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Table 2 Accuracies for the original multiple alignment dataset. SPS and MCC values (%) for the original 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 average 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
IRE 62 29 98 96 93 89 77 83 92
s2m 78 43 96 96 96 96 96 96 95
UnaL2 78 54 95 98 98 96 92 94 82
Hammerhead_3 71 55 96 94 93 89 83 89 91
SECIS 42 64 65 66 65 52 45 56 46
sno_14q_I_II 71 74 90 95 96 93 93 87 71
tRNA 48 76 87 87 87 84 76 82 87
ctRNA_pGA1 74 80 88 86 85 88 84 86 89
Tymo_tRNA 70 83 84 83 82 75 75 79 77
Y 64 95 71 72 72 73 65 64 65
SRP_bact 52 95 71 71 70 66 70 62 66
Purine 55 100 74 77 77 78 75 81 69
5S_rRNA 60 117 88 89 89 86 86 86 83
S_box 66 130 79 80 78 78 68 72 67
U4 67 141 79 81 80 79 79 78 69
RFN 65 150 86 87 87 88 81 80 81
5_8S_rRNA 67 154 91 93 93 90 88 89 78
U1 60 158 81 81 79 79 79 76 74
Telomerase_cil 56 171 48 50 49 43 38 41 37
Lysine 50 180 78 81 79 72 70 76 72
U2 66 185 76 76 75 71 71 73 71
U17 75 214 91 93 93 89 89 87 81
U3 51 246 43 44 44 47 41 40 34
SRP_euk_arch 46 294 50 56 47 42 42 48 44
tmRNA 46 373 48 50 50 47 46 39 42
RnaseP_bact_b 64 387 82 80 79 78 74 74 66
Telomerase_vert 66 463 69 70 69 69 66 64 65
Average(all)    78 79 78 75 72 73 70
Average(sub)    85 85 85 82 78 80 78
SPS:Family RNAlara Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc   
IRE 85 88 (100/100) 87 (99/101) 85 (97/100) 92 90 (101/101) 87 (101/101)   
s2m 96 99 (43/50) 95 (50/50) 95 (47/50) 94 98 (44/50) 93 (50/50)   
UnaL2 93 93 (78/89) 89 (75/89) 86 (87/89) 88 87 (75/89) 75 (89/89)   
Hammerhead_3 88 80 (100/100) 79 (99/100) 77 (97/100) 89 87 (77/100) 94 (100/100)   
SECIS 48 47 (62/63) 46 (63/63) 44 (63/63) 49 39 (63/63) 60 (60/63)   
sno_14q_I_II 78 76 (98/98) 73 (98/98) 61 (97/98) 67 73 (97/98) 89 (97/98)   
tRNA 91 82 (103/103) 90 (100/103) 78 (97/103) 59 86 (103/103) 88 (103/103)   
ctRNA_pGA1 86 74 (20/28) 75 (28/28) 74 (27/28) 79 72 (20/28) 84 (28/28)   
Tymo_tRNA 79 78 (49/59) 68 (59/59) 68 (56/59) 66 71 (49/59) 57 (57/59)   
Y 56 49 (21/24) 50 (24/24) 47 (24/24) 60 43 (11/24) 68 (23/24)   
SRP_bact 63 62 (70/70) 64 (70/70) 56 (67/70) 56 61 (63/70) 60 (67/70)   
Purine 64 65 (45/45) 64 (45/45) 62 (45/45) 64 65 (45/45) 37 (45/45)   
5S_rRNA 85         
S_box 57         
U4 71         
RFN 78         
5_8S_rRNA 81         
U1 74         
Telomerase_cil 32         
Lysine 59         
U2 71         
U17 79         
U3 32         
SRP_euk_arch 42         
tmRNA 34         
RnaseP_bact_b 66         
Telomerase_vert 51         
Average(all) 68         
Average(sub) 77 74 73 69 72 73 74   
MCC:Family %id length MXSCARNA Murlet ProbCons MAFFT ClustalW StrAl RNASampler
IRE 62 29 90 91 75 72 65 43 89
S2m 78 43 84 83 84 84 84 84 81
UnaL2 78 54 52 70 51 53 51 50 51
Hammerhead_3 71 55 99 95 93 86 72 79 96
SECIS 42 64 76 60 55 35 23 37 73
sno_14q_I_II 71 74 93 98 93 93 91 91 95
tRNA 48 76 91 89 86 84 76 83 95
ctRNA_pGA1 74 80 96 93 88 89 81 92 94
Tymo_tRNA 70 83 87 85 75 73 72 80 90
Y 64 95 95 85 86 83 67 83 94
SRP_bact 52 95 81 72 54 50 58 57 83
Purine 55 100 90 94 90 86 80 84 91
5S_rRNA 60 117 75 79 69 70 69 70 70
S_box 66 130 90 87 86 81 76 81 86
U4 67 141 75 71 62 62 54 65 67
RFN 65 150 84 83 84 84 82 83 82
5_8S_rRNA 67 154 58 51 47 45 41 46 52
U1 60 158 70 68 61 56 60 57 71
Telomerase 56 171 65 41 28 21 24 31 60
Lysine 50 180 87 90 76 66 63 71 89
U2 66 185 73 76 58 51 62 59 77
U17 75 214 79 80 78 76 75 72 72
U3 51 246 46 26 22 19 46 21 39
SRP_euk_arch 46 294 72 75 46 37 35 49 72
tmRNA 46 373 51 54 50 49 43 42 49
RNaseP_bact_b 64 387 73 58 63 58 53 60 37
Telomerase 66 463 64 51 47 44 40 36 53
Average(all)    78 74 67 63 61 63 74
Average(sub)    86 85 77 74 68 72 86
MCC:Family RNAlara Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc   
IRE 81 89 85 89 82 89 81   
s2m 84 83 85 86 79 85 84   
UnaL2 53 53 53 51 51 50 45   
Hammerhead_3 95 94 87 91 95 91 98   
SECIS 63 74 74 75 57 67 78   
sno_14q_I_II 92 87 92 84 81 93 85   
tRNA 95 87 95 87 67 90 95   
ctRNA_pGA1 97 95 96 96 95 94 95   
Tymo_tRNA 85 75 87 82 62 82 83   
Y 86 87 94 89 87 83 93   
SRP_bact 65 87 86 83 63 80 69   
Purine 77 89 88 88 82 86 89   
5S_rRNA 72         
S_box 72         
U4 60         
RFN 79         
5_8S_rRNA 46         
U1 60         
Telomerase 39         
Lysine 58         
U2 63         
U17 63         
U3 21         
SRP_euk_arch 42         
tmRNA 40         
RNaseP_bact_b 65         
Telomerase 28         
Average(all) 65         
Average(sub) 81 83 85 83 75 83 83