RNA 3D Hub

JAR3D Query RF03021-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF03021 RT-18 RNA

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
((((....)))).........((((...........(((((((.....(((((...............................)))....))....)))))))..)))).........
>URS0000D6CFA6_12908/1-72
CAGCCCAUGCUGAAAAUU---AUCCGAU--AUA-GGGCCGGGAUAGUAG--------AACC-------------------------------CGAAAUCCCGGCA-GGAGAU-AAGAAA
>URS0000D6D362_12908/1-75
CAGCCCUAGCUGAAAAUU----ACCGA---ACA-GGCGCGGCUUAGUA---------AGCCACAAGCCC-------------------------AAAGGCCGCGA-GGUGAU-AAGAAU
>URS0000D69F92_12908/1-87
UACCCCUUGGUAAAAAUU----GUUGU---AAC-GGCAGGGGUUAGUAAGAGGCUGGUUU--------------------CCAGCCU---GCCCAAUAUCCCUGA-AACUAUAAAAAAG
>URS0000D6BA0F_12908/1-79
UACCACUUGGUAAAAAACUA--UCUCGUA-AAA-GGCACGGUUUAGUAGG-------UCAA---------------------------UUCUCGAAAGACCGUGAGGGACUUAAAAG--
>URS0000D65E88_12908/1-79
CAGCCCUAGCUGAAAAUU---AGUCGA---ACU-GGACUGGCUUAGUAGUU------CCUUUUG----------------------A---AUCGAAAAGUCGGUA-GACAAA-AAUAAG
>URS0000D6C6EE_12908/1-90
CAGCACUUGCUGAAAAUU---AGUCGC---CUU-GGGUUGGGCUAGUAGG-------UUUAUCUCCGUGAGGAAU-------------UUCUCGAAAGCUCGAUA-GACAAA-UAUAAG
>URS0000D67D53_12908/1-76
UGCCCCUUGGCAAAAAUU---AGUCGC---UCU-GGGUUGGCUUAGUAGG-------UUAA---------------------------UUCUCGAAAGGUCGGCA-GGCAAA-UAUAAG
>URS0000D67A13_12908/1-76
UGCCCCUUGGCAAAAAUU---AGUCGC---UCU-GGGUUGGCUUAGUAGG-------UUAA---------------------------UUCUCGAAAAGUCGGCA-GGCAAA-UAUAAG
>URS0000D6A8DF_12908/1-75
CAGCCCUUGCUGAAAAUU---AGUCGU---UCU-GGGCUGGCUUAGUAGG-------UUUA----------------------------UCUCGAAAAGCUGGUA-GGCAAA-UAUAAG
>URS0000D6AFB7_12908/1-81
UGCCCCUUGGCAAAAAUAG--AGUCGCA--ACU-GGACUGGUUUAGUAGC-------UUCUUUUUAG------------------------UCGAAAGACCGGUA-GACAAA-AAUAAG
>URS0000D6D3BA_12908/1-80
UAGCGCUUGCUAAAAAUAA--AGUCGCA--ACU-GGAUUAGUUUAGUAGC-U-----UCUUU--------------------------UAAGUGAAAAACUGAUA-GACAAA-AAUAAG
>URS0000D6BE5D_12908/1-80
UGCCCCUUGGCAAAAAUA---AGUCGCA--ACU-GGAUUGACCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAGCCGAUA-GACUAAAUAAGAA
>URS0000D6C6E9_12908/1-81
UAGCACUUGCUAAAAAUAA--UGUCGAA--ACU-GGACUGGCUUAGUAGU-------UUCUUU-------------------------UAAGCGAAAAGUCGGUA-GACAAAAUAAGAA
>URS0000D6AA2B_12908/1-81
UAGCACUUGCUAAAAAUAG--AGUCGAA--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D6B3B8_12908/1-81
UAGCGCUUGCUAAAAAUAG--AGUCGAA--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D6A304_12908/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCAGUA-GACGAAAUAAGAA
>URS0000D66840_12908/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCGGUA-GACAAAAUAAGAA
>URS0000D682F2_1262800/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUCU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D682F2_12908/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUCU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D67855_12908/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D67855_1262799/1-81
UAGCACUUGCUAAAAAUUG--AGUCGAG--ACU-GGACUGGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUCGGUA-GACGAAAUAAGAA
>URS0000D6D16D_12908/1-79
UGCCCCUUGGCAAAAAUA---UGUCGU---UCU-GGACUGGUCUAGUAGC-------UCCUCU-------------------------UGAGCGAAAAAUCGGUA-GACAAAAUAAGAA
>URS0000D6920E_12908/1-81
UGUCGCUUGGCAAAAAUUA--AGCCGAA--UCU-GGAUUAGUCUAGUAGC-------UCCUUU-------------------------UGAGCGAAAAAUUAAUA-GGCAAAAAAAGAU
>URS0000D6B628_12908/1-82
UGUCGCUUGGCAAAAAUUA--AGCCGAAA-UCU-GGAUUAGUCUAGUAGCU------CCGCA--------------------------UGAGCGAAAAAUUAAUA-GGCAAAAAAAGAU
>URS0000D6C1A3_12908/1-82
GAGCCCUUGCUCAAAAUAG--AGUCGCA--ACU-GGAUUGGAUUAGUAAGCCC----AUUA-----------------------UGG---UUUGAAAAUCCGAUA-GACAAA-AAUAAG
>URS0000D695CF_12908/1-82
GAGCCCUUGCUCAAAAUAG--UGUCGCA--ACU-GGAUUGGACUAGUAAGCCC----AUUA-----------------------UGG---UUUGAAAAUCCGAUA-GACAAA-AAUAAG
>URS0000D6B52F_12908/1-82
GAGCCCUUGCUCAAAAUAG--AGUCGCA--ACU-GGAUUGGACUAGUAAGCCC----AUUA-----------------------UGG---UUUGAAAAUCCGAUA-GACAAA-AAUAAG
>URS0000D6B67A_12908/1-82
UGCCCCUUGGCAAAAAUAG--AGUCGAA--ACU-GGAUUGGCCUAGUAAAUC-----CAUUAU----------------------GA---UGUGAAAAGCCGAUA-GACAAA-AAUAAG
>URS0000D66756_12908/1-81
CACCACAUGGUGGAAAUUUU-CGCAA----CAG-GACGCAGCCUAGUAGACC-----UCUAU-----------------------GG---UUCGGACGGCAGCGA-AGCGAAAAAGGAG
>URS0000D69541_12908/1-82
UGCCACUCGGCAAAAAUA---CGCCACA--UCA-GGUGGGAGCUAGUAGGACC----GGACA----------------------GGU---CUCGAAAACCCUCAA-GGCUAA-AAGAAA
>URS0000D660E0_12908/1-82
UGCCACUCGGCAAAAAUA---CGCCACA--UCA-GGUGGGAGCUAGUAGGACU----GGACA----------------------GGU---CUCGAAAACCCUCAA-GGCUAA-AAGAAA
>URS0000D6682C_12908/1-82
UGCCACUCGGCAAAAAUA---CGCCACA--UCA-GGUGGGAGCUAGUAGGACC----GGAUA----------------------GGC---CUCGAAAACCCUCAA-GGCUAA-AAGAAA
>URS0000D67DED_12908/1-82
UGCCACUCGGCAAAAAUA---CGCCACA--UCA-GGUGGGAGCUAGUAGGACC----GGACA----------------------GGC---CUCGAAAACCCUCAA-GGCUAA-AAGAAA
>URS0000D6C46D_12908/1-83
UGCCACUCGGCAAAAAUA---CGCCAC---UCA-GGUGGGAGUUAGUAGGCCCA---GAUA----------------------CGGG---CUCGAAAGCCCUCAA-GGCUUAAAGAAAG
>URS0000D684CD_12908/1-83
UGCCACUCGGCAAAAAUA---CGCCGC---UCA-GGUGGGAGUUAGUAGGCCCG---GAGA----------------------CGGG---CUCGAAAGCCCUCAA-GGCUUAAAGAAAG
>URS0000D68E85_12908/1-74
CGCCUCUUGGCGAAAAUUA--AGUCGCAG-CAG-GGUG-GGGUUAGUAAA-------GA-------------------------------AUUGAAAGCCCUCAA-GAC-AAUAAGAAA
>URS0000D67412_12908/1-78
CGCCGCUUGGCGAAAAUUU--UCACGA---CAG-GACGCGGCUUAGUAGGC-----------------------------------GAUGCUCGAAAUGCGGCGAAGUGAAAAAAGGAG
>URS0000D6B375_12908/1-76
UGCCGCUCGGCAAAAAUU---AACCGAAA-AAGAGGCAUGGGUUAGUAG--------CAAGU------------------------------CGAAAACUCGUGA-GGUUUAGUAAGAG
>URS0000D69920_12908/1-73
CGCCCCUUGGCGAAAAUU---GCCCGA---GAC-GGCGCGAGUUAGUAGC-------GAAG------------------------------GCGAAAGCCCGCGA-GGGCGA-AGAAAG
>URS0000D6AB38_12908/1-82
UACCGCUUGGUAAAAAUU---CAUCGG---UGC-AGCAGAGGUUAGUAGAAUA----UUAUUU-------------------------UAUUCAAACAUCUUUGA-GAUUAAGAAAGAA
>URS0000D66815_12908/1-81
CACCACUUGGUGAAAAUAUUUUGCGU----CGU-GGUACGGCUUAGUAGGCC-----GCAA------------------------GG---CUCGAAACGCCGUAA-AGCAAAAAAGGAG
>URS0000D6608B_12908/1-83
UACCCCUUGGUAAAGAUGG--UGCCGU---UAG-GGAUGGGGUUAGUACUCCC----GAAA-----------------------GGG-CGAAGGAAAGCUCCAUA-GGC-AGCAAGGAG
>URS0000D65EF3_12908/1-78
UGCCACUUGGCAAAAAUUA--AGCCGACCAAGA-GGUAUGGGUUAGUAAG-------AUUG------------------------------CCGAAAAUCCAUAA-GGCUUAUAAGUAA
>URS0000D667B2_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGG-GCCAGGUCUCGCCUUGGAACACA-CCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D674F9_12908/1-107
CAGCACUUGCUGACGAUG---AGCCAU---CAG-GACACAGCCUGGUACACUUCGGGCCGGGUUUCGCCCCGGAACCA--CCCGCGG-CGAUGGAACGGCUGUGA-GGCUAC-AAGGAG
>URS0000D674DA_12908/1-107
CAGCACUUGCUGACGAUG---AGCCGU---CAG-GACACAGCCUGGUACACUUCGGGCCGGGUUUCGCCCCGGAACCA--CCCGCGG-CGAUGGAACGGCUGUGA-GGCUAC-AAGGAG
>URS0000D6C399_12908/1-107
CAGCACUUGCUGAAGAUG---AGCCGU---CAG-GACACAGCUUAGUACACUUCGGGCCGGGUCCCGCCCCGGAACCA--CCCGCGG-CGAUGGAACAGUUGUGA-GGCUAC-AAGGAG
>URS0000D6C399_658087/1-107
CAGCACUUGCUGAAGAUG---AGCCGU---CAG-GACACAGCUUAGUACACUUCGGGCCGGGUCCCGCCCCGGAACCA--CCCGCGG-CGAUGGAACAGUUGUGA-GGCUAC-AAGGAG
>URS0000D6A0A7_12908/1-107
CAGCACUUGCUGAAGAUA---AGCCGU---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACUA--CCCGCGG-CGAUGGAACAGUUGUGA-GGCUAC-AAGGAG
>URS0000D69495_12908/1-107
CAGCACUUGCUGAAGAUA---AGCCGU---CAG-GACACAGCUUAGUACACUUCGGGCCAAGUCUCGCCUUGGAACCA--CCCGCGG-CGAUGGAACAGUUGUGA-GGCUAC-AAGGAG
>URS0000D68013_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAC--CCCGCGG-AGAUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D6C197_12908/1-107
CAGCACUUGCUUAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAC--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D672AA_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GGCACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAC--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D67810_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAU--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D65DB5_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAAAAC--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D683FD_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAAGUCUCGCCUUGGAACAC--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D6BFF1_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAC--CCCGCGG-CGCUGGAACAGUUGUGA-GGCUAC-AAGGAG
>URS0000D66D30_12908/1-107
CAGCACUUGCUGAAGAAA---AGCCGA---CAG-GACACAGCUUAGUACACUUCGGGCCAGGUCUCGCCUUGGAACAC--CCCGCGG-CGCUGGAACGGUUGUGA-GGCUAC-AAGGAG
>URS0000D6B905_12908/1-78
UGCCCCUUGGCAAAAAUGAA-AGCCGUG--AAU-GGCAUCGGCCAGUAC-C------UUGC-----------------------------GUGGAAAACCGAUGA-GGCUGACAAAGAG
>URS0000D6C2DF_12908/1-78
UGCCCCUUGGCAAAAAUGAA-AGCCGUG--AAU-GGCAUCGGCUAGUAC--------CUUGCUU----------------------------GGAAAACCGAUGA-GGCUGACAAAGAG
>URS0000D6C2DF_411470/1-78
UGCCCCUUGGCAAAAAUGAA-AGCCGUG--AAU-GGCAUCGGCUAGUAC--------CUUGCUU----------------------------GGAAAACCGAUGA-GGCUGACAAAGAG
>URS0000D6A266_12908/1-75
CACCGCUAGGUGAAAAUA---AGCCGCA--AAU-GGCGCCGGCAAGUAG--------CACGAU-----------------------------CGAAACCCGGCGA-GGCUAACAAAGAG
>URS0000D6C2D3_12908/1-76
CACCACUUGGUGAAAAUUA--GGCCGUA--AAU-GGCACUGGUUAGUAG--------CAUGAU-----------------------------CGAAAGCCAGUGA-GGCUGACAAAGAG
>URS0000D697A6_658089/1-76
CACCACUUGGUGAAAAUUA--GGCCGUA--AAU-GGCACUGGUUAGUAG--------UAUGAU-----------------------------CGAAAGCCAGUGA-GGCUGACAAAGAG
>URS0000D67A8C_12908/1-75
CACCGCUUGGUGAAAAUG---GGCCGUA--AAU-GGCACCGGUUAGUAG--------CACGAU-----------------------------UGAAAGCCGGUGA-GGCUAACAAAGAG
>URS0000D68379_12908/1-75
CACCGCUUGGUGAAAAUG---GGCCGUA--AAU-GGCACCGGUUAGUAG--------CAUGAU-----------------------------CGAAAGCCGGUGA-GGCUAACAAAGAG
>URS0000D66FCF_12908/1-75
CACCGCUUGGUGAAAAUG---GGCCGUA--AAU-GGCACCGGUUAGUAG--------CACGAU-----------------------------CGAAAGCCGGUGA-GGCUAACAAAGAG
>URS0000D660A3_12908/1-77
CACCGCUUGGUGAAAAUUAA-GGCCGUA--AAU-GGCACCGGUUAGUAG--------CAAGUC-----------------------------UGAAAGCCGGUGA-GGCUAACAAAGAG
>URS0000D6A14A_12908/1-84
UACCCCCUGGUAAAAAUA---GGCCGCG--AAU-GGCGCUGGUUAGUACGCCA----GGAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D67C25_12908/1-84
UACCCAUUGGUAAAAAUA---GGCCGCG--AAU-GGCGCUGGUUAGUACGCCA----GGAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D6B2E3_12908/1-84
UACCCCUUGGUAAAAAUA---GGCCGCG--AAU-GACGCUGGUUAGUACGCCA----GGAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D6BF33_12908/1-84
UACCCCUUGGUAAAAAUA---GGCCGCG--AAU-GGCGCUGGUUAGUACGCCA----GAAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D6BED7_12908/1-84
UACCCCUUGGUAAAAAUA---GGCUGCG--AAU-GGCGCUGGUUAGUACGCCA----GGAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D6B169_12908/1-84
UACCCCUUGGUAAAAAUA---GGCCGCG--AAU-GGCGCUGGUUAGUACGCCA----GGAA-----------------------UGG-AGCUGGAAAGUCAGCGA-GGCUAACAAAGAG
>URS0000D689A2_12908/1-73
UACCACUUGGUAAAAAUUA--GGCUGAC--AAA-GGCGUGGGUUAGUAG--------GCAA-------------------------------CGAAAAUCUGCGA-GGCUAC-AAGAAA
>URS0000D6650B_12908/1-83
CACCGCUCGGUGAAAAUUU--CGCCGC---AGG-GACACGGCCAAGUAAGCC-----CGAUAU----------------------GG--AUUUGAAAGGUCGUGA-GGUGAAUAAGAAA
>URS0000D6650B_1263002/1-83
CACCGCUCGGUGAAAAUUU--CGCCGC---AGG-GACACGGCCAAGUAAGCC-----CGAUAU----------------------GG--AUUUGAAAGGUCGUGA-GGUGAAUAAGAAA
>URS0000D6C0F6_12908/1-83
CACCGCUCGGUGAAAAUUU--CGCCGC---AGG-GACACGGCCAAGUAAGCCC----GAUA-----------------------UGG--AUUUGAAAGGCCGUGA-GGUGAAUAAGAAA
>URS0000D676DB_12908/1-78
CACCACUUGGUGAAGAUUU--UGUCAU---AGG-GAUAUGGGCUAGUAGGC------AGUU-------------------------G---CUCGAAAACCCGUAA-GACAAACAAGGAA
>URS0000D68821_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGGUUAAGUAGG-------CUUC---------------------------GGCUCGAACAAUCUCGCAGGCAAACAAGGAC
>URS0000D69BCF_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGGUUUAGUAGGC------UUCG-------------------------G---CUCGAACGAUCUCGCAGGCAAACAAGGAC
>URS0000D6B17D_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGGUUUAGUAGGC------UUCG-------------------------G---CUCGAACAAUCUCGCAGGCAAACAAGGAC
>URS0000D68CC2_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGAUUUAGUAGGC------UUCG-------------------------G---CUCGAACAAUCUCGCAGGCAAACAAGGAC
>URS0000D69BDC_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGGUUUAGUAGGC------UUCG-------------------------G---CUCGAAUAACCUCGCAGGCAAACAAGGAC
>URS0000D699CC_12908/1-80
CACCGCUUGGUGAAAAUAU--UGCCGCA--UAG-GACGGGGUUUAGUAGGCCA-------------------------------UGG---CUCGAACGAUCUCGCAGGCAAACAAGGAC
>URS0000D68E92_12908/1-80
CACCGCUUGGCGAAAAUAU--UGCGGCA--UAG-GACGGGGUUUAGUAGGCCA-------------------------------UGG---CUCGAACGAUCUCGCAGGCAAACAAGGAC
>URS0000D6982E_12908/1-79
CACCGCUUGGUGAAAAUAU--UGCCGG---GAG-GACAGGGUUUAGUAGGC------CUCG-------------------------G---CUCGAAAGACCUUGCAGGCAAACAAGGAG
>URS0000D67E8C_12908/1-82
CACCGCUUGGUGAAAAUAU--UGCCGU---CAG-GACAGGGUUUAGUAAGCC-----GAAA------------------------GG--AUUUGAAAGACCUUGCAGGCAAACAAGGAC
>URS0000D6AA15_12908/1-87
CACCGCUUGGUGGAAAUGU--UGCCGCUA-CAG-GACGGGCUCUAGUACGACC----GCAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6CE32_12908/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUCUAGUACGACC----GUAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6C660_12908/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUCUAGUACGACC----GCAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6BCB5_12908/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUCUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAAACCCCGAUGGCAAACAAGGAG
>URS0000D6BB7D_12908/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUUUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D67EE4_12908/1-87
CACCGCUUGGUGAAAAUAU--UGCCGCUA-CAG-GACGGGCUUUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6BCD5_12908/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUCUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6BCD5_1263006/1-87
CACCGCUUGGUGGAAAUAU--UGCCGCUA-CAG-GACGGGCUCUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D69C22_12908/1-87
CGCCGCUUGGCGAAAAUAU--UGCCACUA-CAG-GACGGGCUUUAGUACGGCC----GAAA-----------------------GGU-AUCUGGAAAGACCCCGAUGGCAAACAAGGAG
>URS0000D6B44B_12908/1-84
CACCUCUUGGUGAAGAACGA-UGCCGA---AGG-GACGCGGUUUAGUACAUCC----GAAA-----------------------GGA-CGCUGGAAAGACCGCGA-GGCA-ACAAGGAG
>URS0000D67D05_12908/1-84
CACCUCAUGGUGAAGAUA---GGCAUU---UUG-GGAGCAGGCUAGUACACUCC---GCAG----------------------GGGG-CGAUGGAAAGCCUGUAC-AGCUAA-AAGGAG
>URS0000D675DF_12908/1-84
CACCCCACGGUGAAGAUA---GGCAUU---UUG-GGAGCAGGCUAGUACACUCC---GCAG----------------------GGAG-CGAUGGAAAGCCUGUAC-AGCUAA-AAGGAG
>URS0000D663C8_12908/1-84
CACCCCACGGUGAAGAUA---GGCAUU---UUG-GGAGCAGGCUAGUACACUCC---GCAG----------------------GGAG-CGCUGGAAAGCCUGUAC-AGCUAA-AAGGAG
>URS0000D6A8CD_12908/1-84
CACCUCACGGUGAAGAUA---GGCAUU---UUG-GGAGCGGGCUAGUACACCCC---GCAA----------------------GGGG-CGCUGGAACGUCCGUAC-AGCUAA-AAGGAG
>URS0000D6C6B1_12908/1-84
CACCCCACGGUGAAGAUA---GGCAUU---UUG-GGAGCGGGCUAGUACACCCC---GCAA----------------------GGGG-CGCUGGAACGUCCGUAC-AGCUAA-AAGGAG
>URS0000D6C3BC_12908/1-84
CACCCCAUGGUGAAGAUA---GGCAUU---UUG-GGAGCGGGCUAGUACACCCC---GCAA----------------------GGGG-CGCUGGAACGUCCGUAC-AGCUAA-AAGGAG
>URS0000D6A323_12908/1-86
CACCCCUUGGUGAAGAUA---AGCAAAUU-UGG-GGAGCGGGUUAGUACACCUC---UGCG----------------------GAGG-CGCUGGAAAGCCCGUAC-AGCUAA-AAGGAG
>URS0000D6872E_12908/1-86
CACCCCUUGGUGAAGAUA---AGCAAAUU-UGG-GGAGCGGGUUAGUACACCUC---UACG----------------------GAGG-CGCUGGAAAGCCCGUAC-AGCUAA-AAGGAG
>URS0000D6B0E7_12908/1-85
CACCUCUCGGUGAAGAUA---AGCAGUU--CAG-GGAGCGGGUUAGUACACUCC---GAAA----------------------GGAG-CGCUGGAAAGCUCGUAA-AGCUAA-AAGGAG
>URS0000D6B91D_12908/1-85
CACCUCUCGGUGAAGAUA---AGCAGUU--CAG-GGAGCGGGUUAGUACACCUC---GAAA----------------------GAGG-CGUUGGAAAGCUCGUAC-AGCUAA-AAGGAG
>URS0000D6B91D_1203606/1-85
CACCUCUCGGUGAAGAUA---AGCAGUU--CAG-GGAGCGGGUUAGUACACCUC---GAAA----------------------GAGG-CGUUGGAAAGCUCGUAC-AGCUAA-AAGGAG
>URS0000D677E2_12908/1-83
CACCCCUUGGUGAAGAUA---UGCUAU---AAG-GGCACGGUUUAGUACUCUCC---GAAA----------------------GGAG-CGCAGGAAACACCGUGA-GGCA-A-AAGGAG
>URS0000D6C69F_12908/1-91
CACCCCUUGGUGCAGAUU---AGCCAA---CAG-GACACGGUUUAGUACACUCCCGCAACCG------------------GCGGGAG-CGGGGGGAAGAUCGUGA-GGCUAA-AAGGAG
>URS0000D6B13B_12908/1-91
CACCCCUUGGUGCAGAUU---AGCCAA---CAG-GACACGGUUUAGUACACUCCCGCAACCG------------------GCGGGAG-CGGUGGAAAGAUCGUGA-GGCUAA-AAGGAG
>URS0000D6B13B_658087/1-91
CACCCCUUGGUGCAGAUU---AGCCAA---CAG-GACACGGUUUAGUACACUCCCGCAACCG------------------GCGGGAG-CGGUGGAAAGAUCGUGA-GGCUAA-AAGGAG
>URS0000D66EBC_12908/1-91
CACCCCUUGGUGCAGAUU---AGCCAA---CAG-GACACGGUUUAGUACACUCCCGCAACCG------------------GCGGGAG-CGGGGGAAAGAUCGUGA-GGCUAA-AAGGAG
>URS0000D65EB2_12908/1-91
CACCCCUUGGUGCAGAUU---AGCCAA---CAG-GACACGGUUUAGUACACUCCCGCAACCG------------------GCGGGAG-CGGUGGAAAGAUCGUGA-GGAUAA-AAGGAG
>URS0000D6771B_12908/1-91
CACCCAUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCACAACCC------------------GUGGAGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D6C092_12908/1-91
CACCUCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCACAACCC------------------GUGGAGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D6A08E_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCACAACCC------------------GUGGAGG-CGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D69C4F_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCACAACCC------------------GUGGAGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D6B081_12908/1-91
CACCCCUUGGCGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCACAACCC------------------GUGGAGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D65966_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCAACAACCU------------------GUGGGGG-CGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D6739E_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGAUUUAGUACACUCCCACAACCU------------------GCGGGGG-CGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D68137_12908/1-91
CACCACUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGGUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D6A580_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUUCCGCAACCU------------------GCGGGGG-CGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D65C4A_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGGUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D66E99_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D6A67E_12908/1-92
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGGGCGAUGGAAAGACCGUGA-GGCUAA-AAGGAG
>URS0000D6A9BD_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D66EDF_12908/1-91
CACCCCUUGGCGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGAUGGAAAGGCCGUGA-GGCUAA-AAGGAG
>URS0000D685D4_12908/1-91
CACCCCUUGGUGCAGAUA---AGCCAU---CAG-GACACGGUUUAGUACACUCCCGCAACCU------------------GCGGGGG-CGAUGGAAAGACAGUGA-GGCUAA-AAGGAG
>URS0000D6B669_12908/1-84
CGGCCCUUGCCGGCGAUG---UGCCGA---AGG-GACACGGUUUAGUACACGCC---GGAA----------------------GGCG-CGAUGGAAACACCGUGA-GGCAA-CAAGGAG
>URS0000D67C79_12908/1-84
CGGCCCUUGCCGGAGAUA---UGCCGG---AGG-GACACGGUUUAGUACACGCC---GGAA----------------------GGCG-CGAUGGAAAUACCGUGA-GGC-AACAAGGAG
>URS0000D6D035_12908/1-78
CACCACUUGGUGAAAAUUA--AGUCGUA--AAG-AGCAAAGUUUAGUAGU-------UUAUU----------------------------AUCGAACAACUUUGA-GACUAAUAAGAAA
>URS0000D6B403_12908/1-79
CACCCCAUGGUGAAAAUUA--GGCCGUA--AAG-AGCAAGGUUUAGUAGG-------UUUACUC---------------------------UCGAACCACCUUGA-GGCUAAUAAGAAG
>URS0000D677B7_12908/1-76
CACCUCUUGGUGAAAAUUA--AGCCGAA--AAG-AGCAAGGUUUAGUAG-C------AUA--------------------------G----UCGAAAUACCUUGA-GGCUAAUAAGAAA
>URS0000D66DB7_12908/1-77
CACCCCUUGGUGAAAAUUA--UGCCGAA--AAG-AGCAGGGUUUAGUAG--------CAUUUGU----------------------------CGAAAGACCUUGA-GGCUAAUAAGAAA
>URS0000D69B0F_12908/1-75
CACCACUUGGUGAAGAUUU--UGCCGU----CG-GGAACGGUUUAGUAGG-------UAUUUC----------------------------UCGAAAGACCGUCA-GGCGAA-AAGGAG
>URS0000D6684B_12908/1-93
CACCGCUUGGUGAUGAUUU--UACCGA---UAG-GACACGACUUAGUAU-CGCGGGCGCUAUCACGC-------------GCACGCG---C-AGAAAGGCCGUGA-GGUAAC-AAGGAG
>URS0000D65BFE_12908/1-79
UACCACAUGGUAGAAAUAA--GACCGAU--AAA-GGAAGGGGCUAGUACC-AG----CAA----------------------------CCUGGGAACGUCCUUUA-GGU-AAUAAGAAA
>URS0000D6ADE6_12908/1-79
UACCACACGGUAGAAAUAA--GACCGAC--AAA-GGAAGGGGCUAGUACC-AG----CAA----------------------------CCUGGGAAAGUCCUUUA-GGU-AAUAAGAAA
>URS0000D68962_12908/1-73
UGGCACUUGCCAAAAAUGA--AACCGA---AAC-GGCAGAGAUUAGUAAA-------UC-------------------------------AUUGAAAGUCUUUGA-GGU-AAUAAGAAA

There are no chains in PDB that we map to Rfam family RF03021.

Jump to results for:

  • Loop 1HL Column numbers: 4-9
  • Loop 2IL Column numbers: 25-37, 104-107
  • Loop 3IL Column numbers: 43-49, 93-98
  • Loop 4IL Column numbers: 50-51, 87-92
  • Loop 5HL Column numbers: 53-85

Loop 1 Hairpin loop

Column numbers: 4-9 
    Scored sequences and counts

    
    CCCUUG   43

    
    CACUUG   35

    
    CGCUUG   29

    
    CACUCG    6

    
    CGCUCG    4

    
    CUCUUG    4

    
    CCCACG    3

    
    CCCAUG    3

    
    CUCUCG    3

    
    CACAUG    2

    
    CCAUUG    2

    
    CCCUAG    2

    
    CACACG    1

    
    CCCCUG    1

    
    CGCUAG    1

    
    CUCACG    1

    
    CUCAUG    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_56334.1

Basepair signature:
cWW-F

100.00 48.36 2 1

Mini UNCG

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

100.00 44.37 1 1

3

Motif group HL_56131.2

Basepair signature:
cWW-F-F

96.45 32.87 4 2

4

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

92.20 36.82 3 1

5

Motif group HL_48417.5

Basepair signature:
cWW-F-F

91.49 44.97 2 1

6

Motif group HL_81100.2

Basepair signature:
cWW

88.65 25.31 2 2

7

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

85.82 16.67 4 2

8

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

84.40 20.14 2 2

9

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

65.25 -5.18 3 2

Pseudoknot geometry with 3' bulge

10

Motif group HL_65794.5

Basepair signature:
cWW-F-F-F-F

54.61 7.52 3 2

Pseudoknot geometry

Loop 2 Internal loop

Column numbers: 25-37, 104-107 
    Scored sequences and counts

    
    CAU---CAG-GAC*GA-G   16

    
    CGCUA-CAG-GAC*GAUG    8

    
    CGA---CAG-GAC*GA-G    8

    
    CGCA--UAG-GAC*GCAG    6

    
    CGAG--ACU-GGA*UA-G    6

    
    CGCA--ACU-GGA*UA-G    6

    
    CGUA--AAU-GGC*GA-G    6

    
    AUU---UUG-GGA*AC-A    6

    
    CAA---CAG-GAC*GA-G    5

    
    CGU---CAG-GAC*GA-G    5

    
    CACA--UCA-GGU*AA-G    4

    
    CGAA--ACU-GGA*UA-G    4

    
    CGCG--AAU-GGC*GA-G    4

    
    CGUG--AAU-GGC*GA-G    3

    
    CGC---AGG-GAC*GA-G    3

    
    AAAUU-UGG-GGA*AC-A    2

    
    AGUU--CAG-GGA*AC-A    2

    
    CGAA--AAG-AGC*GA-G    2

    
    CGUA--AAG-AGC*GA-G    2

    
    CGA---AGG-GAC*GA-G    2

    
    CGC---UCU-GGG*CA-G    2

    
    CACUA-CAG-GAC*GAUG    1

    
    CGAAA-AAGAGGC*GA-G    1

    
    CGACCAAGA-GGU*AA-G    1

    
    UCGUA-AAA-GGC*GAGG    1

    
    CGAAA-UCU-GGA*UA-G    1

    
    CGCAG-CAG-GGU*AA-G    1

    
    GGCA--UAG-GAC*GCAG    1

    
    AGUU--CAG-GGA*AA-A    1

    
    CGA---CAG-GAC*GAAG    1

    
    CGAA--UCU-GGA*UA-G    1

    
    CGAC--AAA-GGA*UA-G    1

    
    CGAU--AAA-GGA*UA-G    1

    
    CGAU--AUA-GGG*CA-G    1

    
    CGCA--AAU-GGC*GA-G    1

    
    CGCG--AAU-GAC*GA-G    1

    
    CGG---GAG-GAC*GCAG    1

    
    CGU---CAG-GAC*GCAG    1

    
    UGAC--AAA-GGC*GA-G    1

    
    UGCG--AAU-GGC*GA-G    1

    
    CAC---UCA-GGU*AA-G    1

    
    CAU---AGG-GAU*AA-G    1

    
    CGA---AAC-GGC*GA-G    1

    
    CGA---ACA-GGC*GA-G    1

    
    CGA---ACU-GGA*UA-G    1

    
    CGA---CAG-GGC*GA-G    1

    
    CGA---GAC-GGC*GA-G    1

    
    CGA---UAG-GAC*GA-G    1

    
    CGC---CUU-GGG*UA-G    1

    
    CGC---UCA-GGU*AA-G    1

    
    CGG---AGG-GAC*GA-G    1

    
    CGG---UGC-AGC*GA-G    1

    
    CGU---UAG-GGA*UA-G    1

    
    CGU---UCU-GGA*UA-G    1

    
    CGU---UCU-GGG*UA-G    1

    
    UAU---AAG-GGC*GA-G    1

    
    UGU---AAC-GGC*GA-A    1

    
    AA----CAG-GAC*GA-A    1

    
    CGU----CG-GGA*CA-G    1

    
    GU----CGU-GGU*AA-A    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_37603.1

Basepair signature:
cWW-L-cWW-L-cWW-L-L

17.73 -50.31 6 5

2

Motif group IL_86136.1

Basepair signature:
cWW-tSH-L-cWW-L-L-R-L

4.26 -75.51 5 5

3

Motif group IL_38969.1

Basepair signature:
cWW-L-R-L-cWW-L-L

3.55 -64.14 8 6

Reverse kink-turn related

4

Motif group IL_49971.1

Basepair signature:
cWW-cWH-cWW-cWW-L-L-R

2.84 -70.89 8 6

5

Motif group IL_84665.1

Basepair signature:
cWW-L-cSW-cWW-L-L-R-L-R-L-R-L

0.71 -68.36 7 6

6

Motif group IL_09570.1

Basepair signature:
cWW-L-R-L-R-L-cWW-L-L-R

0.71 -75.86 7 6

7

Motif group IL_89312.1

Basepair signature:
cWW-tSH-L-cWS-cWW-L

0.71 -96.60 8 5

8

Motif group IL_82968.1

Basepair signature:
cWW-L-cWW-L-L-R-L-R-L

0.71 -112.36 6 6

9

Motif group IL_91592.1

Basepair signature:
cWW-L-tHH-L-cWW-L-L

0.71 -119.60 7 6

Loop 3 Internal loop

Column numbers: 43-49, 93-98 
    Scored sequences and counts

    
    UUAGUAC*GGAAAG   35

    
    CUAGUAG*CGAAAA   17

    
    UUAGUAG*CGAAAG   13

    
    CUAGUAC*GGAAAG    9

    
    UUAGUAC*GGAACG    8

    
    UUAGUAG*CGAAAA    6

    
    UUAGUAC*GGAACA    5

    
    CUAGUAC*GGAACG    4

    
    CAAGUAA*UGAAAG    3

    
    CUAGUAA*UGAAAA    3

    
    CUAGUAC*GGAAAA    3

    
    UUAGUAA*UGAAAG    3

    
    UUAGUAG*CGAACA    3

    
    UUAGUAG*CGAACG    3

    
    CUGGUAC*GGAACG    2

    
    UUAGUAC*GGAAAC    2

    
    UUAGUAG*CGAAAU    2

    
    UUAGUAG*UGAAAG    2

    
    AUAGUAG*CGAAAU    1

    
    CAAGUAG*CGAAAC    1

    
    CCAGUAC*GGAAAA    1

    
    CUAGUAG*CGAAAG    1

    
    CUAGUAG*CGGACG    1

    
    UAAGUAG*CGAACA    1

    
    UUAGUAA*CCAAUA    1

    
    UUAGUAA*CGAAAA    1

    
    UUAGUAA*UGAAAA    1

    
    UUAGUAC*GGAAAU    1

    
    UUAGUAC*GGGAAG    1

    
    UUAGUAG*CAAACA    1

    
    UUAGUAG*CGAAAC    1

    
    UUAGUAG*CGAACC    1

    
    UUAGUAG*CGAAUA    1

    
    UUAGUAG*UGAAAA    1

    
    UUAGUAU*AGAAAG    1

    
    UUAGUA-*--AAAG    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

99.29 93.13 2 0

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

99.29 55.64 3 1

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

3

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

99.29 31.92 4 2

8x6 Sarcin-Ricin with inserted A; G-bulge

4

Motif group IL_16458.4

Basepair signature:
cWW-L-R-L-R-cSH-tWH-tHS-cWW

97.87 34.30 3 2

Sarcin-Ricin target in LSU H95; G-bulge

5

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

95.04 10.15 2 2

8x7 Sarcin-Ricin; G-bulge

6

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

87.23 12.31 5 2

8x6 Sarcin-Ricin with inserted Y; G-bulge

7

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

41.13 1.20 7 3

tSH-tSH-tHH-tHS

8

Motif group IL_65594.1

Basepair signature:
cWW-L-R-tSW-tHH-cSH-tWH-tHS-cWW

31.91 -1.93 5 3

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

17.73 -3.15 7 3

8x6 Sarcin-Ricin with bulged A; G-bulge

10

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

17.02 -8.93 6 3

7x7 Sarcin-Ricin with intercalated A; G-bulge

Loop 4 Internal loop

Column numbers: 50-51, 87-92 
    Scored sequences and counts

    
    AC*G-CGAU   22

    
    AC*G-CGCU   15

    
    GC*G---CU   11

    
    GC*G-AGCU    6

    
    GG*U-AUCU    6

    
    AC*G-CGGU    5

    
    GC*G--AUU    4

    
    GA*U-AUCU    3

    
    GC*G---UU    3

    
    AC*G-CGGG    2

    
    AC*G-CGUU    2

    
    GA*C---CU    2

    
    GA*U---CU    2

    
    AC*GGCGAU    1

    
    GC*GAUGCU    1

    
    AC*G-AGAU    1

    
    AU*A-CGCU    1

    
    UC*G-CGAA    1

    
    UC*G-CGCA    1

    
    AA*--UAUU    1

    
    CU*--UGAG    1

    
    AC*G---UU    1

    
    AU*A---UG    1

    
    GA*U---GC    1

    
    UU*A---AU    1

    
    Omitted sequenced and counts

    
    --*------   14

    
    C-*--UGAG   11

    
    G-*--UUCU    4

    
    C-*--CCUG    2

    
    A-*----AU    2

    
    G-*-----U    2

    
    C-*--UAAG    1

    
    G-*--GGCU    1

    
    U-*--UAAG    1

    
    G-*---UCU    1

    
    -C*----GU    1

    
    -C*G----U    1

    
    -C*G---C-    1

    
    U-*----AU    1

    
    C-*-----G    1

    
    C-*-----U    1

    
    G-*-----C    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_20031.1

Basepair signature:
cWW-L-cWW-L

56.84 5.90 4 2

2

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

56.84 -5.42 2 1

Major groove intercalation

3

Motif group IL_07171.1

Basepair signature:
cWW-L-cWW-L

52.63 -2.49 5 1

Bulged stacked bases

4

Motif group IL_25463.1

Basepair signature:
cWW-L-cWW-L-L

42.11 -28.29 5 3

5

Motif group IL_03109.3

Basepair signature:
cWW-cWS-tWH-cWW-L

41.05 -3191.64 3 2

C-loop

6

Motif group IL_26685.1

Basepair signature:
cWW-L-cWW-L

32.63 -8.66 4 2

Multiple bulged bases

7

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

29.47 -13.12 4 2

8

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

29.47 -35.31 4 2

Intercalated cWS

9

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

28.42 -34.59 4 1

10

Motif group IL_29346.2

Basepair signature:
cWW-L-cWW-L-L

28.42 -38.66 4 2

Left turn

Loop 5 Hairpin loop

Column numbers: 53-85 
    Scored sequences and counts

    
    -----UCCUUU----------------------    8

    
    C----GAAA-----------------------G    8

    
    CCCGCAACCU------------------GCGGG    7

    
    UCGGGCCAGGUCUCGCCUUGGAACAC--CCCGC    5

    
    CCCGCAACCG------------------GCGGG    5

    
    UCCACAACCC------------------GUGGA    5

    
    A----GGAA-----------------------U    5

    
    -----UUCG------------------------    4

    
    CC---GCAA----------------------GG    3

    
    CC---GCAG----------------------GG    3

    
    -----CACGAU----------------------    3

    
    -----UCCUCU----------------------    3

    
    C----AUUA-----------------------U    3

    
    UCGGGCCGGGUCCCGCCCCGGAACCA--CCCGC    2

    
    UCGGGCCGGGUUUCGCCCCGGAACCA--CCCGC    2

    
    CC---GAAA----------------------GG    2

    
    CC---GGAA----------------------GG    2

    
    UC---GAAA----------------------GA    2

    
    -----CUUGCUU---------------------    2

    
    C----GGACA----------------------G    2

    
    -----CAUGAU----------------------    2

    
    -----CGAUAU----------------------    2

    
    C----GCAA-----------------------G    2

    
    -----GCAA------------------------    2

    
    -----UUAA------------------------    2

    
    G----CAA-------------------------    2

    
    A-------------------------------U    2

    
    UCGG-GCCAGGUCUCGCCUUGGAACACA-CCGC    1

    
    UCGGGCCAAGUCUCGCCUUGGAACAC--CCCGC    1

    
    UCGGGCCAAGUCUCGCCUUGGAACCA--CCCGC    1

    
    UCGGGCCAGGUCUCGCCUUGGAAAAC--CCCGC    1

    
    UCGGGCCAGGUCUCGCCUUGGAACAU--CCCGC    1

    
    UCGGGCCAGGUCUCGCCUUGGAACUA--CCCGC    1

    
    CGGGCGCUAUCACGC-------------GCACG    1

    
    -----UUUAUCUCCGUGAGGAAU----------    1

    
    CCAACAACCU------------------GUGGG    1

    
    CCCACAACCU------------------GCGGG    1

    
    UCCGCAACCU------------------GCGGG    1

    
    GCUGGUUU--------------------CCAGC    1

    
    -----AGCCACAAGCCC----------------    1

    
    -----UUCUUUUUAG------------------    1

    
    CA---GAUA----------------------CG    1

    
    CG---GAGA----------------------CG    1

    
    UC---UACG----------------------GA    1

    
    UC---UGCG----------------------GA    1

    
    -----CAUUUGU---------------------    1

    
    -----CCUUUUG---------------------    1

    
    -----UUUACUC---------------------    1

    
    A----UUAUUU----------------------    1

    
    C----GGAUA----------------------G    1

    
    U----GGACA----------------------G    1

    
    -----CAAGUC----------------------    1

    
    -----CAUUAU----------------------    1

    
    -----UAUGAU----------------------    1

    
    -----UAUUUC----------------------    1

    
    -----UUCUUU----------------------    1

    
    A----GAAA-----------------------U    1

    
    C----GAUA-----------------------U    1

    
    C----GUAA-----------------------G    1

    
    -----CAAGU-----------------------    1

    
    -----CCGCA-----------------------    1

    
    -----UCUAU-----------------------    1

    
    -----UCUUU-----------------------    1

    
    -----UUAUU-----------------------    1

    
    -----AACC------------------------    1

    
    -----AGUU------------------------    1

    
    -----AUUG------------------------    1

    
    -----CUCG------------------------    1

    
    -----CUUC------------------------    1

    
    -----GAAA------------------------    1

    
    -----GAAG------------------------    1

    
    -----UCAA------------------------    1

    
    -----UUGC------------------------    1

    
    -----UUUA------------------------    1

    
    -----AUA-------------------------    1

    
    -----GA--------------------------    1

    
    -----UC--------------------------    1

    
    Omitted sequenced and counts

    
    ---------------------------------    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_56334.1

Basepair signature:
cWW-F

24.29 -3390.66 3 3

Mini UNCG

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

22.86 -1787.67 3 2

3

Motif group HL_50006.2

Basepair signature:
cWW-F-F

20.71 -1777.48 4 3

4

Motif group HL_37824.7

Basepair signature:
cWW-F-F-F-F

19.29 -1467.64 3 2

GNRA

5

Motif group HL_75660.5

Basepair signature:
cWW-F

17.86 -3463.44 3 3

6

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

16.43 -3248.63 5 4

7

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

15.71 -1725.95 3 3

8

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

15.71 -1839.23 4.5 4

9

Motif group HL_93535.1

Basepair signature:
cWW-F-F-F-F

15.71 -1884.19 4 3

10

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

15.71 -3317.62 3 3

tRNA D-loop

Coloring options: