
SRP 67 300 75 72 68 67 68 65 71 63
Average(all)    80 78 75 73 72 73 78 76
Average(sub)    82 79 76 75 72 75 80 79
MCC:Family Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc     
tRNA 92 96 92 80 93 93     
Intron_gpII 80 76 80 78 76 76     
5S_rRNA 71 72 71 59 70 68     
U5 74 70 69 60 61 78     
SRP 73          
Average(all) 78          
Average(sub) 79 79 78 69 75 79