RNA 3D Hub

JAR3D Query RF02032-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold 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: 9-10, 47-59
  • Loop 2IL Column numbers: 14-17, 42-43
  • Loop 3IL Column numbers: 20-22, 38-39
  • Loop 4HL Column numbers: 26-34
  • Loop 5IL Column numbers: 240-241, 260-262
  • Loop 6IL Column numbers: 241-243, 257-260
  • Loop 7HL Column numbers: 245-255
  • Loop 8IL Column numbers: 272-277, 289-295
  • Loop 9HL Column numbers: 280-286
  • Loop 10IL Column numbers: 306-316, 409-420
  • Loop 11J3 Column numbers: 319-352, 366-371, 405-406
  • Loop 12HL Column numbers: 355-363
  • Loop 13IL Column numbers: 373-375, 401-403
  • Loop 14HL Column numbers: 376-400
  • Loop 15HL Column numbers: 459-469
  • Loop 16IL Column numbers: 483-485, 588-590
  • Loop 17J3 Column numbers: 487-488, 526-534, 580-586
  • Loop 18HL Column numbers: 495-519
  • Loop 19IL Column numbers: 534-535, 578-580
  • Loop 20HL Column numbers: 539-574
  • Loop 21HL Column numbers: 603-619

Loop 1 Internal loop

Column numbers: 9-10, 47-59 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UG*CU--CCCGAAGCA    4

    
    CU*AU--GGCGAUGCG    3

    
    AG*C---CUCAGAGCU    3

    
    UC*AG--AGGUGACCA    2

    
    UU*GU--GACGAGCCG    2

    
    UU*AUGCGUGGUUGCG    1

    
    UU*GGGUGGCGGACCA    1

    
    UU*GGUUGGCGGACCA    1

    
    UU*GUUUGACGAACCG    1

    
    UU*GUUUGACGGACCG    1

    
    UC*GU-GAGGCCAGCA    1

    
    UU*GU-UGGCAGACCG    1

    
    AG*CA--GUGGCAGCU    1

    
    AG*CU--GAGGCAGCU    1

    
    CG*CA--GGUGACGCG    1

    
    GU*UU--UUCGAAGCC    1

    
    UC*AC--GACAGACCA    1

    
    UG*CA--AGACGCGCA    1

    
    UG*CU--GGCGAAGCA    1

    
    UG*CU--GGUAGAGCA    1

    
    UU*AA--GGCAAUGCA    1

    
    UU*AC--GGUGGACCA    1

    
    UU*AU--UUAAGAGCG    1

    
    UU*GU--GAUAGACCG    1

    
    UU*GU--GGCGGACCA    1

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

Motif group IL_18354.1

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

8.57 -39.07 8 4

2

Motif group IL_82968.1

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

2.86 -107.65 8 5

Loop 2 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 3 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 4 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 5 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 6 Internal loop

Column numbers: 241-243, 257-260 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GA-*--UC   10

    
    A-C*GAAU    4

    
    G-G*CAAC    4

    
    A-G*CAAU    3

    
    GG-*--CC    3

    
    G-A*UAAC    2

    
    UGC*AAUA    1

    
    A-A*UAAU    1

    
    G-G*UAAC    1

    
    Omitted sequenced and counts

    
    ---*----    4

    
    U--*--AU    2
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

96.55 30.41 3 1

Multiple bulged bases

2

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

93.10 5.78 2 1

Single stack bend

3

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

89.66 1.59 2 1

Stack and bulge

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

86.21 50.97 4 0

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

86.21 38.56 3 1

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

86.21 20.74 2 1

7

Motif group IL_42771.1

Basepair signature:
cWW-cWW

82.76 7.90 4 1

Multiple bulged bases

8

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

82.76 7.23 4 1

9

Motif group IL_82107.4

Basepair signature:
cWW-cWW

51.72 35.79 2 0

Multiple bulged bases

10

Motif group IL_76709.2

Basepair signature:
cWW-L-cWW-L

51.72 19.20 3 0

Loop 7 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 8 Internal loop

Column numbers: 272-277, 289-295 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    C-A-AG*U-GA--G    4

    
    G-ACAG*C-UU--C    2

    
    U-G-AA*C-GA--U    2

    
    GUA-AA*U-GAGAA    1

    
    CCA-AG*U-GA-GG    1

    
    CGA-UG*CUGA--G    1

    
    AG-UUA*U-CC--U    1

    
    AGG-GA*U-A--CU    1

    
    CU-UUG*C-GG--G    1

    
    GA-CGG*CCUA---    1

    
    GA-UAG*C-UU--C    1

    
    A-A-AC*G-AA--U    1

    
    A-A-AG*C-AA--U    1

    
    A-A-AG*C-GA--U    1

    
    A-A-AG*U-GA--U    1

    
    A-G-AG*U-AA--U    1

    
    AUG-A-*--GA-UU    1

    
    C-G-AA*G-GA--C    1

    
    G-A-AG*C-GA--C    1

    
    G-G-UA*U-CC--U    1

    
    U-A-GA*U-AU--A    1

    
    U-G-AA*G-AC--A    1

    
    U-G-AU*U-GA--C    1

    
    U-G-UA*G-AA--A    1

    
    G-U-GG*C-C---A    1

    
    A-A-A-*--GA--U    1

    
    A-G-A-*--AA--A    1

    
    U-C--G*C-U---A    1

    
    U-G-A-*--GU--C    1

    
    A----A*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_09705.15

Basepair signature:
cWW-tSH-tHS-cWW

45.71 -47.88 3 1

Double sheared

2

Motif group IL_85033.2

Basepair signature:
cWW-cWW-cWW-cWW

42.86 -31.41 4 1

Tandem non-canonical cWW pairs

3

Motif group IL_48444.6

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

34.29 -38.74 4 2

4

Motif group IL_10484.1

Basepair signature:
cWW-tSH-tHS-cWW

31.43 -42.77 5 3

Double sheared

5

Motif group IL_99358.1

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

31.43 -50.73 4 2

6

Motif group IL_80398.1

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

31.43 -57.97 5 2

Minor groove platform

7

Motif group IL_41344.1

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

28.57 -54.29 5 2

8

Motif group IL_58112.2

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

28.57 -61.39 5 2

9

Motif group IL_77691.5

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

25.71 -77.72 4 2

UAA/GAN related

10

Motif group IL_23774.1

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

22.86 -72.85 4 2

UAA/GAN variation

Loop 9 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 10 Internal loop

Column numbers: 306-316, 409-420 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AAAGAGUAA-A*UAAUUGAAAAAU    4

    
    ACCAAAGAC-C*GAGUUGAGUAAU    2

    
    ACGAAAUAC-C*GAGUAGAGUAAC    2

    
    UUGAAAGUU-C*GUGAUGAGUAAG    2

    
    AACAUUCUA-G*CCAAGUCUAAGU    1

    
    AAGAAAGUC-C*GAGAUGAGUAAC    1

    
    AAGAAAGUC-C*GAGAUUAGUAGU    1

    
    AAGAAAGUC-C*GAGGCAAGUAGU    1

    
    AAUGAGUAA-A*UUGAAAAGAAAG    1

    
    ACCAAAAAC-C*GAGUUGAGUAAU    1

    
    ACCAAACAC-C*GAGUCGAGUAAU    1

    
    ACGAAAGUU-C*GUGAUGAGUAAG    1

    
    AUCAAAUAC-C*GAGUAAAGUAGU    1

    
    AUGAAAGGU-C*GAACUGAGUAAU    1

    
    CCCAAACAC-C*GAGUCAAGUAAG    1

    
    GAGAAAGUU-C*GUGAUAAGUACC    1

    
    GAGAACGUU-C*GUAACAAGUACA    1

    
    GCGAAGCGCAC*GGUAGCAG-AAC    1

    
    GUGAAACAA-C*GAUUGGAGUAGU    1

    
    CCUAAAAGC-U*AGCG-GAUUAAG    1

    
    CCUAAAAGC-U*AGUG-GAUUAAG    1

    
    UCGAAAGGU-U*AAAU-AAGUAAG    1

    
    GAGGGGGGU-U*GAAUGGAAU--C    1

    
    GC-GAGUAG-U*GAAUCGAA-AGC    1

    
    GUGAAAUUG-U*GUGAGGA--AGU    1

    
    UCGGAGGAU-U*GGUCCGAUG--A    1

    
    UUAGAAGUU-U*GAG--AAGAAGA    1

    
    GAAAUC-GC-A*GUAA-GAGGA-C    1

    
    GGAAAG----U*GUAGAUAGAA-C    1
No Matches Found View All Results for this Loop

Loop 11 3-way junction loop

Column numbers: 319-352, 366-371, 405-406 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UA-------------------------------A*UGAG-U*AA    3

    
    GU-------------------------------A*UUUAGG*CA    2

    
    GU-------------------------------G*CUUAGA*UA    2

    
    UA-------------------------------G*CGAA-U*AA    2

    
    GGCCGCCUCAACAGAGGACGUCUAUGAAUGGUGA*U--U-G*CA    1

    
    CAC-GUUU-------------------------G*UUAA-C*GG    1

    
    GU-------------------------------A*UUUAGA*UA    1

    
    GU-------------------------------G*CUUAGU*GA    1

    
    GU-------------------------------G*CUUUGU*AA    1

    
    GU-------------------------------U*UUAG-A*UA    1

    
    UA-------------------------------A*CGAG-C*GA    1

    
    UA-------------------------------A*CUAG-U*AA    1

    
    UA-------------------------------A*UAAA-U*AA    1

    
    UA-------------------------------A*UGAA-U*AA    1

    
    UA-------------------------------A*UUCA-C*GA    1

    
    UA-------------------------------A*UUCA-U*AA    1

    
    UA-------------------------------G*CGAA-C*GA    1

    
    UA-------------------------------U*AGAG-U*AA    1

    
    Omitted sequenced and counts

    
    -AGCUUAGACUUUUAGC-GGAGUCU-------U-*--C---*--    3

    
    UA----AGGUGAGGAGGCAUCCUCUU------UA*ACU---*-U    1

    
    UA-----AGUGGUUAGC-ACCACCGA-----AUA*UA----*-A    1

    
    ------GGUGGGUUCGCAGCCCUUUA------CU*AG----*-A    1

    
    -AGCUUAGACCUUUAGC-GGGGUUU-------U-*------*-C    1

    
    ------GAGACGUUAGC-GCGUCUCG------CU*AGA---*--    1

    
    AAC--CGAGUGGGUAGCUCCCAUUU---------*------*-A    1

    
    G-----AGGGCGUAAGC--UGCCCUA------GC*G-----*-A    1

    
    UA------GCGACGGCC-AUCGUU----------*------*-G    1

    
    U--------------------------------A*UUAA-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 J3_80578.1

Basepair signature:
10

56.52 -330.46 4 1

2

Motif group J3_14360.1

Basepair signature:
10

56.52 -387.19 7 2

3

Motif group J3_81015.1

Basepair signature:
11

34.78 -365.23 9 4

4

Motif group J3_47376.1

Basepair signature:
10

8.70 -312.99 9 4

5

Motif group J3_41097.1

Basepair signature:
9

4.35 -322.15 8 4

phi29 pRNA

6

Motif group J3_31041.1

Basepair signature:
12

4.35 -344.92 10 4

Loop 12 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 13 Internal loop

Column numbers: 373-375, 401-403 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GGG*CUC    5

    
    AGU*AUU    3

    
    AGG*CUU    2

    
    AGU*ACU    2

    
    AGU*GUU    2

    
    UGG*CUA    2

    
    AAC*GUU    1

    
    AGA*UCU    1

    
    GGU*AUC    1

    
    UGC*GUA    1

    
    A-A*UAU    1

    
    G-C*GUC    1

    
    G-G*CUU    1

    
    G-C*G-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 IL_31737.3

Basepair signature:
cWW-L-cWW

95.83 33.04 3 1

Stack and bulge

2

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

87.50 46.81 3.5 1

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

87.50 35.93 4 1

Multiple bulged bases

4

Motif group IL_44465.1

Basepair signature:
cWW-L-R-cWW

87.50 32.27 3 1

Isolated non-canonical cWW contact

5

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

83.33 65.50 2 0

Isolated cWS basepair

6

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

83.33 26.62 3 1

Isolated non-canonical cWW pair

7

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

83.33 20.98 2 1

Isolated non-canonical cWW pair

8

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

83.33 14.18 2 1

Isolated non-canonical cWW pair

9

Motif group IL_67095.2

Basepair signature:
cWW-tWW-cWW

83.33 8.28 4 2

Isolated tWW turn

10

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

83.33 7.50 3 1

Isolated non-canonical cWW pair

Loop 14 Hairpin loop

Column numbers: 376-400 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CCGCAA------------------G    5

    
    UCGCAA------------------G    5

    
    GAGGCA-----------------UC    4

    
    GUGGCA-----------------AC    3

    
    CCGGCA-----------------GG    2

    
    UUGCAAAGCGUGGUUUUAAUACCAC    1

    
    AAGGCA-----------------UU    1

    
    GGGGCA-----------------CC    1

    
    UCGGCA-----------------GA    1

    
    UCGGCA-----------------GG    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_85993.1

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

79.17 -338.91 4 2

2

Motif group HL_18565.1

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

70.83 -285.40 4 2

3

Motif group HL_04259.3

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

70.83 -451.92 2 2

GNRA with extra cWW

4

Motif group HL_87553.1

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

58.33 -431.37 3 2

5

Motif group HL_10540.1

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

54.17 -420.63 3 2

6

Motif group HL_37369.2

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

41.67 -330.18 3 2

7

Motif group HL_10453.3

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

41.67 -410.48 3 3

tRNA anticodon loop

8

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

41.67 -507.95 3 2

9

Motif group HL_01609.3

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

33.33 -370.67 3 3

T-loop with 2 bulged bases not stacked

10

Motif group HL_30680.3

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

33.33 -460.31 3 2

Pseudoknot geometry

Loop 15 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 16 Internal loop

Column numbers: 483-485, 588-590 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    G-A*U-C   10

    
    CUU*AGG    3

    
    G-U*A-C    3

    
    U-U*A-A    3

    
    CAG*CUG    2

    
    U-G*C-A    2

    
    CAA*UUG    1

    
    CCU*AGG    1

    
    CUC*GGG    1

    
    CUU*AAG    1

    
    GUA*UAU    1

    
    UAA*UUA    1

    
    UAC*GUA    1

    
    UGG*UUA    1

    
    UUC*GGG    1

    
    C-A*U-G    1

    
    G-G*C-C    1

    
    U-A*U-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_42771.1

Basepair signature:
cWW-cWW

97.14 31.32 3 1

Multiple bulged bases

2

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

97.14 18.27 3 1

Stack and bulge

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

74.29 5.43 3 1

Intercalated cWS

4

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

62.86 6.20 3 1

Major groove platform

5

Motif group IL_84476.1

Basepair signature:
cWW-cWW

60.00 -22.13 3 2

Multiple bulged bases

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

57.14 3.37 3 1

7

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

57.14 -3.56 2 1

Single stack bend

8

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

57.14 -4.93 2 1

Single stack bend

9

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

57.14 -5.46 2 1

Major groove intercalation

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

57.14 -7.07 3 1

Loop 17 3-way junction loop

Column numbers: 487-488, 526-534, 580-586 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AU*G-GACA-AG*CAAAAGU    3

    
    AU*G-GAUA-GG*CUAAAGG    3

    
    AU*G-GACAAUG*CGAAAGA    2

    
    AU*G-GAUA-AG*CAAAAGU    2

    
    AU*G-GAUA-CG*CAAAAGA    2

    
    GU*G-GAAA-UC*GUAAAGU    2

    
    UU*G-GAAA-CG*CCAAAGA    2

    
    AG*G-GAUG-UC*G--AGGU    2

    
    UU*GUGUGUAAA*UAAAAUA    1

    
    GU*G-GACAAAA*UCAAAGU    1

    
    AG*G-GAUA-AG*CAAAGGU    1

    
    AU*G-GACA-AA*GCAAAGG    1

    
    AU*G-GACA-AG*CAAAAGA    1

    
    AU*G-GACA-CG*CAAAAGA    1

    
    AU*G-GAUA-AG*CGAAAGG    1

    
    AU*G-GAUA-CA*CUAAAGA    1

    
    AU*G-GAUA-UU*AUAAAGG    1

    
    CU*G-GACA-AG*CGAGAGG    1

    
    GU*G-GAAA-AU*AGAAAGC    1

    
    UU*G-GAAA-CA*UUAAAGA    1

    
    UU*G-GAAA-CG*CUAAAGA    1

    
    UU*G-GAAA-CG*UAAAAGA    1

    
    UU*G-GAAA-CG*UCAAAGA    1

    
    UU*G-GAAA-CG*UUAAAGA    1

    
    UU*G-GAUA-AA*UGAAAGA    1
No Matches Found View All Results for this Loop

Loop 18 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 19 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 20 Hairpin loop

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

    
    GAA----------ACA---------------AUAAU    4

    
    UAA----------ACU---------------AUAAG    3

    
    GAA----------ACC---------------AUAAU    2

    
    GAA----------UAG---------------AUAAU    2

    
    GAA-CCAAAGGGG----UCGCACCCUACGG-AUAAU    1

    
    GAACGUCUU-ACU----AGCA--CUAGGACGAUAAU    1

    
    GAAGCAGUGCUCG----CAAG---GUGCUGUAUAAU    1

    
    GAAGGUAUGCUCG----CAAG---GUGUACUAUAAU    1

    
    GAACACCGG-CUA----GCUG--CCGGG-AGAUA-U    1

    
    GAAGCCUCGGUGC----CAC-----CGGGGGAUAAU    1

    
    GAAGCCUU--CCC----GCAU---GGAGGGUAUAAU    1

    
    GAACCCAA---UG----UAG-----AAUGGGAUAAU    1

    
    GAAACC------U-UAGU--------ACGGUAUAAU    1

    
    GAAACC------U-UAGU--------CGGGUAUAAU    1

    
    GAA-CCG-----AAAC-A--------AUGG-AUAAU    1

    
    GAA-CCG-----AUUCAA---------UGG-AUAAU    1

    
    GAAGGG------CUACG----------GCU-AUAAU    1

    
    CAA-CC------GAUAU----------AGG-GUAAU    1

    
    GAACAA-------ACUA----------AUU-AUAAU    1

    
    GAAA---------UCAA----------A---AUAAU    1

    
    GAA----------UCAA--------------AUAAU    1

    
    GAAC---------CAC---------------AUAAU    1

    
    GAA----------AAA---------------AUAAU    1

    
    GAA----------UAA---------------AUAAU    1

    
    GAA----------UCA---------------AUAAU    1

    
    UAA----------AAC---------------AUAAG    1

    
    UAA----------GAA---------------AUAAG    1

    
    C------------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_23010.1

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

37.14 -1483.24 6 4

2

Motif group HL_88558.1

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

37.14 -1557.05 5 4

3

Motif group HL_91939.2

Basepair signature:
cWW-tSH-tHH-tWW-F-F-F

31.43 -381.76 7 5

4

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

28.57 -1530.53 6 5

5

Motif group HL_50418.1

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

22.86 -2736.64 6 5

6

Motif group HL_20781.1

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

22.86 -3448.23 6 4

7

Motif group HL_53504.3

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

11.43 -1718.21 5 4

8

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

8.57 -1385.23 6 4

9

Motif group HL_75293.5

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

8.57 -1749.03 7 5

10

Motif group HL_25847.2

Basepair signature:
cWW-F-cSH-tHW-F-F-F

8.57 -2603.41 5 4

Loop 21 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: