RNA 3D Hub

JAR3D Query RF03021-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam 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: 25-36, 105-107
  • Loop 3IL Column numbers: 43-49, 93-98
  • Loop 4IL Column numbers: 50-51, 87-92
  • Loop 5HL Column numbers: 57-81

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: 25-36, 105-107 
    Scored sequences and counts

    
    CAU---CAG-GA*A-G   16

    
    CGCUA-CAG-GA*AUG    8

    
    CGA---CAG-GA*A-G    8

    
    CGCA--UAG-GA*CAG    6

    
    CGAG--ACU-GG*A-G    6

    
    CGCA--ACU-GG*A-G    6

    
    CGUA--AAU-GG*A-G    6

    
    AUU---UUG-GG*C-A    6

    
    CAA---CAG-GA*A-G    5

    
    CGU---CAG-GA*A-G    5

    
    CACA--UCA-GG*A-G    4

    
    CGAA--ACU-GG*A-G    4

    
    CGCG--AAU-GG*A-G    4

    
    CGUG--AAU-GG*A-G    3

    
    CGC---AGG-GA*A-G    3

    
    AAAUU-UGG-GG*C-A    2

    
    AGUU--CAG-GG*C-A    2

    
    CGAA--AAG-AG*A-G    2

    
    CGUA--AAG-AG*A-G    2

    
    CGA---AGG-GA*A-G    2

    
    CGC---UCU-GG*A-G    2

    
    CGU---UCU-GG*A-G    2

    
    CACUA-CAG-GA*AUG    1

    
    CGAAA-AAGAGG*A-G    1

    
    CGACCAAGA-GG*A-G    1

    
    UCGUA-AAA-GG*AGG    1

    
    CGAAA-UCU-GG*A-G    1

    
    CGCAG-CAG-GG*A-G    1

    
    GGCA--UAG-GA*CAG    1

    
    AGUU--CAG-GG*A-A    1

    
    CGA---CAG-GA*AAG    1

    
    CGAA--UCU-GG*A-G    1

    
    CGAC--AAA-GG*A-G    1

    
    CGAU--AAA-GG*A-G    1

    
    CGAU--AUA-GG*A-G    1

    
    CGCA--AAU-GG*A-G    1

    
    CGCG--AAU-GA*A-G    1

    
    CGG---GAG-GA*CAG    1

    
    CGU---CAG-GA*CAG    1

    
    UGAC--AAA-GG*A-G    1

    
    UGCG--AAU-GG*A-G    1

    
    CAC---UCA-GG*A-G    1

    
    CAU---AGG-GA*A-G    1

    
    CGA---AAC-GG*A-G    1

    
    CGA---ACA-GG*A-G    1

    
    CGA---ACU-GG*A-G    1

    
    CGA---CAG-GG*A-G    1

    
    CGA---GAC-GG*A-G    1

    
    CGA---UAG-GA*A-G    1

    
    CGC---CUU-GG*A-G    1

    
    CGC---UCA-GG*A-G    1

    
    CGG---AGG-GA*A-G    1

    
    CGG---UGC-AG*A-G    1

    
    CGU---UAG-GG*A-G    1

    
    UAU---AAG-GG*A-G    1

    
    UGU---AAC-GG*A-A    1

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

    
    CGU----CG-GG*A-G    1

    
    GU----CGU-GG*A-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_18354.1

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

4.26 -64.99 8 5

2

Motif group IL_49971.1

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

4.26 -111.82 7 5

3

Motif group IL_46112.1

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

2.84 -60.29 9 5

4

Motif group IL_33711.1

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

2.84 -78.35 8 5

Minor groove platform

5

Motif group IL_26598.1

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

2.13 -78.07 7 4

6

Motif group IL_82968.1

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

1.42 -73.84 7 5

7

Motif group IL_19897.3

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

0.71 -55.62 6 5

8

Motif group IL_37603.1

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

0.71 -84.29 6 5

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: 57-81 
    Scored sequences and counts

    
    -GAAA--------------------   14

    
    CAACCU------------------G   10

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

    
    -GCAA--------------------    7

    
    -GGAA--------------------    7

    
    GCCAGGUCUCGCCUUGGAACAC--C    5

    
    CAACCC------------------G    5

    
    CAACCG------------------G    5

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

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

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

    
    -GGACA-------------------    3

    
    -AUUA--------------------    3

    
    -GCAG--------------------    3

    
    GCCGGGUCCCGCCCCGGAACCA--C    2

    
    GCCGGGUUUCGCCCCGGAACCA--C    2

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

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

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

    
    -GAUA--------------------    2

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

    
    -CAA---------------------    2

    
    -GCCAGGUCUCGCCUUGGAACACA-    1

    
    GCCAAGUCUCGCCUUGGAACAC--C    1

    
    GCCAAGUCUCGCCUUGGAACCA--C    1

    
    GCCAGGUCUCGCCUUGGAAAAC--C    1

    
    GCCAGGUCUCGCCUUGGAACAU--C    1

    
    GCCAGGUCUCGCCUUGGAACUA--C    1

    
    -UUUAUCUCCGUGAGGAAU------    1

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

    
    CGCUAUCACGC-------------G    1

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

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

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

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

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

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

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

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

    
    -UUAUUU------------------    1

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

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

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

    
    -GGAUA-------------------    1

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

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

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

    
    GUUU--------------------C    1

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

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

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

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

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

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

    
    -GAGA--------------------    1

    
    -GUAA--------------------    1

    
    -UACG--------------------    1

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

    
    -UGCG--------------------    1

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

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

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

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

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

    
    Omitted sequenced and counts

    
    -------------------------    3
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_53890.2

Basepair signature:
cWW-F-F-F

39.13 -1458.63 2.5 1

2

Motif group HL_56334.1

Basepair signature:
cWW-F

33.33 -1615.34 3 2

Mini UNCG

3

Motif group HL_13189.1

Basepair signature:
cWW-F-F

29.71 -1305.81 3 3

4

Motif group HL_37824.7

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

28.26 -1279.84 2 2

GNRA

5

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

25.36 -1494.26 4 2

6

Motif group HL_32346.4

Basepair signature:
cWW-F

20.29 -1629.82 3 2

7

Motif group HL_48778.2

Basepair signature:
cWW-F

16.67 -1620.89 2 2

Mini UNCG

8

Motif group HL_50006.2

Basepair signature:
cWW-F-F

15.94 -1473.24 4 3

9

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

15.94 -1502.46 4 3

10

Motif group HL_13529.1

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

14.49 -1089.36 5 4

Coloring options: