JAR3D on RF03022

RF03022 RT-10 RNA

Input Summary

      000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
((.(((((((.(((.......)))))))))..))).((((((...................)))))).(((((((.......(((.....)))...)))))))........(((((...((((((.....((..........................).).....))))..))))))).
>URS0000D66309_12908_1-118
GGUCGGUUGU----GUUAGGCAU----AUU--GCCCGAUG-------CACUUA----------CACACGCUUGAC--CCACCAGCUUCG-GCAAAUACAUUAAG-A-GGU-ACUG-AG-AACGAGGCGUACC--------GAAA--------------G-GGAGA-CUCG---CGCAGUC
>URS0000D69E83_12908_1-115
ACUAUAGUAC--GC--ACA--GC-GUACUA--UGUUGAUC-------UUUA------------GAUCAGCUUCUU----AUCUGCUUCG-GCAAAUACAAACUU-A-G---AUUGAUG-UAUGCAGAGUAU---------GAAAUAU-------------AGAAA-CGCA--UGUCAAU-
>URS0000D6B3A9_12908_1-119
AACUAUAGAAC-GC-CCCA--GC-UUCU-U--GUUUGAUC-------UUAC------------GAUCAGCUUUCU--UAUC-UGCUUCG-GCAA-AACAAAACUUA-GAU-UUGAUGU--AUGCAGAGUAU---------GAAAUAU-------------AGAAA-CGCA--UUGUCAAU
>URS0000D6B4B6_12908_1-122
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUU-------UUUAC-----------GAUCAGCUUCUU----AUCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAU---------GAAUA---------------UAGAA-CGCA---UGUCAAA
>URS0000D6C3FE_12908_1-119
AACUAUAGUAC-GC-CACA--GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU---UAUCUGCUUC--GC-AAUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAU---------UGAAU---------------AAGAA-CGCA--UUGUCAUA
>URS0000D6B9D3_12908_1-121
AACUAUAGUAC-GC-ACAA--GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU----AUCUGCUUCG-GCAAAUACAAAACUUA--GA-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA---UGUCAAU
>URS0000D6C5C3_12908_1-122
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GUA-AUACAAACUU-A-GAU-UUGAUGU--AUGCAGAGUAU---------GAAUA---------------AAGAA-CGCA--UUGUCAUA
>URS0000D6C46C_12908_1-124
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUAC------------GAUCAGCUUCUU----AUCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-ACAGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D66C86_12908_1-125
AACUAUAGUAACGC-CACAA-GCCUACUAU--AUUUGAUC-------UUAC------------GAUCAGCUUUCU--UAUCCUGCUUCG-GCA-AUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAGU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6727E_12908_1-122
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUC--GCA-AUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAU---------UGAAAAU-------------A-GAA-CGCA---UGUCAAU
>URS0000D66ED2_12908_1-123
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCA-AUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAU---------UGAAAAU-------------A-GAA-CGCA---UGUCAAU
>URS0000D660ED_12908_1-124
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAACUU-A-GAU--UGAUGU--AUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCA-C
>URS0000D699D1_12908_1-124
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCA-AUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAU---------UGAAU-------------A-AAAAA-CGCA--UUGUCAAU
>URS0000D69503_12908_1-123
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCA-AUACAAACUU-A-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAU--------------AUA-AAA-CGCA---UGUCAUA
>URS0000D65997_12908_1-126
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAU---------GAAAUAU-------------AGAAA-CGCA---UGUCACU
>URS0000D6758D_12908_1-128
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAUA
>URS0000D68C0B_12908_1-128
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GUAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D66390_12908_1-128
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D68B93_12908_1-125
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUC--GCA-AUACAAAACUUA-GAU-UUGAUGU--UUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6927E_12908_1-127
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D680E1_12908_1-127
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA---UGUCAAU
>URS0000D6765E_12908_1-126
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAU-CUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D65B13_12908_1-127
AACUAUAGUAACGC-CACAA-GCC-ACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6A68D_12908_1-128
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D669E4_12908_1-127
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA---UGUCAAU
>URS0000D6D29C_12908_1-126
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAU-CUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D69D51_12908_1-127
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCC-GCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D6C4F2_12908_1-127
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D6B071_12908_1-128
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAACACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D659F1_12908_1-128
AACUAUAGUAACGC-CACAA-GCGUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCGUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6AB4E_12908_1-127
AACUAUAGUAACGC-CACAA-GC-UACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCGUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D69374_12908_1-126
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUAC------------GAUCAGCUUUCU--UAU-CUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D67E22_12908_1-129
AACUAUAGUAACGC-CACAA-GCGUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUUGG-UAUGGUGCUUCG-UCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6C161_12908_1-126
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAU---------GAAAUAU-------------AGAAA-CGCUCAUUAUC---
>URS0000D663A0_12908_1-125
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAU---------GAAAUAU-------------AGAAA-CGCA-UCUAAC---
>URS0000D67268_12908_1-124
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUC--GCAAA-ACAAACUU-A-GAU-UUGAUGU-UUUGCAGAGUAU---------UGAAUAU-------------AGAAA-CGCA--UUGUCAAU
>URS0000D67081_12908_1-125
AACUAUAGUAACGC-CACAA-GCCUACUAU--GUUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCCUGCUUCG-GCA-AUACAAAACUUA-GAU-UUGAUGU-A-UUCAGAGUAU---------UGAAUAU-------------AGAAA-CGCA--UUGUCAUA
>URS0000D6C414_12908_1-121
ACUAUAGUAC--GC-CACA--GC-CUACUA--UGUUGAUC-------UUUAC-----------GAUCAGCUUCUA----U-CCGCUUCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAAAAA-CGCA--UUGUCAAU
>URS0000D67FA0_12908_1-124
ACUAUAGUAAC-GC-CACAC-GC--UACUA--UGUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAUCGUGCUUCG-GCA-AUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D67E16_12908_1-122
ACUAUAGUAC--GC-CACAA-GC--UACUA--UGUUGAUC-------UUUAC-----------GAUCAGCUUUCU--UAU-CUGC-UCG-GCAAAUACAAAACUUA-GAU-UUGAUGU-AUUGCAGAGUAUU--------GAAAU-------------AUAGAAA-CGCA--UUGUCAAU
>URS0000D6B16F_12908_1-119
ACUAUAGUAC--GC-CACAA-GC--UACUA--UGUUGAUC-------UUUAC-----------GAUCAGCUUUCU----AUCUGC-UCG-GCAAAUACAAAACUUA-GAU-UUGAUGU--AUGCAGAGUAU---------GAAAUAU-------------AAAAA-CGCA--UUGUCAAU
>URS0000D6AC84_12908_1-131
-AACCCCGGAC-GCCCACG-GGC-UCCGGGACGC---AUCACC----AAAC---------GGUGGUCAGCCCGAA--AGUCUCGCUUCG-GCAAACACACGACA-C-GGUAGGGG----AGCGGCGAGUAGGCC------GCAA------------GGCUCGAAACCCCG--UCACCCCC
>URS0000D6C788_12908_1-129
AAAAUCUGCUC-ACUCAAU-GGU-AUCAGA--UUUAGAGCUCU----AUUAU--------AGAGGUCAGUUUAUU--UUUCCUGCGCAA-GCAAACACAUUACG-A-GGU-CUGU-AA-AAGCCUUAGUAG---------AAUUAA--------------CGAAA-GGGC--AAGACAGC
>URS0000D6593B_12908_1-127
GCUCUGCUGUU-UC-UACG--GG-GCAGCA--GGCCGGUGCU-----AAUCA---------GGUGCCAGCCAUCA--AGUCCAGCUUCG-GCAAACUCAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CUGUCACU
>URS0000D69707_12908_1-127
GCUCUGCUGUU-UC-UACG--GG-GCAGCA--GGCCGGUGCU-----AAUCA---------GGUGCCAGCCAUCA--AGCCCAGCUUCG-GCAAACUCAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CCGUCACC
>URS0000D6C07B_12908_1-127
GCUCUGCUGUU-UC-UACG--GG-GCAGCA--GGCCGGUGCU-----AAUCA---------GGUGCCAGCCAUCA--AGUCCAGCUUCG-GCAAACUCAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CCGUCACC
>URS0000D690D2_12908_1-128
GUUCUUUUGUU-CU-UACG--AG-GCAUUG--GGCGGGUACUU----UACA---------AGGUGCCAGCCUUUG--CAUCCAGCUUCG-GCAAACUUAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CUGUCACU
>URS0000D66AE6_12908_1-128
GUUCCUUUGUU-CU-UACG--AG-GCAUUG--GGCGGGUACUU----UACA---------AGGUGCCAGCCUUUG--CAUCCAGCUUCG-GCAAACUCAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CUGUCACU
>URS0000D68B11_12908_1-128
GUUCCUUUGUU-CU-UAGG--AG-GCAUUG--GGCGGGUACUU----UACA---------AGGUGCCAGCCUUUG--CAUCCAGGUUCG-GCAAACUCAUGUCC-G-AGUGGUGGCAAUGGCAGGGAGUAG---------CUCAU---------------CGAAA-CCUG--CUGUCACU
>URS0000D6BD22_991998_1-121
GCUUUGAAAUG-GU-CAAG--GC-CAUUCA--AGC-GACCA------UUACAU---------UGGUCAGCCGCAA--UAACAUGCUUAG-GCGAAUACAUUAAG-A-GGU-UCAC-A--GUAAGUGAGUAA---------UAAAG---------------UGAAA-GCUG--AAGGUGAC
>URS0000D6B4E9_12908_1-139
CCGCCGGCUUG-GC-UAAG--GC-CUUCCG--GGGCGACCAU-----GAAAGU--------GUGGUCAGCCGUGCC-CUGCCUCCUUCG-GGAAACACACAACU-G-GGU-UCGUGA--AACAGGGCGUAGUG-AGGC--UGCG--------GCCAAUAUCGAGA-CCUG--CGCGCGGC
>URS0000D6942A_12908_1-138
CCGCCGGGAUG-GC-CACG--GC-CGCCCG--GGGCGACC-------UACCUGU---------GGUCAGCCGUGCACCGACCUCCUUCG-GGGAACACACGACC-A-GGU-UCGCGA--AACAGGGCGUAGUG-AGGC--CAAGG-------GCCGACAUCGAGA-CCUG--CGCGCGAC
>URS0000D67093_12908_1-128
GCUCUGUUGU--C--GAUG---G-GCAACA--GGCCGACCAU-----UUAA----------GUGGUCAGCCGAUC--ACACCUGCUUCG-GCAAACACAUUGCA-GGGGU-CGGCCAU-AAGGGGGAGUAGCAA------CAUGA-----------UUG-UGAAA-GCCC--UAGGCCGC
>URS0000D69296_12908_1-129
GCUCUGUUGU--C--GAUG---G-GCAACA--GGCCGACCAU-----GUGA----------GUGGUCAGCCGAUC--ACACCCGCUUCG-GCAAAUACAUUGCA-GGGGU-CGGCCAUAAAGGGGGAGUAGCAA------CAUGA-----------UUG-UGAAA-CCCC--UAGGCCGC
>URS0000D66363_12908_1-135
GCUCUGCCGUU-G--GUGA---C-UCGGCA--GGCCGAUCAC-----UUUUCUU-------GUGGUCAGCCGUUU--AUUCCUGCUUUG-GCAAAUACACUACG-C-GGU-UCGUCAG-AAGGGGGAGUAGCC-------UUUGUUGAUU-------GGUCGAAA-CCCC--UGGACGGC
>URS0000D6712D_12908_1-122
GGUAAGUAAUU-GC-UACG--GC-GUUAUU--UCCCGACC-------AUAU------------GGUCAGCCAUUUU-UAUCCCCCUUCG-GGGAACACACUUAU-A-GGU-UCGGUAG-AACACUUAGUCA---------UUAAUU--------------UAAAA-GGUG--GUGCCGGC
>URS0000D6BB54_12908_1-122
GGUAAGUAAUU-GC-UACG--GC-GUUACU--UCCCGACC-------AUAU------------GGUCAGCCAUUUU-UAUCCCCCUUCG-GGGAACACACUUAU-A-GGU-UCGGUAG-AACACUUAGUCA---------UUAAUU--------------UAAAA-GGUG--GUGCCGGC
>URS0000D6B1AB_12908_1-124
GGUAAGUGACA-GC-UACG--GC-AUCACU--UCCCGACCA------UAUA-----------UGGUCAGCCGUUUU-UAUCCUCCUUCG-GGGAACACACUUAU-A-GGU-UCGAUAG-AACACUGAAUAA---------UUAAUU--------------UAAAA-GGUG--GUGUCGGC
>URS0000D6A556_12908_1-134
GCGCGUGACCC-GC-UAUG--GC-GGGCAC--GGCCGACCAU---UGCAGCAU---CGAAUGUGGUCAGCCCACG--CUUCCUGCUUCG-GCAAACACUCUACU-G-GGU-UCGG-AG-AGCGGCGAGUAGUG-------AGA--------------CAUCGAAA-GCCG---CGCCGAC
>URS0000D6B274_12908_1-132
ACCCGGCGCU--GC-UACG--GC-GUCGUC--GGGCGACCGU-----CAGUUUU-------GUGGUCAGCCCCGCC-CGGCCGGCUUCG-GCAAAUACGUUACG-A-GGU-UCGGAGA-G-CGGCGAGUACGGCG-----GCAA-----------CGCC-CGAAA-GCCG---CGCCGAC
>URS0000D6B5EB_12908_1-146
--GCUGCGUUG-GCCAGAU-GGC--GCGCA--GCCCGAUCA------AGGUCGG--------UGGUCAGCCCGCC--UGUCCUGCCUCG-GCGAACACCUUACG-C-GAU-CCGGUAG-AACGGGGCGUAGCACGGGCGCGGCGCGCA--GCACCCGUGUCGAGA-CCCG--AGGCCGGU
>URS0000D661CA_12908_1-134
GCUUUACACUUACCUUAAG-AGGCGGUGUA--AGCCGGUCAC-----GACAA---------GUGGUCAGCUCAAG--UGUCCUGCUACG-GCGAAUACAUCACG-A-GGU-UCGGUAA-AGCGCAGAGUACCGC------UUCG------------GCG-GGAAA-UGCG--AGACCGGC
>URS0000D679D7_12908_1-128
GCUCUGCACUUACC-ACAA--GGCGGUGCA--GGCCGAUCAC-----CAAG----------GUGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAACACACUACA-G-GGU-CUGGCAA-GCUGCGGAGUAGC--------UACAA-------------G-CGGAA-CGCA--GAACCAGC
>URS0000D6CBDB_12908_1-128
GCUCUGCACUCACC-AAGU--GGCGGUGCA--GGCCGAUCAC-----CAAG----------GUGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAACACACUACA-G-GGU-CUGGCAA-GCUGCGGAGUAGC--------UACAA-------------G-CGGAA-CGCA--GAACCAGC
>URS0000D69F60_12908_1-129
GCUCUGCACUUACC-ACAA--GGCGGUGCA--GGCCGAUCA------CAAUAGA--------UGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAACAAACUACA-G-GGU-CUGGCAA-UCUGCGGAGUAGC--------CUAGA-------------G-CGAAA-CGCG--GCACCAGC
>URS0000D697A4_12908_1-129
GCUCUGCAUUUACC-ACAA--GGCGGUGCA--GGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAACAAACUACA-G-GGU-CUGGCAA-UCUGCGGAGUAGC--------CUAGA-------------G-CGAAA-CGCG--GCACCAGC
>URS0000D67D30_12908_1-129
GCUCUGCAUUUACC-ACAA--GGCGGUGCA--GGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAACAAACUACA-G-GGU-CUGGCAA-UCUGCGGAGUAGU--------UUAGA-------------G-CGAAA-CGCG--GCACCAGC
>URS0000D69D90_12908_1-129
GCUCUGCACUUUCC-AGAU--GGCGGUGCA--GGCAGAUCAU-----CUAGA---------GUGGUCAGCUUGGU--UGUCCUGCUUAG-GCGAAUACAUUGUG-G-GGU-CUGGCAU-AACGCGGAGUAG---------AUGCGCA-------------CGAAA-CGCG--GAGCCAGC
>URS0000D68EAD_12908_1-132
GCUUGGCACUUACC-UUGU--GGCGGUGUC--AGCCGAUCACU----AUUUAG-------GGUGGUCAGCUUGGU--UAUCCUGCUUCG-GCGAACACACAUCU-G-GGU-UUGGUAG-AACGUUGAGUAGC--------CUAGU-------------G-CAAAA-AACG--GAGCCAGC
>URS0000D670A0_12908_1-132
GCUUGGCACUUACC-UUGU--GGCGGUGUC--AGCCGAUCACU----AUUUAG-------GGUGGUCAGCUUGGU--UAUCCUGCUUCG-GCGAACACACAUCU-G-GGU-UUGGUAG-AACGUUGAGUAGC--------CUGGU-------------G-CAAAA-AACG--GAGCCAGC
>URS0000D6BE28_12908_1-132
GCUUUGCACUUACC-AUAU--GGCGGUGCA--GGCCGAUCACU----ACUUAG-------GGUGGUCAGCUUAGU--UGUCCUGCUUAG-GCGAACACACAUCU-G-GGU-UUGGCAU-AACGUCGAGUAGC--------CUUGA-------------G-CAAAA-GACG--GAGCCAGC
>URS0000D67343_12908_1-132
GCUCUGCACUUUCC-AAAU--GGCGGUGCA--GGCCGAUCACU----AUAUAG-------GGUGGUCAGCUUGGU--UGUCCUCCUUCG-GGAAACACACUACA-G-GAU-UCGGUAG-AACGCGGAGUAGC--------CUCGA-------------G-CGGAA-CGCG--GAGCCGGU
>URS0000D6ACE7_12908_1-129
GCUUGGCACUUACC-ACAU--GGCGGUGUC--AGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--CAUCCUCCUUCG-GGAAACACACUACA-G-GAU-UCGGUAG-AACGCGGAGUAGC--------CCAGA-------------G-CGAAA-CGCG--GAGCCGGU
>URS0000D682DB_12908_1-129
GCUUGGCACUUACC-AAAU--GGCGGUGUC--AGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--CAUCCUCCUUCG-GGAAACACAUUACA-G-GAU-UCGGUAG-AACGCGGAGUAGC--------CUAGA-------------G-CGGAA-CGCG--GAGCCGGU
>URS0000D68838_12908_1-129
GCUUGGCACUUACC-ACAU--GGCGGUGUC--AGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--CAUCCUCCUUCG-GGAAACACAUUACA-G-GAU-UCGGUAG-AACGCGGAGUAGC--------CUAGA-------------G-CGGAA-CGCG--GAGCCGGU
>URS0000D6B2D1_12908_1-129
GCUUGGCACUUACC-ACAU--GGCGGUGUC--AGCCGAUCAC-----AAUAG---------GUGGUCAGCUUGGU--CAUCCUCCUUUG-GGAAACACACUACA-G-GAU-UCGGUAG-AACGCGGAGUAGC--------CUAGA-------------G-CGGAA-CGCG--GAGCCGGU
>URS0000D696AD_12908_1-132
GCUCUGCACUUUCC-AAAU--GGCGGUGCA--GGCCGAUCACU----AUUUAG-------GGUGGUCAGCUUGGU--UGUCCUGCUUCG-GCGAACACACAUCU-G-GGU-UUGGUAG-AACGCAGAGUACC--------CACGA-------------G-CGAAA-UGCG--GAGCCAAC
>URS0000D6AE20_12908_1-129
GCUCUGCACUUACC-ACUU--GGCGGUGCA--GGCAGAUCAU-----ACAGA---------GUGGUCAGCUUGGU--UGUCCUGCUUCG-GCAAAUACACUUAG-G-GGU-CUGGUAG-AACGUAGAGUAGC--------AGAAA-------------G-CGAAA-UACG--GAGCCAGU
>URS0000D6D161_12908_1-134
GCUCUGUGUAC-GC-AAGG--GC-UACACA--GGCCGAUCACU----GAAAAACA-----GGUGGUCAGCUCAGU--CAUCCUGCUUCG-GCAAACACACUACU-A-GGU-UUGGCAU-AACGUAGAGUAUGC-------AGAAA------------GC-UGAAA-UACG--AAGCCAGC
>URS0000D6C19B_12908_1-134
GCUCUGUGUAC-GC-AAGG--GC-UACACA--GGCCGAUCACU----GAAAAACA-----GGUGGUCAGCUCAGU--CAUCCUGCUUCG-GCAAACACACUACU-A-GGU-UUGGCAU-AACGUAGAGUAUGC-------AGAAA------------GC-UGAAA-UACG--GAGCCAGC
>URS0000D67D75_12908_1-134
GCUCUGUGUACGC--AAGG---GCUGCACA--GGCCGAUCAC-UG--AAUAU------CAGGUGGUCAGCCCAAU--CAUCCUGCUUCG-GCAAAUACACUACU-G-GGU-CUGGCAU-AACGUAGAGUAUGC-------AGAAA------------GU-UGAAA-UACG--GAGCCAGC
>URS0000D6C117_12908_1-128
GCUUUGGCACGGC--UACG---GCCUGCCA--AGCCGACCUC-----AAAAC---------GUGGUCAGCCCGGU--UAUCCUGCUUCG-GCAAACAACCUGCU-G-GGU-CUGGCAG-AACGUGGAGUAGCC-------CUAG-------------GG-CGGAA-CACG--GAGCCAGC
>URS0000D659A1_12908_1-128
GCUUUGGCACG-GC-UACG--GC-CUGCCA--AGCCGACCUC-----AAAAC---------GUGGUCAGCCCGGU--UAUCCUGCUUCG-GCAAACAACCUACU-G-GGU-CUGGCAG-AACGUGGAGUAGCC-------CUAG-------------GG-CGGAA-CACG--GAGCCAGC
>URS0000D6AE0A_12908_1-128
GCUUUGGCACG-GC-UACG--GC-CUGCCA--AGCCGACCUC-----AAAAC---------GUGGUCAGCCCGGU--UAUCCUGCUUCG-GCAAACAAUCUACU-G-GGU-CUGGCAG-AACGUGGAGUAGCC-------CUAG-------------GG-CGGAA-CACG--GAGCCAGC
>URS0000D673E4_12908_1-134
GCUCUGGCGCAAGC-CAACC-GCAGUGUCACCGGC-GGCAA------UGG------------UGGUCAGCCCGCC--UACCCUGCUUCG-GCAAACACAUUGCG-C-GGU-CCGGUAC-AGCGGGGCGUAGGG-AGC---AUU----------GCUCUU-CGAUA-CCCG--CGACCGGC
>URS0000D6662B_12908_1-131
GAUCCGUAAAC-GC-CACG--GC-UUUGCG--GUCAGACC-UAU---GCAA--------AUGUGGUCAGCCAGUUU-UGUCCUCCUACG-GGAAACACGCUUCA-G-GAU-UCGACAA-AACGCAGAGUAGUG-------AAA--------------CAUCGAAA-GGCG--AGGUCGAU
>URS0000D67697_12908_1-131
GAUCCACAAAC-GC-CACG--GC-UUUGUG--GUCAGACC-UAU---GCAA--------AUGUGGUCAGCCAGUUU-UGUCCUCCUACG-GGAAACACUUUUCG-G-GAU-UCGACAG-AACGCAGAGUAGUG-------AAA--------------CAUCGAAA-GGCG--AGGUCGAU
>URS0000D689F3_12908_1-128
ACUCUGCAAAC-GC-UACG--GC-UUUGCA--GGUCGGCUUU-----UCAACAU-------GUGGUCAGCCGGCAC-UGUCCUCCUUCG-GGAAAUACGCUACA-C-GGU-CUGGUAU-AGCGUCUAGUAG---------CACGU---------------CGAAC-GGCG--CGGCCAGC
>URS0000D6629F_12908_1-128
ACUCUGCAAAC-GC-UACG--GC-UUUGCA--GGUCGGCUCU-----UCAGCAU-------GUGGUCAGCCGGCAC-UGUCCUCCUUCG-GGAAAUACGCUACA-C-GGU-CUGGCAU-AGCGUCUAGUAG---------CACGU---------------CGAAC-GGCG--CGGCCAGC
>URS0000D6D387_12908_1-127
GCUCUGCGCUU-GC-CCCG--GC-UGCGCA--GGCAGGCCA------GUCAACAUG------UGGUCAGCCAGUCC-UGUCCUCC-UCG-GGGAAUACUCAGCU-U-GGU-UCGGCAG-AACGCCUAGUAG---------GAAAU---------------CCAAA-AGCG--CAGCCGAC
>URS0000D6B678_12908_1-136
GCUCUGCCAAC-GC-UACG--GC-UUGGCA--GGCCGACC--UUUCGGUUAU----CGAAGGUGGUCAGCCGGUUU-UGUCCUGCUUCG-GCAAACACGUUUCA-C-GGU-UCGGUAG-AGCGCUGAUUAC---------UGAGAAU-------------GGAAA-GGCG--CGGCCGAC
>URS0000D68EDA_12908_1-128
GCUCUGCCAAC-GC-UCGG--GC-UUGGCA--GGCAGACCA------AUCCACAUG------UGGUCAGCCAGCGC-UGUCCUGCUUCG-GCAAAUACAUUUCG-G-GGU-UCGGCAU-AACGCCUAGUAG---------GAAAU---------------CCAAA-AGCG--CAGCCGAC
>URS0000D65B0F_12908_1-128
GCUCUGCCAAC-GC-UCCG--GC-UUGGCA--GGCAGACCA------AUCCACAUG------UGGUCAGCCAGCGC-UGUCCUGCUUCG-GCAAAUACAUUUCG-G-GGU-UCGGCAU-AACGCCUAGUAG---------GAAAU---------------CCAAA-AGCG--CAGCCGAC
>URS0000D698DE_12908_1-119
GCUCUGCCAAC-GC-UCCG--GC-UUGGCA---GCAGACCA------AUCCACAUG------UGGUCAGCCAGCGC-UGUC-UGCUUC--GC-AAUACAUUUCG-G----GUCGGCAU-AACGCCUAGUAG---------AAU-----------------CC-AA-AGCG--CAGCCGAC
>URS0000D69212_12908_1-127
GCUCUGCCAAC-GC-UACG--GC-UUGGCA--GGCAGACCUC-----UUUAAC--------GUGGUCAGCCAGUUU-UGUCCUGCUUCG-GCAAAUACGUUUAG-C-GGU-UCGGUAG-AGCGCCUAGUAA---------GUUAU---------------UGAAA-AGCG--CAGCCGAC
>URS0000D67A3F_12908_1-133
ACUCUGCCGGUGG--UACG---CCCCGGCG--GGUCGGCC-UUA---CCUUUAU-----UGGUGGUCAGCCGGUUU-CAUCCUGCUUCG-GCAAACACUCUACG-C-GGU-UCGGGCA-AGCGCAGAUUAC---------UGAAAAU-------------GGAAA-AGCG--UACCCGAC
>URS0000D66204_12908_1-129
GCUCUGCAUCU-GC-CAAG--GC-UAUGCA--GGCCGUCCAU-----CUUGU---------GUGGUCAGCCGGGU--UAUCCUCCUUCG-GGAAACACGUUUAU-G-GGU-UGGGCAU-AACGCAGAGUAGUG-------UAAA-------------CAUCGAAA-CGCG--UGGCCUGC
>URS0000D68931_12908_1-128
GCUCUGCACUG-GU-UACG--AC-CGUGCA--GGCCGUCCAU-----AAAGU---------GUGGUCAGCCGGAU--UAUCCUCCUUCG-GGGAAUACGCUUAU-G-GGU-CAGGCAU-AACGCAGAGUAGU--------GCAAU-------------AUCGAAA-CGCG--GGGCCUGC
>URS0000D66333_12908_1-128
GCUCUGUAUUG-GU-UAAG--GC-CAUGCA--GGCCGUCCAU-----ACAGU---------GUGGUCAGCCGGAU--UAUCCUCCUUCG-GGGAAUACACUUAU-G-GGU-UAGGCAU-AACGCAGAGUAGUG-------AAA--------------CAUCGAAA-CGCG--UGGCCUAC
>URS0000D659D8_12908_1-139
GCGCCACGUU--GCUUACG-GGC--GCGUG--GGCCGACCAU-----CAAACCU-------AUGGUCAGCCGUGU--UGUCCUGCUUCG-GCGAAUACCUUUGG-G-GGU-CUGGUAG-AGCGUCUAGUAGCC-UGUG--GCGA--------CACACGG-CGAAC-GACG--CGGCCAGC
>URS0000D69CE5_12908_1-136
GCUCUGCUAUC-GU-UACG--GC-GUAGCA--GGCCGACC-UA----AAAUCU-------UAUGGUCAGCCGUGU--UGUCCUGCUUCG-GCGAAUACCUUUGG-G-GGU-CUGGUAG-AACGCUUAGUAGUCAC-----CAUAUU---------GUGA-CGAAC-AGCG--CGGCCAGC
>URS0000D6706D_12908_1-136
GCUCUGCUAUC-GU-UACG--GC-GUAGCA--GGCCGACC-UA----AAAUCU-------UAUGGUCAGCCGUGU--UGUCCUGCUUCG-GCGAAUACCUUUGG-G-GGU-CUGGUAG-AGCGCUUAGUAGUCAC-----UAUGUU---------GUGA-CGAAC-AGCG--CGGCCAGC
>URS0000D687B2_12908_1-127
GCUCUGCGACG-GC-UACG--GC-CUCGCA--GGCCGACCGCU----UCAU---------GGUGGUCAGCCUCAU--CGACCUGCUUCG-GCGAAUACAUUCAG-A-GGU-UCGGUAA-AGCGGGGAGUAG---------CAGUGU--------------CGAAA-CCCG--CGACCGAC
>URS0000D664D2_12908_1-124
--GC-GCGAUA-GC-UACG--GC-UUCGCA--GGCCGACCGC-----UUCAUG--------GUGGUCAGCCUCAU--CGACCUGCUUCG-GCGAAUACAUUCAG-A-GGU-UCGGUAA-AGCGGGGAGUAGC--------AGC---------------GUCGAAA-CCCG--CGACCGGC
>URS0000D68AFB_1144344_1-149
GCUCGGCACAG-GC-CACG--GC-CUCGCC--GGCCGGUCACAG---CACAA-------CUGUGGUCAGCUCGAC--UCUCCUGCUUCG-GCAAACACACUGCG-C-GGU-CCGGCAG-AGCGGGGCGUAGCGGCGGUUCAGCGCA----GAACUGCCGUCGAGA-CCCG--CGGCCGGC
>URS0000D69AB6_12908_1-126
ACACCGCCGC--GCCGCUUCGGC-GUUGCG--GGCUGG---------UGG---------------UCAGCCCGGC--UGUCCUGCUUCG-GCAAACACACUUCA-C-GGU-CCGGCAG-AGCGGGGCGUAGCGGGC----UUU-----------GCCCGUCGAGA-CCCG--CGGCCGGU
>URS0000D693F9_12908_1-139
GCUCCACCGCU-GC-CACG--GC-ACGGUG--GGCCGACCUUA----CCUAG--------UGUGGUCAGCCAUGC--CGUCCUGCUUCG-GCAAACACCUUUGG-G-GGU-UCAGAAA-AACGACGAGUAGC-CGGGC--GCAA--------GCCCGUG-UGAAA-GUCG--GGUCUGGC
>URS0000D67058_12908_1-129
UCUCGUGCGCA-GU-UACG--GC-UCGCAC--GGAUGACC-U-----GCAAAA-------AGUGGUCAGCUUAUU--UAUCCUGCUACG-GCAAAUACAUUACG-G-GGU-CUGU-AA-AAGUCAGAGUAGU--------GAAAU-------------AUCGAAAAAGAC--AAGACAGC
>URS0000D6A023_12908_1-128
CACUCAUAUA--ACUUAAG-GGU-UAUGUG--GUGGGACUAUU----AAAAAA-------AGUAGUCAGCUUAUU--UGUCCUGCGGAA-GCAAAUACAUAUAG-A-GGU-CUGAAA--GUGUGUGAGUAG---------CAAAA---------------CGAAA-GCAC--AAAUCAGC
>URS0000D6A52D_12908_1-128
CACUCAUCAACAGU-UAAG--GCUUUGGUG--GUGCGACCUGU----AAAU---------AU-GGUCAGCUUGUU--UACCCUGCGUUGAGCGAAUACUUUAAG-A-GGU-CUGU-AA-AAGUACGAGUAA---------UGAAAA--------------UGAAA-CUAU--AAGACAGC
>URS0000D6BA75_12908_1-131
CUCUCGUGAUUAGU-CAAG--GCUUUUACG--GAGCGACCUUA----GAAA---------UAUGGUCAGCUUGCU--UGUCCUACUUCG-GUAAAUACAUUGAG-A-GGU-UUGU-AA-AAGUUGGAGUAGCU-------UUAAG------------AG-UGAAA-GAAC--AAGACAAC
>URS0000D6883B_12908_1-128
CUCUCAUAAUUAGU-CAAG--GCUUUUAUG--GAGCGACCUUA----GAAA---------UAUGGUCAGCUUGUU--UGUCCUGCUUAG-GCGAAUACAUUGAG-A-GGU-CUGU-AA-AAGUUGGAGUAGC--------UUCU--------------G-CGAAA-GAAC--AAGACAGC
>URS0000D6BB08_12908_1-128
ACUCA-UGUAACU--CAAGG--GUUAUGUG--GUGCGGCCAU-----UAAAUU--------AUGGUCAGCUUGUU--UGUCCAGCGUAA-GCAAAUACAUUAAG-A-GGU-CUGUCAC-UG-UGGGAGUAGCG-------CGAU-------------CG-CGAAA-ACAA--CAUACAGC

Rfam family RF03022 maps to these 9 chains: 8UB7|1|I, 8UB8|1|I, 8UB9|1|I, 8UBA|1|I, 8UBB|1|I, 8UBC|1|I, 8UBD|1|I, 8UBE|1|I, 8UBF|1|I See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Jump to results for:

Loop 1IL Column numbers: 2-4, 33-34
Loop 2IL Column numbers: 4-5, 30-33
Loop 3IL Column numbers: 10-12, 24-25
Loop 4HL Column numbers: 14-22
Loop 5HL Column numbers: 42-62
Loop 6IL Column numbers: 75-83, 93-97
Loop 7HL Column numbers: 85-91
Loop 8IL Column numbers: 116-120, 174-175
Loop 9IL Column numbers: 121-122, 170-173
Loop 10IL Column numbers: 125-131, 161-167
Loop 11IL Column numbers: 131-132, 159-161
Loop 12HL Column numbers: 132-159

Loop 1 Internal loop

Column numbers: 2-4, 33-34 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ACU*GU   36

    
    CUC*GG   36

    
    CUU*AG   11

    
    CUA*UG    5

    
    CGC*GG    4

    
    GUA*UC    3

    
    UUC*GG    3

    
    AUC*GU    2

    
    UCU*GA    2

    
    AAA*UU    1

    
    AAC*GC    1

    
    ACU*AU    1

    
    CAC*GG    1

    
    CCC*GG    1

    
    CUC*GU    1

    
    CUU*GG    1

    
    GUC*GC    1

    
    -GC*GC    1

    
    -GC*GG    1

    
    Omitted sequenced and counts

    
    CUC*-G    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_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	71.10	2	0	Single stack bend
2	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	70.55	1	0	Major groove platform
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	60.86	3	0	Major groove platform
4	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	44.98	3	1	Major groove intercalation
5	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	34.66	3	1
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	99.11	70.35	4	0	Intercalated cWS
7	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	99.11	70.31	2	0	Single stack bend
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	99.11	68.49	3	0
9	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	99.11	61.06	2.5	0
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	99.11	48.49	3	1	Multiple bulged bases

Loop 2 Internal loop

Column numbers: 4-5, 30-33 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UA*U--G   34

    
    CU*A--G   32

    
    CC*G--G    9

    
    AU*A--U    6

    
    UG*C--A    6

    
    UU*A--A    5

    
    CG*C--G    4

    
    UC*G--G    4

    
    AA*U--U    3

    
    CU*G--G    2

    
    CC*GACG    1

    
    CU*ACCG    1

    
    CA*G--G    1

    
    CG*U--G    1

    
    UA*U--A    1

    
    UU*A--G    1

    
    Omitted sequenced and counts

    
    C-*A--G    1

    
    CU*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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	99.10	24.07	3	2	Multiple bulged bases
2	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	99.10	15.71	3	1	Intercalated cWS
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	97.30	20.60	2	1	Major groove platform
4	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	97.30	17.31	3	1	Multiple bulged bases
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	94.59	9.95	2	1	Major groove intercalation
6	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	94.59	4.39	1	1	Single bulged G
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	94.59	3.74	3	1
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	67.57	13.44	3	1
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.26	4.73	1	1	Single stack bend
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	59.46	7.28	2	1	Single stack bend

Loop 3 Internal loop

Column numbers: 10-12, 24-25 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AAC*CU   23

    
    UUA*CG   13

    
    UUU*CG    3

    
    AAC*GU    2

    
    UUA*UU    2

    
    AAC*UU    1

    
    ACA*UU    1

    
    ACG*CU    1

    
    CAA*AG    1

    
    CGG*CC    1

    
    GUG*CC    1

    
    UCA*CG    1

    
    AC-*CU    1

    
    Omitted sequenced and counts

    
    AC-*-U   14

    
    UU-*-G    8

    
    AAC*-U    6

    
    UG-*-C    5

    
    CG-*-C    3

    
    U--*-G    3

    
    UC-*-G    2

    
    UU-*-U    2

    
    C--*-G    2

    
    C--*--    2

    
    U--*--    2

    
    AAC*C-    1

    
    AG-*-C    1

    
    CA-*-A    1

    
    CA-*-U    1

    
    CC-*-G    1

    
    CU-*-A    1

    
    CU-*-U    1

    
    UA-*-U    1

    
    UC-*-A    1

    
    A--*-U    1

    
    AC-*--    1

    
    C--*-C    1

    
    UG-*--    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	60.79	4	0	Major groove platform
2	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	53.43	1	0	Single stack bend
3	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	52.66	2	0	Major groove platform
4	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	51.76	2	0	Single stack bend
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	98.04	58.36	3	0
6	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	98.04	47.65	2	0	Multiple bulged bases
7	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	98.04	45.08	3	1	Intercalated cWS
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	98.04	43.88	2	0	Major groove intercalation
9	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	98.04	43.42	4	1
10	Motif group IL_51454.3 View motif instance in 3D Basepair signature: cWW-cSH-cWW	98.04	33.27	2	0	Minor groove platform

Loop 4 Hairpin loop

Column numbers: 14-22 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    C-CACAA-G   34

    
    C-UACG--G   15

    
    C-ACAA--G    5

    
    C-CACG--G    5

    
    C-AAAU--G    3

    
    C-ACAU--G    3

    
    U-CAAG--G    3

    
    U-UACG--A    3

    
    U-UACG--G    3

    
    C-AAGG--G    2

    
    C-CACA--G    2

    
    C-UCCG--G    2

    
    C-UUGU--G    2

    
    U-UAAG--G    2

    
    --GAUG---    2

    
    --UACG---    2

    
    CCGCUUCGG    1

    
    -GUUAGGCA    1

    
    CCAGAU-GG    1

    
    CCCACG-GG    1

    
    CUCAAU-GG    1

    
    CUUAAG-AG    1

    
    CUUAAG-GG    1

    
    CUUACG-GG    1

    
    C-CAACC-G    1

    
    C-CACAC-G    1

    
    C-AAGU--G    1

    
    C-ACUU--G    1

    
    C-AGAU--G    1

    
    C-AUAU--G    1

    
    C-CAAG--G    1

    
    C-CCCA--G    1

    
    C-CCCG--G    1

    
    C-UAAG--G    1

    
    C-UAUG--G    1

    
    C-UCGG--G    1

    
    U-UAGG--A    1

    
    --CAAGG--    1

    
    C--ACA--G    1

    
    --AAGG---    1

    
    --GUGA---    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_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	82.30	13.53	2	2
2	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.10	-562.30	3	2	Pseudoknot geometry with 3' bulge
3	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	44.25	-11.58	3	2
4	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	42.48	-19.42	2	2
5	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	40.71	-11.48	2	2
6	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	38.94	2.04	2	2
7	Motif group HL_34617.5 View motif instance in 3D Basepair signature: cWW-tSW-F	38.05	-21.31	2	2	UNCG
8	Motif group HL_87954.2 View motif instance in 3D Basepair signature: cWW-tSW-F	35.40	-22.55	3	2
9	Motif group HL_87553.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	32.74	-47.35	3	2
10	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	31.86	-642.57	3	2	Purine riboswitch

Loop 5 Hairpin loop

Column numbers: 42-62 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ------UUUAC----------   35

    
    C-----AAUAG---------G    6

    
    ------UUAC-----------    4

    
    CU----AUUUAG-------GG    3

    
    ------AUCCACAUG------    3

    
    UU----UACA---------AG    3

    
    C-----AAAAC---------G    3

    
    U-----AAUCA---------G    3

    
    CU----GAAAAACA-----GG    2

    
    UA----AAAUCU-------UA    2

    
    UAU---GCAA--------AUG    2

    
    UA----GAAA---------UA    2

    
    C-----CAAG----------G    2

    
    ------AUAU-----------    2

    
    ------UGG------------    2

    
    -UUUCGGUUAU----CGAAGG    1

    
    U---UGCAGCAU---CGAAUG    1

    
    UUA---CCUUUAU-----UGG    1

    
    C-UG--AAUAU------CAGG    1

    
    CAG---CACAA-------CUG    1

    
    CU----ACUUAG-------GG    1

    
    CU----AUAUAG-------GG    1

    
    UU----AAAAAA-------AG    1

    
    ------GUCAACAUG------    1

    
    C-----UUUUCUU-------G    1

    
    CU----AUUAU--------AG    1

    
    U-----CAAACCU-------A    1

    
    U-----CAGUUUU-------G    1

    
    U-----GCAAAA-------AG    1

    
    U-----UCAACAU-------G    1

    
    U-----UCAGCAU-------G    1

    
    UA----CCUAG--------UG    1

    
    C-----UUCAUG--------G    1

    
    C-----UUUAAC--------G    1

    
    CC----AAAC---------GG    1

    
    CU----UCAU---------GG    1

    
    GU----AAAU---------AU    1

    
    U-----GAAAGU--------G    1

    
    U-----UAAAUU--------A    1

    
    ------AGGUCGG--------    1

    
    ------CAAUAGA--------    1

    
    ------UACCUGU--------    1

    
    C-----GACAA---------G    1

    
    U-----AAAGU---------G    1

    
    U-----ACAGA---------G    1

    
    U-----ACAGU---------G    1

    
    U-----CUAGA---------G    1

    
    U-----CUUGU---------G    1

    
    ------CACUUA---------    1

    
    ------UUACAU---------    1

    
    U-----GUGA----------G    1

    
    U-----UUAA----------G    1

    
    ------UAUA-----------    1

    
    ------UUUA-----------    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_46501.1 View motif instance in 3D Basepair signature: cWW-cWS	38.94	-398.79	3	3
2	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	38.94	-637.44	3	3
3	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	38.94	-753.39	3	2	Mini UNCG
4	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	35.40	-833.84	3	3
5	Motif group HL_43517.1 View motif instance in 3D Basepair signature: cWW-F-F-F	30.97	-286.18	4	3
6	Motif group HL_59735.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	15.04	-2141.63	4	3
7	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	13.27	-100.93	3	3
8	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	12.39	-323.26	4	3
9	Motif group HL_13529.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	11.50	-97.99	3	3
10	Motif group HL_39243.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	11.50	-3703.63	5	3

Loop 6 Internal loop

Column numbers: 75-83, 93-97 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--UAUCCU*AAAUA   14

    
    U--UAUCCU*A-AUA    8

    
    U--CAUCCU*AAACA    6

    
    U--UGUCCU*AAACA    6

    
    U--UAUCCU*AAACA    5

    
    U--UGUCCU*GAAUA    5

    
    U----AUCU*AAAUA    5

    
    U--UAU-CU*AAAUA    4

    
    UU-UGUCCU*AAACA    3

    
    G--CAUCCA*AAACU    3

    
    U--UGUCCU*AAAUA    3

    
    AC-UGUCCU*AAAUA    2

    
    GC-UGUCCU*AAAUA    2

    
    UU-UAUCCC*GAACA    2

    
    A--AGUCCA*AAACU    2

    
    U--CGACCU*GAAUA    2

    
    U--UAUCCU*GAACA    2

    
    U--UAUCCU*GAAUA    2

    
    U--UAUCGU*AAAUA    2

    
    U--UGUCCU*GAACA    2

    
    CACCGACCU*GAACA    1

    
    CC-CGGCCG*AAAUA    1

    
    CC-CUGCCU*AAACA    1

    
    CC-UGUCCU*GAAUA    1

    
    GG-UAUGGU*AAAUA    1

    
    UU-CAUCCU*AAACA    1

    
    UU-UAUCCU*GAACA    1

    
    UU-UGUCCU*AAAUA    1

    
    A--AGCCCA*AAACU    1

    
    A--AGUCUC*AAACA    1

    
    A--UAACAU*GAAUA    1

    
    C--ACACCC*AAAUA    1

    
    C--ACACCU*AAACA    1

    
    C--CCACCA*AAAUA    1

    
    C--CGUCCU*AAACA    1

    
    C--UACCCU*AAACA    1

    
    C--UCUCCU*AAACA    1

    
    C--UGUCCU*AAACA    1

    
    C--UGUCCU*GAACA    1

    
    G--CUUCCU*AAACA    1

    
    G--UGUCCU*GAAUA    1

    
    U--AUUCCU*AAAUA    1

    
    U--CAUCCU*AAAUA    1

    
    U--UACCCU*GAAUA    1

    
    U--UGUCCA*AAAUA    1

    
    U--UUUCCU*AAACA    1

    
    GC-UGUC-U*-AAUA    1

    
    U--UAUCC-*AAAUA    1

    
    U--UAUCCU*AAA-A    1

    
    U--UAUCGU*A-AUA    1

    
    U---UAUCU*-AAUA    1

    
    U--UAUC-U*AA-AA    1

    
    A----U-CC*AAAUA    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_85652.1 View motif instance in 3D Basepair signature: cWW-tSH-L-R-L-R-L-cWW-L	45.13	-10.93	6	4
2	Motif group IL_31084.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L	33.63	-12.02	6	4
3	Motif group IL_99498.1 View motif instance in 3D Basepair signature: cWW-L-R-tHW-cWW	25.66	-30.22	7	4
4	Motif group IL_06691.1 View motif instance in 3D Basepair signature: cWW-cWS-L-R-L-R-cWW-L	21.24	-60.28	7	4
5	Motif group IL_18472.4 View motif instance in 3D Basepair signature: cWW-tSW-R-L-R-L-R-cWW	7.96	-47.77	6	3
6	Motif group IL_96236.1 View motif instance in 3D Basepair signature: cWW-tWW-cWW-L-cWW	4.42	-101.63	7	5
7	Motif group IL_96788.1 View motif instance in 3D Basepair signature: cWW-tHW-tHS-cWW-cWW	4.42	-117.44	8	5
8	Motif group IL_29223.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-cWW-cWW	3.54	-68.99	5	5
9	Motif group IL_80412.1 View motif instance in 3D Basepair signature: cWW-tSW-L-cWW-L-L-R-L	1.77	-30.34	7	4
10	Motif group IL_11344.2 View motif instance in 3D Basepair signature: cWW-cSS-L-cWW	1.77	-92.80	7	4	180 degree turn

Loop 7 Hairpin loop

Column numbers: 85-91 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUUCG-G   88

    
    CUUC--G    5

    
    CUACG-G    4

    
    CUUAG-G    4

    
    C-UCG-G    3

    
    CUUUG-G    2

    
    CGUUGAG    1

    
    CCUCG-G    1

    
    CGCAA-G    1

    
    CGGAA-G    1

    
    CGUAA-G    1

    
    CUUCG-U    1

    
    GUUCG-G    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_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	57.96	0	0
2	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	99.12	90.00	0	0
3	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	97.35	12.53	2	2
4	Motif group HL_32392.1 View motif instance in 3D Basepair signature: cWW-F-F	96.46	77.37	2	0
5	Motif group HL_43517.1 View motif instance in 3D Basepair signature: cWW-F-F-F	93.81	41.42	1	1
6	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	93.81	4.75	1	1	Mini UNCG
7	Motif group HL_34617.5 View motif instance in 3D Basepair signature: cWW-tSW-F	92.92	81.05	0	0	UNCG
8	Motif group HL_56676.1 View motif instance in 3D Basepair signature: cWW-F-F	92.04	78.55	0	0
9	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	92.04	27.56	3	2
10	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	92.04	7.72	2	2

Loop 8 Internal loop

Column numbers: 116-120, 174-175 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UGU-A*UG   31

    
    UAG-A*AG   10

    
    CAU-A*AG    9

    
    UAG-A*GG    5

    
    -AA-A*AG    5

    
    UGU--*UG    5

    
    CAAUG*UG    4

    
    CAG-A*AG    4

    
    CAG-A*GG    4

    
    CAU-A*GG    4

    
    CAA-U*CA    3

    
    UAA-A*GA    3

    
    UAG-A*UG    3

    
    CAAUG*CG    2

    
    CAA-G*AA    2

    
    UGU-A*UA    2

    
    -AG-A*CG    2

    
    GA--A*GC    2

    
    CAUAA*AG    1

    
    AAA-A*GU    1

    
    AGA-G*CG    1

    
    AUG-U*GU    1

    
    CAA-A*GG    1

    
    CAC-U*AU    1

    
    GCA-A*AC    1

    
    UAC-A*GA    1

    
    UAU-A*GG    1

    
    UGU-U*UG    1

    
    AA--G*AA    1

    
    -A--G*AG    1

    
    Omitted sequenced and counts

    
    ----A*CA    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_82107.4 View motif instance in 3D Basepair signature: cWW-cWW	91.96	47.18	2	0	Multiple bulged bases
2	Motif group IL_76709.2 View motif instance in 3D Basepair signature: cWW-L-cWW-L	83.04	24.51	3	1
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	79.46	16.78	4	1	Intercalated cWS
4	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	69.64	38.29	2	0	Major groove intercalation
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	66.96	12.77	3	1
6	Motif group IL_79895.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	66.07	15.16	5	1
7	Motif group IL_59877.1 View motif instance in 3D Basepair signature: cWW-L-cWW	65.18	-87.02	2	1
8	Motif group IL_95583.2 View motif instance in 3D Basepair signature: cWW-L-cWW	58.93	9.67	3	1	Minor groove platform, major groove intercalation
9	Motif group IL_50694.7 View motif instance in 3D Basepair signature: cWW-tSH-cWW-L	56.25	-14.43	2	1	Major groove platform; stack outside cWW
10	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	53.57	-7.70	2	1	Major groove platform

Loop 9 Internal loop

Column numbers: 121-122, 170-173 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UU*A--U   23

    
    AC*G--G   21

    
    GC*G--C   17

    
    AC*G--C    7

    
    AU*A--U    5

    
    AC*G--A    4

    
    AG*C--A    4

    
    AG*C--U    3

    
    CU*G--G    3

    
    AC*G--U    2

    
    CU*A--G    2

    
    GC*G--U    2

    
    UU*UCAU    1

    
    UU*A-UC    1

    
    AG*U--A    1

    
    CA*A--U    1

    
    GC*G--A    1

    
    UA*G--A    1

    
    UG*C--A    1

    
    Omitted sequenced and counts

    
    UU*A---    8

    
    -U*A--U    1

    
    AC*G---    1

    
    G-*A--C    1

    
    GC*G---    1

    
    -C*G---    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	96.00	6.00	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	72.00	11.18	3	2	Multiple bulged bases
3	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	39.00	-12.96	2	1	Single bulged G
4	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	36.00	1.79	4	1	Multiple bulged bases
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	36.00	1.59	3	1
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	34.00	1.46	3	1	Intercalated cWS
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	31.00	-4.59	2	1	Major groove intercalation
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.00	-6.91	2	1	Single stack bend
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.00	-9.29	2	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	31.00	-10.62	4	1

Loop 10 Internal loop

Column numbers: 125-131, 161-167 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AGAGUAU*AGAAA-C   22

    
    GGAGUAG*CGAAA-C   14

    
    AGAGUAU*AAAAA-C   11

    
    GGAGUAG*CGGAA-C    9

    
    GGCGUAG*CGAGA-C    5

    
    AGAGUAG*CGAAA-C    3

    
    AGAGUAU*UGAAA-U    3

    
    CUAGUAG*CCAAA-A    3

    
    CUAGUAG*CGAAC-G    3

    
    AGAGUAG*CGAAA-G    2

    
    AGAGUAU*AAGAA-C    2

    
    GGAGUAG*UGAAA-G    2

    
    UGAGUAG*CAAAA-A    2

    
    UUAGUAG*CGAAC-A    2

    
    UUAGUCA*UAAAA-G    2

    
    AGAGUAU*A-GAA-C    2

    
    AGAGUAG*CGAAAAA    1

    
    CGAGUAG*CGAAACC    1

    
    AGAGUAC*CGAAA-U    1

    
    AGAGUAC*GGAAA-U    1

    
    AGAGUAG*AGAAA-C    1

    
    AGAGUAG*CGAAA-U    1

    
    AGAGUAU*UAGAA-C    1

    
    AGAUUAC*GGAAA-A    1

    
    CGAGUAA*UGAAA-C    1

    
    CGAGUAC*CGAAA-G    1

    
    CGAGUAG*CAAAA-G    1

    
    CGAGUAG*CGAAA-G    1

    
    CGAGUAG*UGAAA-G    1

    
    CUAGUAA*UGAAA-A    1

    
    GGAGUAG*CGAAA-A    1

    
    GGAGUAG*CGAAA-G    1

    
    GGAGUAG*UGAAA-C    1

    
    GGCGUAC*GGAGA-C    1

    
    GGCGUAG*CGAUA-C    1

    
    UGAAUAA*UAAAA-G    1

    
    UGAGUAA*UGAAA-G    1

    
    UGAGUAG*CGAAA-G    1

    
    UGAUUAC*GGAAA-G    1

    
    UUAGUAG*CGAAA-G    1

    
    AGAGUAU*A-AAA-C    1

    
    CUAGUAG*CC-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_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	96.46	79.74	2	0	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	92.92	28.49	3	1	8x6 Sarcin-Ricin with inserted Y; G-bulge
3	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	90.27	21.75	6	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
4	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	80.53	21.30	5	2	8x6 Sarcin-Ricin with bulged A; G-bulge
5	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	72.57	10.21	5	2	7x7 Sarcin-Ricin with intercalated A; G-bulge
6	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	69.91	13.89	5	2	tSH-tSH-tHH-tHS
7	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	57.52	0.20	6	3	8x6 Sarcin-Ricin with inserted A; G-bulge
8	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	55.75	-0.86	4	2	8x7 Sarcin-Ricin; G-bulge
9	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	23.01	-11.80	7	3	Sarcin-Ricin target in LSU H95; G-bulge
10	Motif group IL_69543.3 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tSS-tHS-L-R-cWW	9.73	-27.54	7	4

Loop 11 Internal loop

Column numbers: 131-132, 159-161 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UU*AUA   25

    
    GC*G-C   19

    
    GU*AUC    9

    
    GC*GUC    5

    
    GC*G-U    4

    
    CC*G-G    2

    
    GU*A-C    2

    
    UG*C-U    2

    
    GG*CUC    1

    
    GU*AUA    1

    
    CC*G-C    1

    
    CG*C-C    1

    
    GG*U-C    1

    
    GU*G-C    1

    
    UG*U-U    1

    
    Omitted sequenced and counts

    
    G-*--C   16

    
    U-*--A   12

    
    A-*--U    6

    
    C-*--G    2

    
    U-*A-A    1

    
    U-*--U    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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	97.33	17.85	3	1	Multiple bulged bases
2	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	94.67	40.85	4	0	Major groove platform
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	93.33	42.56	3	1	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	92.00	58.47	2	0
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	86.67	59.83	3	0	Intercalated cWS
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	86.67	50.28	2	0
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	86.67	36.82	3	1	Major groove intercalation
8	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	86.67	8.59	2	1	Single bulged G
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	85.33	49.82	2	0	Single stack bend
10	Motif group IL_89505.4 View motif instance in 3D Basepair signature: cWW-L-cWW	85.33	46.76	0	0	Single bulged U

Loop 12 Hairpin loop

Column numbers: 132-159 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--------GAAAU-------------A   26

    
    ---------GAAAUAU------------    6

    
    ---------CUCAU--------------    6

    
    C--------CUAGA-------------G    5

    
    CC-------CUAG-------------GG    3

    
    ---------UGAAAAU------------    3

    
    UG-------AAA--------------CA    3

    
    ---------UUAAUU-------------    3

    
    ---------GAAAU--------------    3

    
    CAA------CAUGA-----------UUG    2

    
    GC-------AGAAA------------GC    2

    
    ---------UGAAUAU------------    2

    
    C--------UACAA-------------G    2

    
    ---------CACGU--------------    2

    
    ---------GAAUA--------------    2

    
    CACGGGCGCGGCGCGCA--GCACCCGUG    1

    
    CGGCGGUUCAGCGCA----GAACUGCCG    1

    
    UG-AGGC--CAAGG-------GCCGACA    1

    
    C-CGGGC--GCAA--------GCCCGUG    1

    
    CC-UGUG--GCGA--------CACACGG    1

    
    UG-AGGC--UGCG--------GCCAAUA    1

    
    CC-------UUUGUUGAUU-------GG    1

    
    GG-AGC---AUU----------GCUCUU    1

    
    UCAC-----CAUAUU---------GUGA    1

    
    UCAC-----UAUGUU---------GUGA    1

    
    CGGGC----UUU-----------GCCCG    1

    
    GGCG-----GCAA-----------CGCC    1

    
    CGC------UUCG------------GCG    1

    
    GCC------GCAA------------GGC    1

    
    CU-------UUAAG------------AG    1

    
    GC-------AGAAA------------GU    1

    
    CG-------CGAU-------------CG    1

    
    UG-------UAAA-------------CA    1

    
    ---------AUGCGCA------------    1

    
    ---------UGAGAAU------------    1

    
    C--------AGAAA-------------G    1

    
    C--------CACGA-------------G    1

    
    C--------CCAGA-------------G    1

    
    C--------CUAGU-------------G    1

    
    C--------CUCGA-------------G    1

    
    C--------CUGGU-------------G    1

    
    C--------CUUGA-------------G    1

    
    U--------GCAAU-------------A    1

    
    U--------UUAGA-------------G    1

    
    UG-------AGA--------------CA    1

    
    ---------AAUUAA-------------    1

    
    ---------CAGUGU-------------    1

    
    ---------UGAAAA-------------    1

    
    ---------UGAAU-------------A    1

    
    C--------GAAA--------------G    1

    
    C--------UUCU--------------G    1

    
    U--------GAAU--------------A    1

    
    ---------CAAAA--------------    1

    
    ---------GUUAU--------------    1

    
    ---------UAAAG--------------    1

    
    ---------UGAAU--------------    1

    
    C--------AGC---------------G    1

    
    ---------AAU----------------    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_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	50.44	-605.55	2	2
2	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	42.48	-359.01	3	2
3	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	41.59	-264.72	3	2
4	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	39.82	-1002.43	4	3
5	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	39.82	-1159.14	3	2	Pseudoknot geometry with 3' bulge
6	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	39.82	-1275.49	3	2
7	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	37.17	-616.25	3	3
8	Motif group HL_97917.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	37.17	-725.49	4	3
9	Motif group HL_87954.2 View motif instance in 3D Basepair signature: cWW-tSW-F	34.51	-633.09	3	2
10	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	34.51	-1008.38	3	3