RNA 3D Hub

JAR3D Query RF02032-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF02032 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222233333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555566666666666666666666666
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222
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.........(((((..((((.(((((.......))))))))))))))...(((((((.................(((((((((.(((((((.)))))))))))))))).........................................................................................)))))))...............................((((((((((.........))).)).))))).((((((..(((((.....)))).))..))))).(((((((....(((.((((.....(((((((.....))))))).......(((((.......)))))...(((((((.....................))))))))))).))).....)))))))............................((((((.........))))))......((((((((.((((((.......................)))))).........((((((...(((.....(.............)))).....))))).)....))))))))......(.(((...............))))
>URS0000710B35_12908_1-408
UCGGGGCGUUC--UAUCUAAACUUCU-CAAAA-GGAAGCAAGGUAGAUGCGUGGUUGCGCGUCCUGA-----------AUUAU-GGCAUUGUUUUCGGGUUAAAUCCCACUUAAC----------------------------------------------------------AAUUAAAAAAUUAAGCAA-AAGA-CAACCAC--CUUUCCCGCU---GACAAUAGCGUU-AU-CCCUCUGCAC-UUCG----GUAAUAUGAGGG-CACAGUA-AAUCCCGCAAGGAU-GAGAAUGUGAUGUGGAAUGAGUAA-AUCUA----AGGUGAGGAGGCAUCCUCUU------UAGUC-CGCAA-GACACU-------------------------------------UGGUUGAAAAGAAAGC-AUAUAUA-AGCUGGAAAGUACA-----UGGUAGUUAG--U------CU-ACUCGCUAUCCU-AGUUACUUUGG----------AGUAA-------UCUAAAGUGUGUGUAAACGGGC------------GAAA------------------GUCUG-UAAAAUACU-GGGGACAUAG-GGU---CAACACUCA---GCCU
>URS0000D6852E_12908_5-498
--GUGGUGUCUGGUAUUUCG-U-GUU-GAAA--GAU-ACGAAGUCAGU-GAGGCCAGCACGUCAUGGUAGGUUACUAGCGGAC-UCAUACUCCGUUGGGUUGUAGCUCAUUUGGGUAGAGCACUCGUUUUUGGAACGAAUGGUAGCCGGUUCAAAUCCGGUCAACUCAUCCUUGAAAGAUGAAAAAACGCA-AAGA-CUGGCCUCACAGGUAGUAC---GAAAAUGGCUUA-AU-GCUUCA-GUC-CUUCG---GGCAAU-GAAGC-CCUUC-G-AAGCUCGCAAGGCG-GA--CAAGGUUAGUAGCGAAGCGCACUAUA------GCGACGGCC-AUCGUU---------------------------------------------------------------GUAGGUAGCAG-AACUACUGAGUA--CGCUACUUGAUACG--UGAAUCGCCACA-CGUUAA-AAAAGGCAGUCAUGCUGGCAGACUCAGGAGCAUCCUUGA----UGG-AUGGCUUGGGUG-GAUA-AGCUGGGAA-CCAAAGGGG----UCGCACCCUACGG-AUAAUCCAG-CAAAGGUGUUAGCGGUGAA--GGU---GUAAUCUCA---GCCU
>ABOX02000006.1_193416-192978
--AAGGCGUGCAGUAUAGCG-UGAUC-CAAAA-GAUCAUGAAGCUGCA--AGACGCGCACGUCUUGGUAGGAUUGCUGCUGCA-GGCAACUGUAGCACCUGACUGAA-------------------------------------------------------------------AAUCAGGCUAAACGCAA--AGU-CGCGUCUUCUGUUGGAUUG---GAAAGUAGCUUA-AU-CCCUGA-AUCCUGCG---GGAUAAU-CAGGG-CGUCCGA-UGCUCCGCAAGAGCUGA--GGACGUUGGUUGAAAUC-GC-AU-------GGUGGGUUCGCAGCCCUUUA------CUGCC-CGCAA-GGCAG--------------------------------------ACAGUAA-GAGGA-CAGCCGAG---CGAUCCAAUGGUGAACUGGCAAUGCCACCAGUAUAA--AACGGCAGCUAUCGG-ACUUACCAGAUUGU----GGCU----UCGGCCUGGUUUGGUG-GAAA-CGUUGGGAAGCCUU--CCC----GCAU---GGAGGGUAUAAUCCAA-UCAAAGAGU-CCGAACCAAA-ACU---GUAUUCUCA---GGUU
>ABHI01000002.1_126521-126020
AGGAGAAGGUUGGUAUUUUG-UAGG--CAAAAA-UCUACGAAGCCAUU--UUCGAAGCCCUUCUCCUAGGUCAAAGUUUUGAA-GUCUAGGUUCGAUUCCUAGUAUCUCAACCGAAAAGGGGAUAUAGUUCAAC--------------------UGGUAGAGCACUGUAUUUUUCAUACAGCGAAAGGCAC-AAGA-CUUCGAA--CAUUAUAGCAGUUAGUAGUUGCCUA-AA-CCCAUU-----GCAAU-------AU-AUGGG-ACAGU-A-GAGGUCGCAAGCCU-AU--ACUGUGCGGUGAACAUUCUA-GUAGGCCGCCUCAACAGAGGACGUCUAUGAAUGGUGAGGGAGCCAA-CCCU--U-GUA-AUUGCAAAGCGUGGUUUUAAUACCACUAUGCAAGCCAAGUCUAAGUCGCUGAA--CAUCUAUAAUG---------------------UAUUA--------GGCAUCAGGUAAGUACACAAUUCUCU-AAGCG---AUG---AGAAGCGUGUG-GAAA-AUUAGGGAAGGG------CUACG----------GCU-AUAAUCCUA-AGAAAGCUUAUCUACAA----GCGGAGGUAUUCUCAGAACGCU
>URS0000D6AFE5_12908_1-419
AGAAGGAGCGCGGCAUUCGG-CAUCUCGAAA-GGGGUGUCGAACCGCA--GGUGACGCGCUUCU--CGAUCGGUUUCCUACAC-UGGGAAGUGGUU------------------------------------------------------------------------------GCGAACCAUUAAAGCAA-AAGC-CGUCACC--CCUGGUCGAG---CGCAACGACUUA-AC-ACUGCG-GGC-GCAA----GCCAAC-GCAGU-CGGUU-G-A-UUCUGCAAGGA--GU--CACCGUUGAUCUCGGAGGAU-UCGG-----AGGGCGUAAGC--UGCCCUA------GCCGGACGCAAAGCGG---------------------------------------ACGGGUCCGAUG--AGGUCGAAAG-CAAGAUCAGCAGGGA--UGAAAUGCCACA-UCUUAA-AAAAGGCAGUCGUGCU-GGAUACGC-CGCA-------GUGAGAGC----CGCGAGCGUG-GACA-AAGCGGGAACACCGG-CUA----GCUG--CCGGG-AGAUA-UCCGC-GCAAAGGCC-AGCGAUGAC--GGC---AUAGUCUCA---GCCC
>URS0000D6B11A_12908_2-427
--GAGGCGUGCGGCAUAGAG-UGGCU-CAAAA-AGUCAUUCAACCGCU--GGUAGAGCACGUCUUUGUCAGUUCCUCGCUAGA-GGGCAAACACUACGGAU-------------------------------------------------------------------------GUUCUUGUUAAACGCCA--AGU-CUCUACC--CGCGAGCCGC---GAAAGCGGCAUA-AU-GCUCGG-GGC-UUCG----GCCAAC-CGAGU-CGGCGA-CGGUCCCGCAAGGGCCUA---UCUGUUGAUCGUGAAAUUG-UCG------GAGACGUUAGC-GCGUCUCG------CUGCC-CCGAA-GGCAGA--------------------------------------CGGUGAGGA--AGUGAUCGUGUA-GUGGUUCGUCAGGGG--UGAAACGCCACA-CCCUAA-AAAAGGCAGUCGUGAU-GGCUACGCCGGA---------AGUGAUGA-GCUACGGUUGUG-GACA-AG-CGGGAAGCCUCGGUGC----CAC-----CGGGGGAUAAUCCGA-CGAGAGGCC-AUCGAUGAAG-GGU---AUAGUCUCA---GCCC
>URS000070F468_12908_1-413
CGUGGACGUGUUGUAUUUUG-UGGGU-CAAAA-GCCUAUGAAGCAAC---GGCGGCACGCGGACACAGACUAAAAAAUAACUU-UCACGAUUA---------------------------------------------------------------------------------UGAAAAUAAACAUGCAA--AGU-UGUCGCC--AAGAAUUGAU---GAUAGAACCGUA-AU-GCUCAA-CGG-GUAA----CCGAAU-UGAGC-CAGUCCA-AGACUCGCAAGGUU-GA-GGGUUGUU-GUGGGAAAG----UCGCAC-GUUU-------------------------GGGG-UCGAA-CCCUUAA-CUG-CUCGCAA------------------GG-CAGGCGGUAGAUAGAA-CCAU-GAGUA-AUCAAUUCUUAUAGU--GGAAAUGCCACC-ACUCAAAACAAGGCCGGUUCGGU-UGAUUCGUCC------------AUGA---------GGACGAG-GAUA-AGGGUAGAACGUCUU-ACU----AGCA--CUAGGACGAUAAUGACC-CGAAAGGCA-ACCUUCAAAU-GCU---UUAAUCUCA---AGCA
>URS0000D66A22_12908_2-459
--UUGGUGAGUUGUAUACUG-UAUGC-CAAAA-GCAUAUGGAGCAACU--GAGGCAGCUCAUCAAGGUAGGUUGCAACGUAGA-UCAAUGGUAGAUCGUCUGUCUCUUAAACAGGAUGUUGCGG---------------------------------------GUUCGAUCCCCGCCGUAAUAAAAUGCAA--AGA-CUGCCUC--GGUUAUCAGU---GAAAAGCAUCUA-AU-GCUUGA-CAC-GCAA----GUGAAU-CAAGU-CCAUU-G-UAGCUCGCAAGGCG-AA--AGUGGUUUGUGUUAGAAGUU-UCGU--------------------------------AGUU-CGCAA-GACUUAA-UGG-CUCGCAA------------------GGUCAA-CGGAG--AAGAAGACACAGAGUA-GCUGGUAACGACAAG--CCUACUGCCUGG-CUUUAAAAAC-GGCGAUGCUGACAACAGACAGUGAUA-------CCGCAAG-----GGUCGCUGUG-GAUG-UCUAGAGAAGCAGUGCUCG----CAAG---GUGCUGUAUAAUGCUA-G--AGGUGUUGUUGGCUUAA-GGU---GUAAUCUCA---ACCU
>URS0000624918_12908_1-465
--GUGGUGAGUUGUAUUCAG-CAUUC-CAAAA-GAUUGUUGAGCAACA--GUGGCAGCUCAUCGCGGUAGGUUGCAAUUAGCC-UAAUGGUAAGGCAUCAGUCGCUUAAACUGGAGACUGUAGGUU-----------------------------------CAAAUCCUACAUUGUAAAUCAAAAAUGCAA--AGA-CUGCCAC--GGUCAUGUGU---GAAAAGUAUCUA-AU-ACUUGA-CAC-GUAA----GUGAAU-CAAGU-UUAGU-G-AAGCUCGCAAGGUG-AC--ACUAAUUUGUGGAGGGGGGU-UCGUA-----AGUGGUUAGC-ACCACCGA-----AUAGCU-CGCAA-GGCUA--------------------------------------ACGGAAUGGAAU--CCGCAGAAUA-GCACAUGAUGACAAG--ACUACAGCCUGU-CUUUAAAAAC-GGCGAUACUGGUAACAGACAUAGAUA-------CCGAAAG-----GGUUUAUGUG-GAUG-UCAAGAGAAGGUAUGCUCG----CAAG---GUGUACUAUAAUGCUU-G--AGGUGUUACUGGUUAA--GAU---GUAAUCUCA---GUCU
>CP000416.1_1118883-1118471
CGGCCCAGUGAAGCAUUUGC-UUUCU-CAAAA-GGAAAGCGAACUUCU--GGCGAAGCACUGGGUUCCGAAUAAGAUGAAUUA-UUCCUAGCUAAGGAAUAGUAUGUUAAACCAUUAAA--------------------------------------------------UAUAACAUUAUCUAAAAUGCAA-AAGU-CUUCGCC--UGCUGUAUCU---GAAAGUAGUCUA-AU-GCUCCA-CACACAAGGGGUGUGAAU-GGAGC-GUCGAUG-A-ACUCGCAAGGU--GA-UUCGAUUCAGUAGC-GAGUAG-UGCAAC--CGAGUGGGUAGCUCCCAUUU--------------------------------------------------------------AGUGAAUCGAA-AGCUGCUGAGUA-GGAUGCAGUAUGAAC---G----GGUGGA-A-CUCC-UUCCACCGACUAUGGC-AGUUACACGA------------GGGA---------UCGUGUG-GAAA-CGCGACUAA----------GAA---------------AUAAGGUCG-UUAAAGACU-GCUGCUAACG-GAU---GUAUUCUCA---AUCU
>URS00006982F9_12908_1-422
GGAGAUUGUUUACAGUAUUC-UUGUCUGAAA-GGAUGAGAGCUGUAAU--UUAAGAGCGCAAUCUUCACUUCGCCCCUUUUCU-GCAUAAUCCUUGUUUAGCCAAAAGGCGUAGAUAAC-------------------------------------------------AAGUUCAUUAACAAGAAAAGCAAAGAGU-CUCUUAA--CGGUUAAGAG---CAUAGGGCACUU--U-ACCUCU-----GAAAC--A----AU-GAGGUGCAUUA----AACCCGCAAGGUU-----UGGUGUUCAUGAUGAAAGGU-CAGGU-------------------------------UGGUUCGUAC-CCAUUAG-ACG-GUCGGCA-----------------GACUUGUACUGAACUGAGUAAUUGUGUAGAU-AACUUAACCGAUAA-----GACUGAUGAG--CUAUA--CUCAUUGUGCCUGAUACUGUACUAAUC-----------GCAA--------GAUUGGUG-GACAAAAGAGGGAA----------UAG---------------AUAAUCCUC-UCAAAGUGGUAUCGC-AAAG-CCU---GUAGUCUCA---AGGC
>JX409894.1_31726-31351
AGCAGGCGUUGCGCAUUUUG-UUGUU-CAAAA-GGCGACGAAACGCAA--GGCAAUGCACGUCUGCGAUACACGAAAACAAUG-CUAUUUGUUGAAA-----------------------------------------------------------------------------AUAUUGGAAUAAAGCAA-AAGU-CAUUGCC--CGUCGCAAAC---GAAAGUGUGCUU--C-GGUAG------CUAGG----------CUACC-UGCUA-G-AGUCUCGCAAGGAU-AA--UAGCAA-AGUCAAAGAGUAA-AGC-AGCUUAGACCUUUAGC-GGGGUUU-------U------------------------------------------------------CGUUAAUUGAAAAAUGGCUUAGUA-GUUUGUGACGUAAG-----GAGUGGUUAG--CGAUA--CUAACCGCGCAUGGU-UGUUACUUGAA-----------GGGA--------UUUGAGUG-GAUA-AAAAACUAA----------AAC---------------AUAAGGUUU-UGAAAGACA-ACUGACUAAA-CGU---GUAAUCUCA---GCGU
>HG799490.1_23999-23607
AGCAGGCGCUGUGCAUUUUG-UUCUU-CAAAA-GAGAAUGAAACACAU--GGCGAUGCGUGUCUGUGAUAGAUGAAAGAUGAU-UUUUAUAUUUUAAGGCUAUUCAAGAUAGAA------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUCGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA------UUAGA----------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA--GAGUAA-AGUCAAAGAGUAA-AGC-AGCUUAGACUUUUAGC-GGAGUCU-------U----------------C--------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGAUGUGAG-----GAGUGAUUGG--UCUAA--CCAAUCGUGCAUGAG-UGAUACAAGUA-----------GGAA--------UAUUUGUG-GACA-AGAUAAUAA----------ACU---------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
>HG799496.1_23475-23083
AGCAGGCGCUGUGCAUUUUG-UUCUU-CAAAA-GAGAAUGAAACACAU--GGCGAUGCGUGUCUGUGAUAGAUGAAAGAUGAU-UUUUAUAUUUUAAGGCUAUUCAAGAUAGAA------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUCGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA------UUAGA----------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA--GAGUAA-AGUCAAAGAGUAA-AGC-AGCUUAGACUUUUAGC-GGAGUCU-------U----------------C--------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGAUGUGAG-----GAGUGAUUGG--UCUAA--CCAAUCGUGCAUGAG-UGAUACAAGUA-----------GGAA--------UAUUUGUG-GACA-AGAUAAUAA----------ACU---------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
>KT337365.1_17794-17402
AGCAGGCGCUGUGCAUUUUG-UUCUU-CAAAA-GAGAAUGAAACACAU--GGCGAUGCGUGUCUGUGAUAGAUGAAAGAUGAU-UUUUAUAUUUUAAGGCUAUUCAAGAUAGAA------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUCGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA------UUAGA----------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA--GAGUAA-AGUCAAAGAGUAA-AGC-AGCUUAGACUUUUAGC-GGAGUCU-------U----------------C--------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGAUGUGAG-----GAGUGAUUGG--UCUAA--CCAAUCGUGCAUGAG-UGAUACAAGUA-----------GGAA--------UAUUUGUG-GACA-AGAUAAUAA----------ACU---------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
>URS00006D7BBB_12908_1-421
GAAAGUUGAGUGGCAUUUGC-UUCUU-CAAAA-GAGAAGUUAACCAC---CUCAGAGCUCAACUUUCAUUACACUCACUAUGU-UGGAUUAAUUAAAAAUU-------------------------------------------------------------------------AAAACUACAGAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-GGUAGAAAU---ACUAAC-AAGGA-GAUUG-ACAGGACCCCAAGUCC-UU--CAGUUUUGACUAAGAAAGUC-CUAGU-------------------------------ACCUGGGCAC-GGGUUUAGGGAGUCCGCAA------------------GAUUCCAUAGAGAUGAGUAACAGUUGAGUA-GGGUUAACCGAAAC-----GAGUGAUUGA--CGUAA--ACAAUCGGUGAUGACUUGAUACCUUUG-----------GCAA--------CAUCGGUG-GACA-CGGGAGGAACCCAA---UG----UAG-----AAUGGGAUAAUCUCA-CAAAAGACAGGUCAACGAAA-CGU---AUAGUCUCA---GCGU
>URS00006945ED_12908_1-421
GAAAGUUGAGUGGUAUUUCC-UUCUU-CAAAA-GAGAAGCUAGCCAC---CUCAGAGCUCAACUUUCAUGACUCUCACUAUGU-UGAUUUAUUUAUGAAAAAA-----------------------------------------------------------------------UAAACUACAGAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-AGUAGAAAU---ACUAAC-GAGGA-AAUUGA-UAGGACCCCAAGUCC-UU--CAGUUUUAACUAAGAAAGUC-CUAGU-------------------------------ACCUGGGCAC-GGGUUUAGGGAGUCCGCAA------------------GAUUCCAUAGAGAUUAGUAGUAGUUGAGUA-GGGUUAACCGAAAC-----GAGUGAUUGA--CGUAA--ACAAUCGGUGAUGACUUGAUACAGAUG-----------GCAA--------CAUUUGUG-GAUA-CGGAAGGAAACC------U-UAGU--------ACGGUAUAAUCUUCACAAAAGACAGGUCAGUUAAA-CGA---GUAAUCUCA---UCGU
>URS000072C429_12908_1-421
GAAAGGUGAGUGGUAUUUAC-UUCUU-CAAAA-GAGAAGCUAUCCAC---CUCAGAGCUCAUCUUUCAUCACACUCACUAUGU-UGAUUUAUUAUGAAAAAAU-----------------------------------------------------------------------AAACUACAGAAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-GGUAGAAAU---GCCAAC-AAGGA-AAUUG-ACAGGACCCCAAGUCC-UU--CAGUUUUGACUAAGAAAGUC-CUAGU-------------------------------ACCUGGGCAC-GGGUUUAGAGAGUCCGCAA------------------GAUUCUAUAGAGGCAAGUAGUAGUUGAGUA-AGUUUGACCGAAAC-----GUGUGAUUGU--CGUAA--ACAAUCGGUGAUGACUUGAUACUGAUG-----------GCAA--------CAUUAGUG-GAUA-CGAGAGGAAACC------U-UAGU--------CGGGUAUAAUCUCUACAAAAGACAGGUCACUUAAA-CGA---GUAAUCUCA---UCGU
>URS000063E4BF_12908_1-412
CGGAGUCGUCCAGUAUUCUU-GAGUU-CAAAA-GAUUUGAGAGCUGAG--AGGUGACCACGACUUCGACAAAUCUACACGGCACUAAAUUUCUAACUGUUAAUUGGAAACAUUU------------------------------------------------------------AAAAAAGAAGAAAUCGA-AAGU-GUUACCU--AGUUGUUGAC---GAAAGGUGUCUACAUAGUUAUGG----GUUGU-------CC-AUAGC-CA-CU-G-AAGCUCGAAAGGCC-GA--UG-UGAUUUCACCUAAAAGC-UUAUA-------------------------------GAGGGUCGAG-CCUCGAA-UCAGUCCGGCA-----------------GGGUUGAAUAAGUG-GAUUAAGUG-AGAGUA-GUUAACAACUUAAG-----UAGUGAUUGG--UCUAA--CCAAUCGACACUGACAGAAUACUUCU------------CAAA-------A-GGAAGUG-GAUA-AGAAGGGAA----------ACC---------------AUAAUCUGA-CAAAAGUUCUGUCUUUAUAA-GGU---GUAAUCUCA---GCCC
>URS000065D934_12908_1-396
CGGAGUCGUCCAGUAUUCUU-GAGUU-CAAAA-GAUUUGAGAGCUGAG--AGGUGACCACGACUUCGACAAAUCUACAGGCAC-UAAAUUUCUAACUU----------------------------------------------------------------------------UAAAAAGAAGAAAUCGA-AAGU-GUCACCU--AGUUACUGAC---GAAAGGUGUCUACAUAGUUAUGG----GUCGU-------CC-AUAGC-CA-CU-G-AAGCUCGAAAGGCC-GA--UG-UGAUUUCACCUAAAAGC-UUAUA-------------------------------GAGGGUCGAA-CCUCGAA-UCAGUCCGGCA-----------------GGGUUGAAUAAGCG-GAUUAAGUGGAGAGUA-GUUAGUAACUCAAG-----UAGUGAUUGG--UCUAA--CCAAUUGACACUGACAGAAUACUUCU------------CAAA-------A-GGAAGUG-GAUA-AGAAGGGAA----------ACC---------------AUAAUCUAA-CAAAAGUUCUGUCUUUAUAA-GGU---GUAAUCUCA---GCCU
>URS000066C161_12908_1-412
GAGAGUAGUUGAGUAUCAGG-UCGCU-CAAAA-GGUGAUUUGGCUCGGGUGGCGGACCACUACUUUCACAAUCCACGACACAC-AACUUAUGGAAACUAUUAAUUCCCAAAUUA------------------------------------------------------------AAAAGAUCAUUAAGGAA-AAGU-GUCCGUC--AGGUCUAAUU---GAAAGGUGACUACUUAGUCGUGA----GCUGU-------UC-ACGGC-AC-AC-A-AGGAUCCCAAGUCU-GA--GU-GUAAUUUUACCAAAGAC-CUCUA-------------------------------AUCC-CGCAA-GGACGAG-CUGGGGAGGCA-----------------UCCUCGGAGAGAGUUGAGUAAUGAGAGAGUA-GAUUAGACCUCAAG-----GAGUGGUUUA--CCUAA--AUAACCGUCACUGAG-AAAUACUUCU------------CAAA-------A-GGAAGUG-GAUA-GGAGUAGAA----------UAA---------------AUAAUGACU-CUAAAGGUU-CUCACAAAAA-ACU---GUAAUCUCA---GGUU
>URS000065E4E8_12908_1-405
CGGAGUAGUCUAGUAUUUGG-UCGUU-CAAAA-GAUGACUAAGCUUAC--GACAGACCACUACUUCGACACAUCCACGACACA-CACUUAAAAUGAAUUUAAGUCAAAU-----------------------------------------------------------------UAAAUACAAUUAAGCAA-GAGU-GUCUGUC--AGGUAUCAGU---GAAAGGUGACUACAUAGUAAUGA----GCCGU-------UC-AUUGC-AC-AU-G-AUGACCGCAAGUCU-GA--CU-GUAAUCUUACCAAAGAC-CUCUA-------------------------------UUCC-CGCAA-GGAAGAG-UUGGGGAGGCA-----------------UCCUCAAAGAGAGUUGAGUAAUUAGAGAGUA-AUUGAUACCUCAAG-----GAGUGGUGUA--CCUAA--AAGACCGUCAUUGAG-AAAUACUUUC------------CAAA-------A-GAAAGUG-GAUA-UUAAGGGAA----------ACA---------------AUAAUCCUU-AUAAAGGUU-CUCACAAAUA-GGU---GUAAUCUCA---GCCU
>URS00006C3EDA_12908_1-411
GAGAGUAGUUGAGUAUUUCG-UUGUU-CAAAA-GAUAACGAAGCCCGU--GGCGGACCACUACUUUCACAAUCCACAACACAA-AAACUUAUGACACUGAUUAAGUCAAAUUAA-----------------------------------------------------------UUAUUAAGAAAUAAGCAA-AAGU-GUCCGUC--AGGUAAUAGU---GAAAGGUGACUACAUAGUAAUGA----GCCGU-------UC-AUUGC-AC-GA-A-AGGAUCGCAAGUCU-GA--UC-GUAUUCUUACCAAACAC-CUCUA-------------------------------AUCC-CGCAA-GGACUAG-UUGGGGAGGCA-----------------UCCUCGAAGAGAGUCGAGUAAUAAGAGAGUA-ACUAUUAUCUCAAG-----GAGUGGUACA--CCUAA--AAGACCGUCACUGAG-AAAUACUUCU------------CAAA-------A-GGAAGUG-GAUA-GGAGUAGAA----------ACA---------------AUAAUGACU-CUAAAGGUU-CUCACAAACA-GGU---GUAAUCUCA---GCCU
>URS00006B2A5C_12908_1-412
GAGAGUAGUUAAGUAUCGAC-UCAUC-CAAAA-GAUGGGUUGGCUUGGUUGGCGGACCACUACUUUCACAAUCCACAACACAA-AACUUAUGACUCUGAUUAAGUCAAAUUAAU------------------------------------------------------------UAUUAUGAAGUAAGGAA-AAGU-GUCCGUC--AGGUUUGAAU---GAAAGGUGACUACAUAGUAAUGA----GCCGU-------UC-AUUGC-ACACA-A-A-GAUCCCAAGUC--GA--UGUGUAAUUAUCCCAAACAC-CUUUA-------------------------------GUCC-CGCAA-GGACGAA-CUGGGAAGGCA-----------------UUCUCAGAAAGAGUCAAGUAAGAUGAGAGUA-AUUUAAACCUUAAG-----GAGUGGUAAA--CCUAA--AAGACCGUCACUGAG-AAAUACUUCU------------CAAA-------A-GGAAGUG-GAUA-GGAGUAGAA----------ACA---------------AUAAUGACU-CUAAAGGUU-CUCAAUCAAA-CGU---GUAAUCUCA---GCGU
>URS00006672EE_12908_1-413
AGGAGUAGUUUAGUAUUCUG-UUGUU-CAAAA-GAUAACGGAGCUUAC--GGUGGACCACUACUUCUAUCAUCACGACACACA-ACUUUAUUUUACGUUCAGAAGUAAAAUUCAU----------------------------------------------------------GAUAUAAACAUAAAGCAA-AAGU-GUCCAUC--AGGUUUUGAU---GAAAGUCGCCUACACAGUCAUGG----GUUGU-------CC-AUGGC-ACACA-G-A-GACCGCAAGUC--AA--AGUGUAUUUUUACCAAAAAC-CUCUA-------------------------------AGGGGUCGAA-CCCUGAG-UCAGGUCGCAA------------------GCUUGAAGAGAGUUGAGUAAUGAAAGAGUA-GUUAAAACCUUAAG-----AAGUGAUUGG--UCUAA--CCAAUCGGCGAUGAG-AGUUACCAUU------------CAAA-------A-GAUGGUG-GAAA-CGAAGGGAAC---------CAC---------------AUAAUCCUU-UAAAAGAUU-CUCAAAAUUA-GGU---GUAUUCUCA---ACCU
>URS0000627B57_12908_1-410
GAGAGUAGUUCAGUAUCGAG-UCGUU-CAAAA-GAUGACUUGUCUGGU-UGGCAGACCGCUACUUUCACCAUCCACAGACCAA-AAACUUUGCAUUUUUGAAGUAUGCAAAU--------------------------------------------------------------ACUAAGAGACAAAGGAA-AAGU-GUCUGUC--AGUCGUAGGC---GAAAGGUGACUACAUAGUAAUGA----GAUGU-------UC-AUUGC-CGUUG-U-GGGUUCCCAAGACC-C---AAACGAUUCUUGAGAACGUU-CUCUA-------------------------------AUCC-CGCAA-GGAUUCA-CUGGGGUGGCA-----------------ACCUCGGAGAGUAACAAGUACAAAGAGAGUA-ACCGACGACUCAAG-----GAAUGGUAAC--CCUAA--GUGACCGUCACUGAG-AAUUACUACU------------CAAA-------A-GGUAGUG-GAAA-CGGGAAGAA----------AAA---------------AUAAUGUCC-CCAAAGAUU-CUUAAUCAAA-GGU---GUAUUCUCA---ACCU
>URS0000668E35_12908_1-407
GAGGGUAGUUUAGUAUCGUG-UCGUU-CAAAA-GAUGACAUGGCUGGU--GACGAGCCGCUACCUUCCUUAUCCGUAAACCAA-CUUUGGAAUUGCAAUGUCCAAAACAU----------------------------------------------------------------UAAAAUUAACAAAGGAG-AAGU-GCUCGUC--AGUUGUGUGU---GACAGGUCACUACAUAGUCGUGA----GAUGU-------UC-ACGGC-CG-UG-A-AGGGUCCCAAGCCC-GA--CA-UGAGUUUCGAGAAAGUU-CUCUA-------------------------------AUCC-CGCAA-GGAUAAA-UUGGUGGGGCA-----------------CCAUCGAAGAGUGAUAAGUACCGAGAGAGUU-GCAGACAACUUAAG-----GAUUGGUUAA--UCUAA--UUGACCGUGACUGAG-GGUUACCGUU------------CAAA-------A-GACGGUG-GAAA-CGAAGGGAA----------UCAA--------------AUAAUCCUU-CCAAAGAUC-CUCACAAAAU-GGU---GUAUUCUCA---ACCU
>URS000072667B_12908_1-411
AGGUGUAGUUCAGUAUCGUC-UCGUU-CAAAA-GAUGAGACAUCUGGUUUGACGGACCGCUACAUCUAUUAUCCACAAAUCAC-AACUUUGUUAAUUAAGGUUUAACAACUU--------------------------------------------------------------AUAAAUCAAUAAAGGAA-AAGU-GUUCGUC--AGUCGUGGUA---GACAGGUCACUACUUAGUCAUGA----GUUGU-------UC-AUGGC-CG-UA-A-AGGGUCCCAAACCC-GA--UA-CGAUUGUUUUGAAAGUU-CUCUA-------------------------------AUCC-CGCAA-GGAUGAG-UUUGGGUGGCA-----------------ACCUAGAAGAGUGAUGAGUAAGAAUAGAGUA-UAUUACCACUUUAG-----GAUUGGUUAA--UCUAA--UUGACCGUGACUGAG-AGGUACUUCU------------CAAA-------A-GGAAGUG-GAAA-UCGGAGGAA----------ACA---------------AUAAUCUCCUGUAAAGUCU-CUCACAAGAU-GGU---GUAUUCUCA---ACCU
>URS00006D2122_12908_1-411
AGGUGUAGUUCAGUAUCGUC-UCGUU-CAAAA-GAUGGGAUGGCUGGUUUGACGAACCGCUACAUCUAUUAUCCACAAAUCAA-ACUUUUACUUUCAAAUGGUGAAAAC-----------------------------------------------------------------UAAUAAAUUAAAAGAAA-AAGU-GUUCGUC--AGUCGUGGUA---GAUAGGUCACUACUUAGUCAUGA----GUUGU-------UC-AUGGC-CG-UA-A-AGGGUCUCAAACCC-AA--UA-CGAUUGUUUUGAAAGUU-CUCUA-------------------------------AUCC-CGCAA-GGAUGAG-UUUGGGUGGCA-----------------ACCUAGAAGAGUGAUGAGUAAGAAUAGAGUA-UAUUACGACUUUAG-----GAUUGGUUAA--UCUAA--UUAACCGUGACUGAG-AGGUACUUCU------------CAAA-------A-GGAAGUG-GAAA-UCGGAGGAAA---------UCAA----------A---AUAAUCUCCUGUAAAGUCU-CUCACAAGAU-GGU---UUAUUCUCA---ACCU
>URS00006C4A8F_12908_1-413
UCGGGUAGUUAAGUAUUCUG-UCGUU-CAAAA-GGCGGCGGAGCUUGU--GAUAGACCGCUACCUGAAACCACUGCAAAACCA-AACUUAUAUUUGCAUUUAGGAUUGCAAAAUCA--------------------------------------------------------UAAAAAUCAAAAUAAGAAA-AAGU-GUCUAUC--AGUUUUGACC---GAAAGGUGUCUACAUAGUAAUGA----GUUGU-------UC-AUUGC-CA-CA-A-ACACUCUCAAGGUG-AA--UG-UGAUUCUUUCGAAAGGU-UUCUA-------------------------------ACAC-CGCAA-GUGUGAA-UCUGCUCGGCA-----------------GGGUAGAAGAAAAU-AAGUAAGAAGAGAGUA-GGUUAAAACUCAAA-----GAGUGGUUCA--CUUAA--AUAACCGACAUUGGU-UGUUACAUCU------------CAAA-------A-GGAUGUG-GAAA-CAAAGGGAA----------UAG---------------AUAAUCCUU-UUAAAGACA-ACUACAAUAU-GGU---GUAUUCUCA---GCCU
>URS0000647792_12908_1-413
GAGGGUAGUUUAGUAUCGUG-UCAUU-CAAAA-GAUGAUUUGGCUUGU--GACGAGCCGCUACCUUCCACAUCCGUAAACCAA-ACCUUAAUUGUUAAUUCUGGUUUAACAACUA----------------------------------------------------------UUAAUUAAAAUCAAGGAA-AAGU-GCUCGUC--AGUCGUUGGA---AACAGGUGACUACUUAGUCUUGA----GAUGU-------UC-AUGAC-CGCGU-C--GGGUCCCAAGCCC-U---ACACGAUUUUCACGAAAGUU-CUCUA-------------------------------ACCC-CGCAA-GGGUUCA-UCAGGGAGGCA-----------------UCCUUGAAGAGUGAUGAGUAAGGAGAGAGUA-UUCAGCGACUUCAC-----GAAUGGUUCA-ACGUAA-UUG-ACCGUCACUGAG-AGUUACUACU------------CAAA-------A-GGUAGUG-GAAA-CGGAGGGAA----------UCA---------------AUAAUCCUU-CUAAAGAUU-CUCAUCAGAA-CUU---GUAUUCUCA---GAGU
>URS000070E2B3_12908_1-426
GGGUGGUGUGAAGCAUUUUG-UU-CC-CAAAA-GG-AACGAACCUUCU--CCCGAAGCACAUCGUCCAUUCUUCCACAACUGC-UAAUUAUCCUGCAACGAUAAUGUUACU---------------------------------------------------------------AAUAAUUAUGCAAGCGA-AAGU-CUUCGGG--CGUUGACAGU---GAAAGGUGUCUA-AU-ACUUCA-GAC-AUUG----GUCAAU-GGAGU-CAUCAGG-GAGACCGCAAGUCU-A--CUGAUGUCAAUCACGAAAUAC-CUGGU-------------------------------GGGACGGCCA-UCCCUUAGAGAGUCCGCAA------------------GACUUUACAGAGUAGAGUAACGGUUGAGUA-ACUGGCAACGAAAC-----GAGUGGUUCA-UCGUA--CUGAACCGACACUGAUUCGAUACUACGG-----------GCAA--------UCGUAGUG-GACAAUGUGAGGAA-CCG-----AAAC-A--------AUGG-AUAAUCUCA-CGAAAGACGGGUCACAUAAA-CGU---AUAGUCUCA---GCGU
>URS0000648352_12908_1-424
GGGUGGUGUGAAGCAUUUUG-UU-CU-CAAAA-GG-AACGGAACUUCU--CCCGAAGCACAUCGUCCAUUUUUCCACAAUUGC-UAAUUAUCCUGCAACGAUAAUGUUAC----------------------------------------------------------------AUAAGAUAAUACAGCGA-AAGC-CUUCGGG--CGUUGACAGU---GAAAGGUGUCUA-AU-ACUUCA-GAC-AUUA----GUCAAU-GAAGU-CAUCAG-UUAGAACGCAAUUCU-CC--UGAUGUCAAUCACGAAAUAC-CUGGU-------------------------------GGGACGGCCA-UCCCUUAGAGAGUUCGCAA------------------GACUUUACAGAGUAGAGUAACGGUUGAGUA-GCUGGCAACGAAAA-----GAGUGGUAAA--CUUAA--AUUACCGACACUGACUCGAUACUACGG-----------GCAA--------UCGUAGUG-GACAAUGUGAGGAA-CCG-----AUUCAA---------UGG-AUAAUCUCA-CGAAAGACGGGUCACAUAAA-CGU---GUAGUCUCA---GCGU
>URS0000631864_12908_1-406
GAGAGGUGUGAAGCAUUUUG-UU-UU-CAAAA-GA-AACGAAACUUCU--CCCGAAGCACAUCUUUCUCAUUUCCAUCGUUAC-UUUUACUA----------------------------------------------------------------------------------AAACUAAAAGAGAGCAA-AAGUUCUUCGGG--CGUUGACAAC---GAAAGGUGUCUA-AC-ACUUCG-AGUCAAUA---GACUAAC-GAAGU-CAUCG-G-UAGACCGCAAGUCU-CC--UGAUGUCAAUUAUCAAAUAC-CUGGU-------------------------------GGGAUGGCCG-UCCCUUAGUGAACUCGCAA------------------GGUUUGACAGAGUAAAGUAGUAGUUGAGUA-GUUGUUAACGAAAA-----GAGUGGUUCA--CUCAA--AUAACCGACACUGACUUGAUACUUUCG-----------GCAA--------CGAGAGUG-GAUA-CAUGAGCAA-CC------GAUAU----------AGG-GUAAUCUCA-CUAAAGACAAGUCACCAUAAACGU---GUAAUCUCA---GCGU
>URS00006DBC20_12908_1-407
GAGAGGUGUGAAGCAUUCUG-UA-CU-CAAAA-GG-UACGGACCUUCU--CCCGAAGCACAUCUUUCAUAAAUCCACAUUUGC-UAACUUUUAAUUC-----------------------------------------------------------------------------AAUGAUUAAAAAAGCAA-GAGU-CUUCGGG--CGUUGAUGAC---GAAAGGUGUCUA-AU-ACUUCG-GAC-CUUA----GUCAAC-GAAGU-CAUCCU-UUGAACCGCAAGUUC-GG--GGAUGUCAAUUGUGAAACAA-CUCGU-------------------------------GGGUUGGCCG-ACCCUUUGUGAGACCGCAA------------------GUCUUAAGAGAUUGGAGUAGUAGUUGAGUA-GUUAUCGACGAUAC-----GAAUGGUAGC--CGUAA--GCGACCGACACUGACCUGAUACCUCU------------GUCA-------A-UGAGGUG-GACA-AGUGGGGAACAA-------ACUA----------AUU-AUAAUCCCA-CAAAAGACAGGUUAUUCAAA-CGU---GUAGUCUCA---GCGU

Rfam family RF02032 maps to these 73 chains: 9L0R|1|A, 9L0R|1|B, 9L0R|1|C, 9L0R|1|D, 9L0R|1|E, 9L0R|1|F, 9L0R|1|G, 9L0R|1|H, 9L0R|1|I, 9L0R|1|J, 9L0R|1|K, 9L0R|1|L, 9LEC|1|J, 9LEE|1|A, 9LEE|1|B, 9LEE|1|C, 9LEE|1|D, 9LEE|1|E, 9LEE|1|F, 9LEE|1|G, 9LEE|1|H, 9LEE|1|I, 9LEE|1|J, 9LEL|1|J, 9LEM|1|A, 9LEM|1|B, 9LEM|1|C, 9LEM|1|D, 9LEM|1|E, 9LEM|1|F, 9LEM|1|G, 9LEM|1|H, 9LEM|1|I, 9LEM|1|J, 9LHK|1|G, 9LHL|1|A, 9LHL|1|B, 9LHL|1|C, 9LHL|1|D, 9LHL|1|E, 9LHL|1|F, 9LHL|1|G, 9LHL|1|H, 9LHL|1|I, 9LHL|1|J, 9LHL|1|K, 9LHL|1|L, 9LHL|1|M, 9LHL|1|N, 9LMF|1|A, 9LMF|1|B, 9LMF|1|C, 9LMF|1|D, 9LMF|1|E, 9LMF|1|F, 9LMF|1|G, 9LMF|1|H, 9LMF|1|I, 9LMF|1|J, 9MEE|1|A, 9MEE|1|B, 9MEE|1|C, 9MEE|1|D, 9MEE|1|E, 9MEE|1|F, 9MEE|1|G, 9MEE|1|H, 9MEE|1|I, 9MEE|1|J, 9MEE|1|K, 9MEE|1|L, 9MEE|1|M, 9MEE|1|N 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: 14-17, 42-43
  • Loop 2IL Column numbers: 20-22, 38-39
  • Loop 3HL Column numbers: 26-34
  • Loop 4IL Column numbers: 57-75, 108-198
  • Loop 5IL Column numbers: 83-85, 99-100
  • Loop 6HL Column numbers: 91-93
  • Loop 7IL Column numbers: 240-241, 260-262
  • Loop 8IL Column numbers: 242-243, 257-259
  • Loop 9HL Column numbers: 245-255
  • Loop 10IL Column numbers: 272-273, 292-295
  • Loop 11IL Column numbers: 273-276, 291-292
  • Loop 12IL Column numbers: 276-277, 289-291
  • Loop 13HL Column numbers: 280-286
  • Loop 14IL Column numbers: 307-312, 413-419
  • Loop 15IL Column numbers: 314-316, 409-411
  • Loop 16J4 Column numbers: 319-325, 343-351, 367-371, 405-406
  • Loop 17HL Column numbers: 331-337
  • Loop 18HL Column numbers: 355-363
  • Loop 19HL Column numbers: 377-399
  • Loop 20HL Column numbers: 459-469
  • Loop 21J3 Column numbers: 488-490, 524-534, 580-585
  • Loop 22HL Column numbers: 495-519
  • Loop 23IL Column numbers: 534-535, 578-580
  • Loop 24IL Column numbers: 539-543, 568-574
  • Loop 25IL Column numbers: 545-551, 565-566
  • Loop 26HL Column numbers: 551-565
  • Loop 27IL Column numbers: 599-601, 621-622
  • Loop 28HL Column numbers: 603-619

Loop 1 Internal loop

Column numbers: 14-17, 42-43 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UAUU*AG   11

    
    CAUU*AA    9

    
    UAUC*GG    6

    
    CAUU*AC    2

    
    UAUA*AG    2

    
    AGUA*CU    1

    
    CAUA*AA    1

    
    UAUC*AU    1

    
    UAUC*GU    1

    
    UAUU*AU    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_76709.2

Basepair signature:
cWW-L-cWW-L

100.00 84.44 2 0

2

Motif group IL_82107.4

Basepair signature:
cWW-cWW

100.00 78.06 2 0

Multiple bulged bases

3

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 73.27 2 0

Major groove intercalation

4

Motif group IL_79895.1

Basepair signature:
cWW-L-cWW-L

100.00 68.94 2 0

5

Motif group IL_50694.7

Basepair signature:
cWW-tSH-cWW-L

100.00 51.54 1 0

Major groove platform; stack outside cWW

6

Motif group IL_84476.1

Basepair signature:
cWW-cWW

100.00 49.75 2 0

Multiple bulged bases

7

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 32.92 4 1

8

Motif group IL_59877.1

Basepair signature:
cWW-L-cWW

97.14 60.12 2 0

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

97.14 25.65 2 0

Single stack bend

10

Motif group IL_42626.2

Basepair signature:
cWW-cWW

94.29 24.60 4 1

Loop 2 Internal loop

Column numbers: 20-22, 38-39 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    G-U*AC   12

    
    G-U*AU    9

    
    C-U*AG    6

    
    C-U*GG    2

    
    G-C*GU    2

    
    U-G*UG    2

    
    AAC*GC    1

    
    G-U*GC    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

Basepair signature:
cWW-L-cWW

100.00 14.74 3 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

94.29 14.40 4 1

Multiple bulged bases

3

Motif group IL_84476.1

Basepair signature:
cWW-cWW

91.43 20.31 3 2

Multiple bulged bases

4

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

85.71 3.88 1 1

Single bulged G

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

62.86 11.43 3 1

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

54.29 11.70 3 1

Intercalated cWS

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

54.29 7.38 2 1

Major groove intercalation

8

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

54.29 6.72 2 1

Single stack bend

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

54.29 2.50 2 1

Single stack bend

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

54.29 0.39 4 1

Loop 3 Hairpin loop

Column numbers: 26-34 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U-CAAAA-G   25

    
    C-CAAAA-G    5

    
    CUGAAA-GG    1

    
    UCGAAA-GG    1

    
    U-CAAAA-A    1

    
    --CAAAAA-    1

    
    U-GAAA--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

Basepair signature:
cWW-F-F-F

94.29 35.05 1 1

2

Motif group HL_87553.1

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

94.29 31.00 3 2

3

Motif group HL_10540.1

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

94.29 9.43 3 2

4

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

91.43 46.26 1 1

5

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

91.43 31.41 2 1

Pseudoknot geometry with 3' bulge

6

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

91.43 10.50 3 2

7

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

91.43 9.39 2 2

8

Motif group HL_65794.5

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

91.43 2.84 3 1

Pseudoknot geometry

9

Motif group HL_31585.4

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

88.57 20.27 2 1

Purine riboswitch

10

Motif group HL_02817.2

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

88.57 16.63 2 1

Loop 4 Internal loop

Column numbers: 57-75, 108-198 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GCGUGUCUGUGAUAGAUGA*GAUAGAA------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-C    3

    
    GCACGUCAUGGUAGGUUAC*CAUUUGGGUAGAGCACUCGUUUUUGGAACGAAUGGUAGCCGGUUCAAAUCCGGUCAACUCAUCCUUGAAAGAUGAAAAAACGCA-AAGA-C    1

    
    GCCCUUCUCCUAGGUCAAA*UCAACCGAAAAGGGGAUAUAGUUCAAC--------------------UGGUAGAGCACUGUAUUUUUCAUACAGCGAAAGGCAC-AAGA-C    1

    
    GCUCAUCGCGGUAGGUUGC*AAACUGGAGACUGUAGGUU-----------------------------------CAAAUCCUACAUUGUAAAUCAAAAAUGCAA--AGA-C    1

    
    GCUCAUCAAGGUAGGUUGC*UAAACAGGAUGUUGCGG---------------------------------------GUUCGAUCCCCGCCGUAAUAAAAUGCAA--AGA-C    1

    
    GCGCAAUCUUCACUUCGCC*GGCGUAGAUAAC-------------------------------------------------AAGUUCAUUAACAAGAAAAGCAAAGAGU-C    1

    
    GCACUGGGUUCCGAAUAAG*UAAACCAUUAAA--------------------------------------------------UAUAACAUUAUCUAAAAUGCAA-AAGU-C    1

    
    CCGCUACCUGAAACCACUG*GCAAAAUCA--------------------------------------------------------UAAAAAUCAAAAUAAGAAA-AAGU-G    1

    
    CCACUACUUCUAUCAUCAC*AAAUUCAU----------------------------------------------------------GAUAUAAACAUAAAGCAA-AAGU-G    1

    
    CCGCUACCUUCCACAUCCG*AACAACUA----------------------------------------------------------UUAAUUAAAAUCAAGGAA-AAGU-G    1

    
    CCACUACUUUCACAAUCCA*AAAUUAA-----------------------------------------------------------UUAUUAAGAAAUAAGCAA-AAGU-G    1

    
    CCACGACUUCGACAAAUCU*AACAUUU------------------------------------------------------------AAAAAAGAAGAAAUCGA-AAGU-G    1

    
    CCACUACUUUCACAAUCCA*AAUUAAU------------------------------------------------------------UAUUAUGAAGUAAGGAA-AAGU-G    1

    
    CCACUACUUUCACAAUCCA*CAAAUUA------------------------------------------------------------AAAAGAUCAUUAAGGAA-AAGU-G    1

    
    CCGCUACAUCUAUUAUCCA*AACUU--------------------------------------------------------------AUAAAUCAAUAAAGGAA-AAGU-G    1

    
    CCGCUACUUUCACCAUCCA*CAAAU--------------------------------------------------------------ACUAAGAGACAAAGGAA-AAGU-G    1

    
    GCACAUCGUCCAUUCUUCC*UACU---------------------------------------------------------------AAUAAUUAUGCAAGCGA-AAGU-C    1

    
    CCGCUACCUUCCUUAUCCG*CAU----------------------------------------------------------------UAAAAUUAACAAAGGAG-AAGU-G    1

    
    GCACAUCGUCCAUUUUUCC*UAC----------------------------------------------------------------AUAAGAUAAUACAGCGA-AAGC-C    1

    
    CCACUACUUCGACACAUCC*AU-----------------------------------------------------------------UAAAUACAAUUAAGCAA-GAGU-G    1

    
    CCGCUACAUCUAUUAUCCA*AC-----------------------------------------------------------------UAAUAAAUUAAAAGAAA-AAGU-G    1

    
    GCACAUCUUUCUCAUUUCC*-------------------------------------------------------------------AAACUAAAAGAGAGCAA-AAGUUC    1

    
    GCGCGUCCUGA--------*CACUUAAC----------------------------------------------------------AAUUAAAAAAUUAAGCAA-AAGA-C    1

    
    CCACGACUUCGACAAAUCU*-------------------------------------------------------------------UAAAAAGAAGAAAUCGA-AAGU-G    1

    
    GCACAUCUUUCAUAAAUCC*-------------------------------------------------------------------AAUGAUUAAAAAAGCAA-GAGU-C    1

    
    GCACGUCUGCGAUACACGA*-------------------------------------------------------------------AUAUUGGAAUAAAGCAA-AAGU-C    1

    
    GCUCAACUUUCAUGACUCU*-------------------------------------------------------------------UAAACUACAGAAAGGAA-AAGU-C    1

    
    GCUCAACUUUCAUUACACU*-------------------------------------------------------------------AAAACUACAGAAAGGAA-AAGU-C    1

    
    GCUCAUCUUUCAUCACACU*-------------------------------------------------------------------AAACUACAGAAAAGGAA-AAGU-C    1

    
    ACGCGGACACAGACUAAAA*-------------------------------------------------------------------UGAAAAUAAACAUGCAA--AGU-U    1

    
    GCACGUCUUGGUAGGAUUG*-------------------------------------------------------------------AAUCAGGCUAAACGCAA--AGU-C    1

    
    GCACGUCUUUGUCAGUUCC*-------------------------------------------------------------------GUUCUUGUUAAACGCCA--AGU-C    1

    
    GCGCUUCU--CGAUCGGUU*-------------------------------------------------------------------GCGAACCAUUAAAGCAA-AAGC-C    1
No Matches Found View All Results for this Loop

Loop 5 Internal loop

Column numbers: 83-85, 99-100 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    U-U*GC    3

    
    A-A*AU    2

    
    A-A*UU    2

    
    C-U*CG    2

    
    U-U*AA    2

    
    ACU*UU    1

    
    A-A*GA    1

    
    A-A*UC    1

    
    A-A*UG    1

    
    A-C*UG    1

    
    A-C*UU    1

    
    A-G*CC    1

    
    A-G*CU    1

    
    A-G*GA    1

    
    A-U*AU    1

    
    A-U*UC    1

    
    C-A*AG    1

    
    C-A*AU    1

    
    C-U*CA    1

    
    C-U*GU    1

    
    U-G*GU    1

    
    U-G*UA    1

    
    U-U*AU    1

    
    Omitted sequenced and counts

    
    C-U*--    4

    
    G-C*--    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_07039.3

Basepair signature:
cWW-L-cWW

44.83 0.44 3 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

44.83 -4.32 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

31.03 -10.24 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

27.59 -11.61 4 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

24.14 -11.88 4 1

6

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

24.14 -18.01 2 1

Single stack bend

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

24.14 -19.01 3 1

Major groove intercalation

8

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

24.14 -21.92 5 1

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

24.14 -23.27 2 1

Single stack bend

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

24.14 -23.44 3 1

Loop 6 Hairpin loop

Column numbers: 91-93 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    AUU    6

    
    GUU    4

    
    UCC    4

    
    AAU    2

    
    UCU    2

    
    UUA    2

    
    AAA    1

    
    ACA    1

    
    ACU    1

    
    AUG    1

    
    GCU    1

    
    GUA    1

    
    GUG    1

    
    UAA    1

    
    UAU    1

    
    UGA    1

    
    UGC    1

    
    UGG    1

    
    UGU    1

    
    UUU    1

    
    UA-    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_78677.1

Basepair signature:
cWW-F-F

45.71 -299.68 3 1

2

Motif group HL_32346.4

Basepair signature:
cWW-F

25.71 -311.78 2 1

3

Motif group HL_70782.2

Basepair signature:
cWW-F

22.86 -327.74 3 2

Loop 7 Internal loop

Column numbers: 240-241, 260-262 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UG*C-A   15

    
    CA*U-G    4

    
    CG*C-G    3

    
    GA*U-C    3

    
    CU*AUG    1

    
    AA*U-U    1

    
    CU*U-G    1

    
    GG*C-C    1

    
    UG*C-G    1

    
    UU*U-A    1

    
    Omitted sequenced and counts

    
    A-*--U    3

    
    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_07039.3

Basepair signature:
cWW-L-cWW

100.00 18.87 2 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

96.77 30.61 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

93.55 24.54 1 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

93.55 22.37 3 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

93.55 21.88 3 1

6

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

90.32 14.96 3 1

Single stack bend

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

90.32 14.03 3 1

Major groove intercalation

8

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

90.32 12.64 1 1

Single stack bend

9

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

90.32 11.63 3 1

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

90.32 8.81 2 1

Loop 8 Internal loop

Column numbers: 242-243, 257-259 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GC*AAU    1

    
    Omitted sequenced and counts

    
    A-*--U   10

    
    -G*CAA    7

    
    -C*GAA    4

    
    --*---    4

    
    -A*UAA    3

    
    G-*--C    3

    
    --*--A    2

    
    -G*UAA    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

Basepair signature:
cWW-L-cWW

100.00 50.43 3 0

Major groove platform

2

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 50.02 3 0

Single stack bend

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 48.54 3 0

Multiple bulged bases

4

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

100.00 45.09 3 0

Stack and bulge

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 42.53 3 0

6

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 41.39 2 0

Single stack bend

7

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

100.00 41.25 1 0

Single bulged A

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 38.77 3 0

Major groove intercalation

9

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 28.91 2 0

Major groove platform

10

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 22.91 3 1

Loop 9 Hairpin loop

Column numbers: 245-255 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    --GUUGU----    5

    
    --GAUGU----    3

    
    --GCCGU----    3

    
    --UUAGA----    3

    
    UAGAAAU---A    2

    
    C-GCAA----G    2

    
    C-UUCG----G    2

    
    CACAAGGGGUG    1

    
    CCUGCG---GG    1

    
    UAGAAAU---G    1

    
    UCAAUA---GA    1

    
    C-CUUCG---G    1

    
    --GAAAC--A-    1

    
    C-AUUA----G    1

    
    C-AUUG----G    1

    
    C-CUUA----G    1

    
    C-GUAA----G    1

    
    G-GUAA----C    1

    
    --CUAGG----    1

    
    --GCAAU----    1

    
    --GCUGU----    1

    
    --GUCGU----    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_48417.5

Basepair signature:
cWW-F-F

62.86 -1.81 3 2

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

45.71 -1.28 3 2

3

Motif group HL_50006.2

Basepair signature:
cWW-F-F

37.14 -23.49 3 3

4

Motif group HL_75660.5

Basepair signature:
cWW-F

34.29 -25.78 2 2

5

Motif group HL_57875.1

Basepair signature:
cWW-F-F

34.29 -39.42 3 2

6

Motif group HL_32392.1

Basepair signature:
cWW-F-F

31.43 -63.35 3 3

7

Motif group HL_56131.2

Basepair signature:
cWW-F-F

28.57 -35.33 3 3

8

Motif group HL_81100.2

Basepair signature:
cWW

28.57 -342.67 3 2

9

Motif group HL_69752.2

Basepair signature:
cWW-F

25.71 -48.75 3 3

10

Motif group HL_70782.2

Basepair signature:
cWW-F

25.71 -53.51 3 3

Loop 10 Internal loop

Column numbers: 272-273, 292-295 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GU*AGAA    1

    
    AU*A-UU    1

    
    CC*A-GG    1

    
    AG*--CU    1

    
    AG*C--U    1

    
    CG*A--G    1

    
    CU*G--G    1

    
    GA*U--C    1

    
    Omitted sequenced and counts

    
    A-*A--U    6

    
    C-*A--G    4

    
    G-*U--C    2

    
    U-*A--U    2

    
    A-*A--A    1

    
    C-*A--C    1

    
    G-*A--C    1

    
    G-*C--U    1

    
    GA*A---    1

    
    U-*A--A    1

    
    U-*A--C    1

    
    U-*C--A    1

    
    U-*U--A    1

    
    U-*U--C    1

    
    A-*---U    1

    
    G-*---A    1

    
    U-*---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_73452.2

Basepair signature:
cWW-L-cWW

87.50 26.04 3 1

2

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

87.50 25.60 4 1

Intercalated cWS

3

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

87.50 25.48 2 1

Major groove platform

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

75.00 25.71 2 1

Major groove intercalation

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

75.00 17.37 3 1

6

Motif group IL_42771.1

Basepair signature:
cWW-cWW

75.00 13.43 3 1

Multiple bulged bases

7

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

75.00 6.26 1 1

Single bulged G

8

Motif group IL_84476.1

Basepair signature:
cWW-cWW

75.00 4.64 3 2

Multiple bulged bases

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

62.50 15.27 2 1

Single stack bend

10

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

62.50 12.71 2 1

Single stack bend

Loop 11 Internal loop

Column numbers: 273-276, 291-292 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    -A-A*GA    8

    
    -G-A*GA    4

    
    -ACA*UU    2

    
    -A-A*AA    2

    
    -G-A*AA    2

    
    A-CG*UA    1

    
    A-UA*UU    1

    
    CA-A*GA    1

    
    G-UU*CC    1

    
    GA-U*GA    1

    
    U-UU*GG    1

    
    UA-A*GA    1

    
    UG-A*GA    1

    
    -A-G*AU    1

    
    -G-A*AC    1

    
    -G-A*GU    1

    
    -G-U*AA    1

    
    -G-U*CC    1

    
    Omitted sequenced and counts

    
    GG-G*A-    1

    
    -U-G*C-    1

    
    -C--*U-    1

    
    ----*--    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

Basepair signature:
cWW-L-cWW

100.00 24.27 3 0

Major groove platform

2

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 3.19 3 0

Single stack bend

3

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 -88.93 2 0

Major groove platform

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

96.77 5.57 3 0

Major groove intercalation

5

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

67.74 -3.81 3 0

Single stack bend

6

Motif group IL_42771.1

Basepair signature:
cWW-cWW

64.52 0.86 3 1

Multiple bulged bases

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

64.52 -6.66 3 0

8

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

64.52 -16.75 3 1

Stack and bulge

9

Motif group IL_51454.3

Basepair signature:
cWW-cSH-cWW

64.52 -94.70 2 0

Minor groove platform

10

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

58.06 -111.72 3 1

Loop 12 Internal loop

Column numbers: 276-277, 289-291 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AG*U-G    6

    
    AG*C-U    3

    
    AA*C-G    2

    
    AG*C-G    2

    
    GA*U-A    2

    
    UA*U-C    2

    
    GG*CCU    1

    
    UG*CUG    1

    
    AA*G-A    1

    
    AA*G-G    1

    
    AA*U-G    1

    
    AC*G-A    1

    
    AG*C-A    1

    
    AG*U-A    1

    
    AU*U-G    1

    
    GG*C-C    1

    
    UA*G-A    1

    
    UG*C-G    1

    
    Omitted sequenced and counts

    
    A-*--G    3

    
    -G*C-U    1

    
    -A*U--    1

    
    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_07039.3

Basepair signature:
cWW-L-cWW

58.62 7.59 2 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

37.93 -5.81 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

24.14 -8.62 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

24.14 -8.93 4 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

24.14 -10.50 3 1

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

20.69 -13.45 2 1

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

20.69 -16.65 3 1

8

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

20.69 -17.16 2 1

Single stack bend

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

20.69 -20.81 2 1

Single stack bend

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

20.69 -21.37 3 1

Loop 13 Hairpin loop

Column numbers: 280-286 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UCGCAAG   11

    
    CCGCAAG    9

    
    UCCCAAG    5

    
    CCCCAAG    3

    
    UCGAAAG    2

    
    ACGCAAU    1

    
    CUGCAAG    1

    
    UCCCAAA    1

    
    UCUCAAA    1

    
    UCUCAAG    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_87553.1

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

100.00 43.75 3 2

2

Motif group HL_10453.3

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

94.29 41.08 3 1

tRNA anticodon loop

3

Motif group HL_37369.2

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

94.29 38.22 2 1

4

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

82.86 12.06 1 1

5

Motif group HL_18565.1

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

74.29 3.21 4 2

6

Motif group HL_10540.1

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

68.57 10.78 3 2

7

Motif group HL_85993.1

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

62.86 1.68 4 2

8

Motif group HL_56131.2

Basepair signature:
cWW-F-F

60.00 -1.03 3 2

9

Motif group HL_70782.2

Basepair signature:
cWW-F

45.71 -6.48 3 2

10

Motif group HL_04259.3

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

34.29 -10.84 2 1

GNRA with extra cWW

Loop 14 Internal loop

Column numbers: 307-312, 413-419 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AAGAGU*UGAAAAA    4

    
    UGAAAG*UGAGUAA    3

    
    CCAAAG*UGAGUAA    2

    
    CGAAAU*AGAGUAA    2

    
    CUAAAA*-GAUUAA    2

    
    ACAUUC*GUCUAAG    1

    
    AGAAAG*CAAGUAG    1

    
    AGAAAG*UAAGUAC    1

    
    AGAAAG*UGAGUAA    1

    
    AGAAAG*UUAGUAG    1

    
    AGAACG*CAAGUAC    1

    
    AUGAGU*AAAGAAA    1

    
    CCAAAA*UGAGUAA    1

    
    CCAAAC*CAAGUAA    1

    
    CCAAAC*CGAGUAA    1

    
    CGAAAG*UGAGUAA    1

    
    UCAAAU*AAAGUAG    1

    
    UGAAAC*GGAGUAG    1

    
    CGAAAG*-AAGUAA    1

    
    CGAAGC*GCAG-AA    1

    
    UAGAAG*-AAGAAG    1

    
    AGGGGG*GGAAU--    1

    
    C-GAGU*CGAA-AG    1

    
    CGGAGG*CGAUG--    1

    
    GAAAG-*AUAGAA-    1

    
    UGAAAU*GGA--AG    1

    
    AAAUC-*-GAGGA-    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

51.43 5.01 4 2

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_41756.4

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

51.43 -34.42 6 3

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

3

Motif group IL_24254.1

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

40.00 -32.39 7 3

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

4

Motif group IL_47346.2

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

31.43 -36.56 6 3

tSH-tSH-tHH-tHS

5

Motif group IL_61286.1

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

31.43 -37.25 7 4

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

6

Motif group IL_29198.2

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

28.57 -40.85 6 3

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

7

Motif group IL_87284.1

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

25.71 -33.31 5 3

tSH-tHW-tWH-tHS

8

Motif group IL_02349.4

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

25.71 -49.86 6 4

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

9

Motif group IL_04346.10

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

25.71 -62.22 5 3

8x7 Sarcin-Ricin; G-bulge

10

Motif group IL_16458.4

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

14.29 -52.34 6 4

Sarcin-Ricin target in LSU H95; G-bulge

Loop 15 Internal loop

Column numbers: 314-316, 409-411 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    C-C*GAG   11

    
    A-A*UAA    4

    
    U-C*GUG    4

    
    CAC*GGU    1

    
    A-A*UUG    1

    
    A-C*GAU    1

    
    A-G*CCA    1

    
    C-A*GUA    1

    
    C-U*AGC    1

    
    C-U*AGU    1

    
    G-U*GAA    1

    
    G-U*GUG    1

    
    U-C*GAA    1

    
    U-C*GUA    1

    
    U-U*AAA    1

    
    U-U*GAA    1

    
    U-U*GAG    1

    
    U-U*GGU    1

    
    Omitted sequenced and counts

    
    --U*GUA    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

Basepair signature:
cWW-L-cWW

97.06 66.80 2 0

Single stack bend

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

97.06 60.32 3 0

Major groove platform

3

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

97.06 54.02 2 0

Major groove platform

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

97.06 51.91 3 1

Intercalated cWS

5

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

94.12 61.91 2 0

Single stack bend

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

94.12 58.68 2 0

Major groove intercalation

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

94.12 56.75 3 0

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

94.12 52.16 2.5 1

9

Motif group IL_42771.1

Basepair signature:
cWW-cWW

91.18 62.03 2.5 0

Multiple bulged bases

10

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

91.18 57.11 3 0

Loop 16 4-way junction loop

Column numbers: 319-325, 343-351, 367-371, 405-406 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GGCCGCC*UGAAUGGUG*--U-G*CA    1

    
    Omitted sequenced and counts

    
    UA-----*---------*GAG-U*AA    4

    
    -AGCUUA*U-------U*-C---*--    3

    
    GU-----*---------*UUAGA*UA    3

    
    UA-----*---------*GAA-U*AA    3

    
    GU-----*---------*UUAGG*CA    2

    
    CAC-GUU*---------*UAA-C*GG    1

    
    -AGCUUA*U-------U*-----*-C    1

    
    GU-----*---------*UUAGU*GA    1

    
    GU-----*---------*UUUGU*AA    1

    
    UA----A*UU------U*CU---*-U    1

    
    GU-----*---------*UAG-A*UA    1

    
    UA-----*---------*AAA-U*AA    1

    
    UA-----*---------*GAA-C*GA    1

    
    UA-----*---------*GAG-C*GA    1

    
    UA-----*---------*UAG-U*AA    1

    
    UA-----*---------*UCA-C*GA    1

    
    UA-----*---------*UCA-U*AA    1

    
    UA-----*GA-----AU*A----*-A    1

    
    AAC--CG*U--------*-----*-A    1

    
    ------G*CG------C*GA---*--    1

    
    ------G*UA------C*G----*-A    1

    
    G-----A*UA------G*-----*-A    1

    
    U------*---------*UAA-U*A-    1

    
    UA-----*---------*-----*-G    1
No Matches Found View All Results for this Loop

Loop 17 Hairpin loop

Column numbers: 331-337 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    UUAGC-G    5

    
    AGAGGAC    1

    
    GGAGGCA    1

    
    GUAGCUC    1

    
    UUCGCAG    1

    
    CGGCC-A    1

    
    UUAGC-A    1

    
    UAAGC--    1

    
    Omitted sequenced and counts

    
    -------   23
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_04783.2

Basepair signature:
cWW-F-F-F

58.33 16.74 2.5 0.5

2

Motif group HL_93535.1

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

58.33 -12.58 2 2

3

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

58.33 -14.42 3 2

4

Motif group HL_59843.1

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

58.33 -17.47 3 2

5

Motif group HL_37824.7

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

58.33 -22.91 1.5 0

GNRA

6

Motif group HL_56131.2

Basepair signature:
cWW-F-F

50.00 -19.96 2 1.5

7

Motif group HL_99040.1

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

50.00 -753.33 2.5 2

8

Motif group HL_97917.2

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

16.67 -17.04 3 3

9

Motif group HL_51447.1

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

16.67 -4710.48 3 2

10

Motif group HL_89893.1

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

8.33 -23.22 3.5 2

Loop 18 Hairpin loop

Column numbers: 355-363 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    C-CGCAA-G   12

    
    UGGGCAC-G    3

    
    ACGGCCA-U    2

    
    GGUCGAA-C    2

    
    U-CGCAA-G    2

    
    GACGCAAAG    1

    
    AUGGCCG-U    1

    
    GAGCCAA-C    1

    
    GGUCGAG-C    1

    
    UUCGUAC-C    1

    
    UUGGCCG-A    1

    
    C-CCGAA-G    1

    
    G-UCGAA-C    1

    
    Omitted sequenced and counts

    
    ---------    6
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_85993.1

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

62.07 -5.89 4 3

2

Motif group HL_87553.1

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

58.62 10.36 3 2

3

Motif group HL_10453.3

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

55.17 -3.63 3 2

tRNA anticodon loop

4

Motif group HL_10540.1

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

55.17 -6.53 3 2

5

Motif group HL_18565.1

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

55.17 -8.44 4 3

6

Motif group HL_04259.3

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

51.72 -17.76 2 1

GNRA with extra cWW

7

Motif group HL_37369.2

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

48.28 -3.18 2 2

8

Motif group HL_13963.3

Basepair signature:
cWW-F-F

48.28 -28.34 4 2

9

Motif group HL_56131.2

Basepair signature:
cWW-F-F

48.28 -31.72 3 2

10

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

48.28 -38.33 2 2

Loop 19 Hairpin loop

Column numbers: 377-399 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CGCAA------------------   10

    
    AGGCA-----------------U    5

    
    CGGCA-----------------G    4

    
    UGGCA-----------------A    3

    
    UGCAAAGCGUGGUUUUAAUACCA    1

    
    GGGCA-----------------C    1

    
    Omitted sequenced and counts

    
    -----------------------   11
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_82710.2

Basepair signature:
cWW-F-F-F

95.83 -416.11 3 1

2

Motif group HL_13963.3

Basepair signature:
cWW-F-F

95.83 -432.18 3 2

3

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

95.83 -434.22 2 2

4

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

95.83 -444.54 3 2

tRNA D-loop

5

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

58.33 -439.99 1 1

6

Motif group HL_37824.7

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

58.33 -504.39 1 1

GNRA

7

Motif group HL_71391.1

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

54.17 -445.00 3 1

8

Motif group HL_56131.2

Basepair signature:
cWW-F-F

54.17 -445.05 4 2

9

Motif group HL_50006.2

Basepair signature:
cWW-F-F

54.17 -447.31 2 2

10

Motif group HL_56334.1

Basepair signature:
cWW-F

54.17 -451.62 3 1

Mini UNCG

Loop 20 Hairpin loop

Column numbers: 459-469 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    G--UCUAA--C    6

    
    A--CCUAA--A    4

    
    A--UCUAA--U    3

    
    A--CGUAA--A    2

    
    A--CUUAA--A    2

    
    C-ACUCAAAAC    1

    
    G-CUUUAAAAA    1

    
    U-CUUUAAAAA    1

    
    A-ACGUAA-UU    1

    
    A-CCCUAA-AA    1

    
    A-CGUUAA-AA    1

    
    A-UCUUAA-AA    1

    
    CAGUAUAA--A    1

    
    A-A-CUCC-UU    1

    
    A-UCGUA--CU    1

    
    A--CUCAA--A    1

    
    C--CCUAA--G    1

    
    C--CGUAA--G    1

    
    G--CGAUA--C    1

    
    G--CUAUA--C    1

    
    U--CGUAA--A    1

    
    ---UAUUA---    1

    
    G--U------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 HL_10453.3

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

60.00 -268.29 4 2

tRNA anticodon loop

2

Motif group HL_87553.1

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

57.14 -18.61 4 2

3

Motif group HL_70782.2

Basepair signature:
cWW-F

45.71 -50.76 3 2

4

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

40.00 -36.62 3 2

5

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

31.43 -57.50 4 2

6

Motif group HL_56131.2

Basepair signature:
cWW-F-F

28.57 -31.69 3 2

7

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

28.57 -269.49 3 3

tRNA anticodon loop with synthetase

8

Motif group HL_25967.2

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

25.71 -46.45 4 3

9

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

20.00 -259.82 6 4

Other HL

10

Motif group HL_73266.9

Basepair signature:
cWW-F-F-cSW-cSH-F

17.14 -34.39 3 3

Loop 21 3-way junction loop

Column numbers: 488-490, 524-534, 580-585 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UAC*GUG-GACA-AG*CAAAAG    4

    
    UAC*GUG-GAUA-GG*CUAAAG    3

    
    UAC*GUG-GACAAUG*CGAAAG    2

    
    UAC*GUG-GAAA-CG*CCAAAG    2

    
    UAC*GUG-GAAA-UC*GUAAAG    2

    
    UAC*GUG-GAUA-AG*CAAAAG    2

    
    UAC*GUG-GAUA-CG*CAAAAG    2

    
    GAC*GUG-GAUG-UC*G--AGG    2

    
    UAC*GUGUGUGUAAA*UAAAAU    1

    
    UAC*GUG-GACAAAA*UCAAAG    1

    
    GAC*GUG-GAUA-AG*CAAAGG    1

    
    UAC*GUG-GAAA-AU*AGAAAG    1

    
    UAC*GUG-GAAA-CA*UUAAAG    1

    
    UAC*GUG-GAAA-CG*CUAAAG    1

    
    UAC*GUG-GAAA-CG*UAAAAG    1

    
    UAC*GUG-GAAA-CG*UCAAAG    1

    
    UAC*GUG-GAAA-CG*UUAAAG    1

    
    UAC*GUG-GACA-AA*GCAAAG    1

    
    UAC*GUG-GACA-AG*CGAGAG    1

    
    UAC*GUG-GACA-CG*CAAAAG    1

    
    UAC*GUG-GAUA-AA*UGAAAG    1

    
    UAC*GUG-GAUA-CA*CUAAAG    1

    
    UAC*GUG-GAUA-UU*AUAAAG    1

    
    UUC*GAG-GAUA-AG*CGAAAG    1
No Matches Found View All Results for this Loop

Loop 22 Hairpin loop

Column numbers: 495-519 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    ------------CAAA-------A-   13

    
    G-----------GCAA--------C    4

    
    A-----------GGAA--------U    3

    
    G-----------GCAA--------U    2

    
    GAGCAUCCUUGA----UGG-AUGGC    1

    
    UUCUCU-AAGCG---AUG---AGAA    1

    
    UUGU----GGCU----UCGGCCUGG    1

    
    GA---------AGUGAUGA-GCUAC    1

    
    GCA-------GUGAGAGC----CGC    1

    
    AUA-------CCGAAAG-----GGU    1

    
    AUA-------CCGCAAG-----GGU    1

    
    G----------AGUAA-------UC    1

    
    A-----------GGGA--------U    1

    
    C-----------GCAA--------G    1

    
    ------------GUCA-------A-    1

    
    ------------AUGA---------    1

    
    ------------GGGA---------    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_04783.2

Basepair signature:
cWW-F-F-F

71.43 -397.95 2 2

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

68.57 -962.32 2 1

3

Motif group HL_75660.5

Basepair signature:
cWW-F

68.57 -2143.13 1 2

4

Motif group HL_38168.1

Basepair signature:
cWW-F

37.14 -2164.06 4 2

5

Motif group HL_37824.7

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

34.29 -487.98 2 1

GNRA

6

Motif group HL_56334.1

Basepair signature:
cWW-F

34.29 -2162.81 3 3

Mini UNCG

7

Motif group HL_50006.2

Basepair signature:
cWW-F-F

31.43 -983.04 3 2

8

Motif group HL_13963.3

Basepair signature:
cWW-F-F

31.43 -998.42 5 4

9

Motif group HL_93535.1

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

31.43 -1019.36 3 2

10

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

31.43 -1562.66 3 2

Loop 23 Internal loop

Column numbers: 534-535, 578-580 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GA*U-C    7

    
    GU*A-C    3

    
    CG*CUG    2

    
    AA*U-U    2

    
    GA*A-C    2

    
    GG*C-C    2

    
    GA*UAC    1

    
    GG*CAC    1

    
    AC*G-U    1

    
    AG*C-G    1

    
    AG*C-U    1

    
    AU*A-C    1

    
    CA*U-G    1

    
    CU*A-G    1

    
    GA*U-U    1

    
    GC*G-C    1

    
    GC*G-U    1

    
    GG*A-C    1

    
    GG*U-C    1

    
    GU*A-U    1

    
    UA*U-A    1

    
    UU*A-A    1

    
    Omitted sequenced and counts

    
    G-*A-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_84476.1

Basepair signature:
cWW-cWW

97.06 22.77 3 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

94.12 21.39 3 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

85.29 23.93 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

76.47 22.33 4 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

76.47 22.29 3 1

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

76.47 17.61 2 1

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

76.47 16.44 2 1

Major groove intercalation

8

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

76.47 4.53 1 1

Single bulged G

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

73.53 16.22 3 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

73.53 12.56 2 1

Single stack bend

Loop 24 Internal loop

Column numbers: 539-543, 568-574 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GAA--*--AUAAU   12

    
    UAA--*--AUAAG    5

    
    GAA-C*G-AUAAU    3

    
    GAAAC*GUAUAAU    2

    
    GAAGC*GUAUAAU    2

    
    GAACC*GGAUAAU    1

    
    GAACG*CGAUAAU    1

    
    GAAGC*GGAUAAU    1

    
    GAAGG*CUAUAAU    1

    
    GAACA*AGAUA-U    1

    
    GAACA*U-AUAAU    1

    
    GAAGG*U-AUAAU    1

    
    CAA-C*G-GUAAU    1

    
    GAAA-*--AUAAU    1

    
    GAAC-*--AUAAU    1

    
    Omitted sequenced and counts

    
    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_59258.1

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

32.35 -20.18 5 2

2

Motif group IL_21667.1

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

26.47 -7.16 4 1

3

Motif group IL_80231.1

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

23.53 -36.74 5 2

Other IL

4

Motif group IL_53448.1

Basepair signature:
cWW-tWH-cSH-cWW

14.71 -55.88 5 2

Receptor of 11-nt loop-receptor motif

5

Motif group IL_14177.2

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

14.71 -57.11 5 2

6

Motif group IL_77045.1

Basepair signature:
cWW-L-tSW-L-tHW-cWW-L

14.71 -70.20 7 4

Kink-turn

7

Motif group IL_22564.1

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

14.71 -4175.70 7 4

8

Motif group IL_90346.1

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

11.76 -26.11 4 2

9

Motif group IL_34737.1

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

11.76 -45.60 5 2

10

Motif group IL_11344.2

Basepair signature:
cWW-cSS-L-cWW

11.76 -53.17 5 3

180 degree turn

Loop 25 Internal loop

Column numbers: 545-551, 565-566 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    AAAGGGG*AC    1

    
    AUGCUCG*GU    1

    
    GUGCUCG*GC    1

    
    UCGGUGC*GG    1

    
    CGG-CUA*GG    1

    
    CUU-ACU*GG    1

    
    UU--CCC*AG    1

    
    AA---UG*AU    1

    
    G-----A*AU    1

    
    Omitted sequenced and counts

    
    -------*--   19

    
    -------*-A    2

    
    ------U*AC    1

    
    ------U*CG    1

    
    G-----A*-U    1

    
    ------C*-G    1

    
    ------G*-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_99380.1

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

22.22 -61.74 6 3

2

Motif group IL_51191.1

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

11.11 -68.07 7 4

3

Motif group IL_26685.1

Basepair signature:
cWW-L-cWW-L

11.11 -103.37 5 3

Multiple bulged bases

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

11.11 -112.76 3 2

Major groove intercalation

5

Motif group IL_25463.1

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

11.11 -115.34 5 3

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

11.11 -120.98 5 3

7

Motif group IL_00881.1

Basepair signature:
cWW-L-cWW-L

11.11 -142.54 5 3

8

Motif group IL_79895.1

Basepair signature:
cWW-L-cWW-L

11.11 -154.93 5 3

9

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

11.11 -158.29 6 3

Intercalated cWS

10

Motif group IL_56987.1

Basepair signature:
cWW-L-cWW

11.11 -166.50 5 3

Loop 26 Hairpin loop

Column numbers: 551-565 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    -ACA-----------    4

    
    -ACU-----------    3

    
    G----CAAG---GUG    2

    
    -UCAA----------    2

    
    -ACC-----------    2

    
    -UAG-----------    2

    
    G----UCGCACCCUA    1

    
    A----GCUG--CCGG    1

    
    U----AGCA--CUAG    1

    
    C----GCAU---GGA    1

    
    AAAC-A--------A    1

    
    AUUCAA---------    1

    
    C----CAC-----CG    1

    
    G----UAG-----AA    1

    
    U-UAGU--------A    1

    
    U-UAGU--------C    1

    
    CUACG----------    1

    
    GAUAU----------    1

    
    -ACUA----------    1

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

    
    -AAA-----------    1

    
    -AAC-----------    1

    
    -CAC-----------    1

    
    -GAA-----------    1

    
    -UAA-----------    1

    
    -UCA-----------    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_75660.5

Basepair signature:
cWW-F

37.14 -5218.25 2 1

2

Motif group HL_32346.4

Basepair signature:
cWW-F

22.86 -369.39 3 2

3

Motif group HL_56334.1

Basepair signature:
cWW-F

22.86 -373.76 3 2

Mini UNCG

4

Motif group HL_70782.2

Basepair signature:
cWW-F

20.00 -50.76 4 2

5

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

20.00 -74.89 3 2

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

17.14 -74.24 3 2

7

Motif group HL_48778.2

Basepair signature:
cWW-F

17.14 -74.63 2 1

Mini UNCG

8

Motif group HL_13189.1

Basepair signature:
cWW-F-F

17.14 -110.69 4 3

9

Motif group HL_56131.2

Basepair signature:
cWW-F-F

14.29 -92.06 3 2

10

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

11.43 -97.87 3 2

tRNA D-loop

Loop 27 Internal loop

Column numbers: 599-601, 621-622 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    A-C*GU    9

    
    A-G*CU    9

    
    U-G*CU    4

    
    A-A*UU    2

    
    G-G*CU    2

    
    AAC*GU    1

    
    A-G*CC    1

    
    G-C*GC    1

    
    G-G*CC    1

    
    U-G*CA    1

    
    Omitted sequenced and counts

    
    --G*CU    3

    
    --G*CC    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

Basepair signature:
cWW-L-cWW

100.00 16.05 3 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

96.77 26.77 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

83.87 20.12 3 1

Multiple bulged bases

4

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

83.87 17.69 3 1

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

83.87 17.41 3 1

Intercalated cWS

6

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

83.87 3.33 2 1

Single bulged G

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

77.42 13.81 2 1

Major groove intercalation

8

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

77.42 12.70 2 1

Single stack bend

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

77.42 9.65 1 1

Single stack bend

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

77.42 8.02 4 1

Loop 28 Hairpin loop

Column numbers: 603-619 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U---GUAAUCUCA---G   10

    
    U---GUAUUCUCA---A    5

    
    A---GUAGUCUCA---U    3

    
    U---AUAGUCUCA---G    3

    
    U---GUAUUCUCA---G    3

    
    A---GUAAUCUCA---U    2

    
    U---GUAGUCUCA---G    2

    
    GGAGGUAUUCUCAGAAC    1

    
    C---AUAGUCUCA---G    1

    
    U---CAACACUCA---G    1

    
    U---GUAAUCUCA---A    1

    
    U---GUAGUCUCA---A    1

    
    U---UUAAUCUCA---A    1

    
    U---UUAUUCUCA---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 HL_85434.1

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

77.14 -0.71 4 2

2

Motif group HL_94376.1

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

11.43 -22.60 6 5

Pseudoknot geometry

3

Motif group HL_15118.1

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

2.86 -40.18 7 6

4

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

2.86 -43.32 6 5

5

Motif group HL_50418.1

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

2.86 -202.18 6 5

Coloring options: