JAR3D on RF03087

RF03087 ROOL RNA

Input Summary

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........................(((((..............((..(((((............))))).)))))))(..((((.(((.......................(((..(((.....(..((.((..((((....................))))..)).)).)......).))..))).(((.((.(...((((.(................................)).))).).)).)))....(((((.................................))))).........).....................................))).)).).)............................................................((((.((.......................((((...............(.)...................)))).............()((((((..........((((.............((((................)))).....))))................................................))))))............................................................................................................................)))))).......().....((.....((((((................)))))).))........................((.........((((((......()........................................................................................(.....).................))))))........)).((.(((.........................))).))(((((................................(((((.................................................................)))))....((((((((..(((.(((..(((((.())....))))..)))...................................................)))......))))))))..)))))..................................................((((...................))))......................
>URS0000D6BDF8_12908_1-591
CCCUCACUGCUUA--UAUGAGGAAGCGUG-UGU--------AUA---AACCU--AUGACA----GGGUU---CACGCC--AUUC-AAUCUAUAAAUCGAC-----------AG---CGAC----G--UU-CU--GCCG-----------G-GAUA--CCGAC--GG-AA-UU-----U-CAGA-CA-AGC-CA-A---AG---G-------------GUAA---------------UA-GCU-U-UG-GUU-GACCUACACC--------GAAAAGGAAAUA---------GGUGUCG------UU-------------------------------------GGUUG-AG-UGAGAAAGCA-------UUAAAUU-------A----UUGAUAAAGUAGGCAAC--AAUGUCAG-CAG-AAUUACAAU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCCGGCGGAGAUUUAGGCGCUCCGUGUAAAGCAGUCUCACGCUAAUCUGGCAGACAUGUCAGGGAACCACGAGAUAAAUGUAAGUUA-----------------------AAA-UUCUGG-----UCCACGAUGAU-----CCGCA----GAAA----------UGCGG-GUAUAA-CUGAUACG-----UGCCGUACGAGUA----GCCCAAAA--CGUGGAAAUUACAAUACAGGUUUUUGCAUAA-----------------------------------------------------CCAUCAAUCGCAUUG-----------------UUGGGU----GAAAGUUGG-AGG----------A--UAAAU-------CCU-CACCAAGAUUUAAA-------------------------------------------------------------------------------------------------------UUAAGCAAG-AGA--UAU--AAGGCCGCU----CCUU--AUA----------------------------------------------------UUGCGA--CUUGCUUAAACUUG-UGACU-GAAUA---AUCAAC-----------GAUUUAACAAGUUCAA---GUGGUUAAUAG------------CCAC-CCG-CAUAACUAGGAAUAUAG
>URS0000D66DD5_575596_1-591
CCCUCACUGCUUA--UAUGAGGAAGCGUG-UGU--------AUA---AACCU--AUGACA----GGGUU---CACGCC--AUUC-AAUCUAUAAAUCGAC------------AG--CGAC----G--UU-CU--GCCG-----------G-GAUA--CCGAC--GG-AA-UU-----U-CAGAC--AAGC-CA-A---AG---G-------------GUAA---------------UA-GCU-U-UG-GUU-GACCUACACC--------GAAAAGGAAAUA---------GGUGUCG-----UUGA--------------------------------------UUG-AG-UGAGAAAGCA-------UUAAAUU-------A----UUGAUAAAGUAGGCAAC--AAUGUCAG-CAG-AAUUACAAU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCCGGCGGAGAUUUAGGCGCUCCGUGUAAAGCAGUCUCACGCUAAUCUGGCAGACAUGUCAGGGAACCACGAGAUAAAUGUAAGUUA-----------------------AAA-UUCUGG-----UCCACGAUGAU-----CCGCA----GAAA----------UGCGG-GUAUAA-CUGAUACG-----UGCCGUACGAGUA----GCCCAAAA--CGUGGAAAUUACAAUACAGGUUUUUGCAUAA-----------------------------------------------------CCAUCAAUCGCAUUG-----------------UUGGGU----GAAAGUUGG-AGG----------A--UAAAU-------CCU-CACCAAGAUUUAAA-------------------------------------------------------------------------------------------------------UUAAGCAAG-AGA--UAU--AAGGCCGCU----CCUU--AUA----------------------------------------------------UUGCGA--CUUGCUUAAACUUG-UGACU-GAAUA---AUCAAC-----------GAUUUAACAAGUUCAA---GUGGUUAAUAG------------CCAC-CCG-CAUAACUAGGAAUAUAG
>URS0000D6B8CE_12908_1-588
GUCCGUCCGUAGUCUUAGGCAAAACCUAUCUGU--------AA----GGGCA--UUGACA----AGCCU-AGGUAGGUGCGUAA-CCUUAAAAUC-----------------CG-UGAAG----C-------------------CGUCCGUGUCU---------------GA-----U-UA--AG-GUAC-UG-A---UUGU-G-------------AUGA---------------CGAUAG-U-AA-GUC---AGCAGGUG--------GAAG-----------------CACUUGU--ACGGU----------------------------------------GGU-UA-CUGCAGCCU--------CAUAUACAU-----GAA--UGACUGAUGUAGAG-----UUCGGUUGGAGC-G-AC--AAG---UAU--U-------UAGC---------------UUGAGAU--------------AGCUA-A----A-----U-CACCUCG---GUAUGA-UU---------------AGG----GUGAGA--------CCU-------AGGAACCGU-----------------------------------------AGGGGUA---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA---GCUU------UUGCAGUGACG----CCCAU----GUAA----------GUGGG-AUAUAA-CAACAGAA------CUCGUAUGAGUA----GCCUAAUU-CUGCAACCCUCUUUAGGGUAUGUGUUAGCCAUAUUUUAGGAUGGAAACAUGAAUACAAGAUAU-------------------------AUUUACUCUUG------------------UUAGGU----GAAAGUUGA-UGG-------UC-G--CCGUG-------UCAGUCCAUGCCUUUGAAAAC-----------------------------------------------------------------------------------------------------AGUUCUA------------------------------------------UGUAGUAGGGAGUCGAGAACCUAUGA--------------------GAGU---UAGAACUU-GCACGAAACAUUCUAU--UGUCUGCA--------GUGUAUGUGUG-------GUAGGGCUAAAA--------------ACCC-UUG-CCUAUU-UUAUAAGUUC
>URS0000D6BFAD_12908_1-562
---------GGUUUUAGGCAAAACCUAUC-UGU--------AA----GGGU---GUGACGA----GCCU--AGAUAGG--UACU-UAACCUCUAAUU--------------CGA--UAAG----C--CGUCAGUGUCC-------------GAUA---GGGUACUGAUU-GUG----A-UG--ACGA-------C-U--------------------AGAA---------------------AG--------UCAGCGGGUG--------GAAG-----------------CAUCUGU-GCGUGGGU--------------------------------------UAG-GU-AGCCUC-----------AUAUACAU------GAA--CGACUGAUGUAGAG-----UUCGAUUGGGGA-G-AU--AAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUCUAAUGCGUGUCAUUAGGUCACCUCGGUAUGACUAGGGUGAGAGCUAGGAACCGUAGAGGUGUUCUCAAGG------------------------------------GAA---UCCU------UUGCAGUGAC-----GUCCUC---GUAA---------GUGGAC--UAUAA-CAGUAGAA------CUCGUAUUAGUA----GCCUAAUA-CUGCAGCCCUUUUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUAUUACAAGAU----------------------------AUUUACUCUUG------------------UUAGGU----GAAAGUUGA-UGG-------UC-G--CCGAG-------CCAGUCCGUACAUCCAAAAAG-----------------------------------------------------------------------------------------------------GACUCUA------------------------------------------UGUAGUAGGAAGUCGAGAGCCUAUGA--------------------GAGU---UAGAGUCG-GUACGAAACA-UCUAU---UGUCUGCA--------GUGUAUGUGUUG-----GUAGGGCUAAAA--------------ACCC--UU-GCCUAUUU---------
>URS0000D66B34_12908_1-561
---------GGUUUUAGGCAAAACCUGUC-UGU--------AA----GGGU---GUGACGA----GCCU--AGAUAGG--UACU-UAACCUCUAAUU--------------CGA--UAAG----C--CGUCAGUGUUC-------------GAUA---GGGUACUGAUU-GUG----A-UG--ACGA-CU---------------------------AGAA---------------------------AG--UCAGCAGGUG--------GAAG-----------------CAUCUGU-GCGUGGGU--------------------------------------UAG-GU-AGCCUC-----------AUAUACAU------GAA--CGACUGAUGUAGAG-----UUCGAUUGGGGA-G-AU--AAG---UAUC-U-------AAUG---------------CGUGU-----------------CAUU-A----G-----GUCACCU-----C------GGUAUGA----------CUAG--GGUGAGAG------CUAG----GAACCGUAG----------------------------------------------GGGUG---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA---UCCU------UUGCAGUGAC-----GUCCUC---GUAA---------GUGGAC--UAUAA-CAGUAGAA------CUCGUAUUAGUA----GCCUAAUA-CUGCAGCCCUUUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUAUUACAAGAU-----------------------------AUUUACUCUUG------------------UUAGGU----GAAAGUUGA-UGG-------UC-G--CCAAG-------CCAGUCCGUACAUCCAAAAAG-----------------------------------------------------------------------------------------------------GACUCUA------------------------------------------UUUAGUAGGAAGUCGAGAGCCUAUGA--------------------GAGU---UAGAGUCG-GUACGAAACA-UCUAU---UGUCUGCA--------GUGUAUGUGUUG-----GUAGGGCUAAAA--------------ACCC--UU-GCCUAUUU---------
>URS0000D6570B_12908_1-579
AUCCGACCGUAGUCUUAGGUAAAACCUAUCUGU--------AA----GGGU---UUGACAA----GCCU-AGAUAGGUACUUAA-CCUCUAAAUCGAU-----------------AAGCC----G-UCA-GU--GUCC-------------GAUG---GGGU--AC-UGAUU-----G-U----G--AUG-ACG-AUA-------------------GUAA------------------------GU-CA--GCAGGUGG----------AAA--------------------C-ACU-UUGUGCGUG-------------------------------------GGU-UA-GGUAGC-----------CUCAUAUACAU---GAA--CGACUGAUGUAGAG-----UUCGGUUGGGGA-G-AU--AAG---UAUC-U-------AAUG---------------CGUGU-----------------CAUU-A----G-----GUCACCU-----C------GGUAUGA----------UUAGU--GUGAGA------GCUAG----GAACCGUAG----------------------------------------------GGGUG---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA---UCCU------UUGCAGUGAC-----GUCCUC---GCAA---------GAGGAC--UAUAA-CAACAGAA------CUCGUAUUAGUA----GCCUAAUAC-UGCAGCCCCUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUUGAAUCAAG---ACAU------------------------AUUUACUCUUG------------------UUAGGU----GAAAGUUGG-UGG-------UU-G--CCAUG-------CCA-GCCCGUACAUCCGAGAAG----------------------------------------------------------------------------------------------------GACUCUA------------------------------------------UGUAGUAGGAAGUCGAGAGCCUAUGA--------------------GAGU---UAGAGUCGGUACG-AAACA-UCUA---UUGUCUGCA-----GUGUAUAUUGG---------GUAGAGCUAAAA--------------ACUC-UUA-CCUA---UUUUAUUAAG
>URS0000D66442_12908_1-591
AUCCGACCGUGGUUUUAGGCAAAUCCUAUCUGU--------AA----GGGCU--UUGACA----AGUCU-AGAUAGGUGUUUAA-CCUUUAAAUAC---------------CGA--UAAG----C--CGUCCGUGUCC-------------GAUAU--GGGUACGGAUU-GUG----A-UG--ACGA-------C-U--------------------AGAA---------------------AG--------UCAGCAAGUG--------GAAG-----------------CACUUGU-----GCGUA-------------------------------------GGU-UA-AGCAGCCU---------CAUAUACAU-----GAA--AGACUGAUGUAGAG-----UUCGGUUGGAGC-G-AC--AAG---------UACC-UA-GCUU--------------GAGA-----------------UAGU-UA-GGUC--------GCCU-----U------GGUAUGA----------CUAGU--GUGAGAA-----GCUAG----GAACCGUAG----------------------------------------------AGGUA----------------------------------------------------------------------------------------------------------UCUCAAA----AACAA---GCUU------UUGCAGUGAC-----GUCCUC---GUAA---------GUGGAC--UAUAA-CAACAGAA------CUCGUAUUAGUA----GCCUAAUU-CUGCAAUCCCUUGGUUGGGAAGUGUUGUCCAUAUAGUUCAAGAUGGAGACAUGAAUACAAGAUUA-----------------------UAUUACUCUUG------------------UUAGGU----GAACGUUGG-UGG-------UC-G--UCGAG-------CCA-GCCCCUCCUUUGUAAAG-----------------------------------------------------------------------------------------------------GACUCUA------------------------------------------UGUAGUAGGAAGUCGAGAGCCUAUGA--------------------GAGU---UAGAGUCG-GAGAGAAACA-UCUA---UUGUCUGCA-------GUGUAUGUGUG-------GUAGAGCUAAAA--------------ACUC-UUG-CCUAUUUUAUAAGUUCC
>URS0000D6A43E_12908_1-580
UAUAUUAUAGAAGACGCUGCUGAUACGGA-UGU--------AUA---ACGGA--CUGAUAA---UCCUU---UCCGUAA-AUUG-CCUGUAAGUC----------------AGA--UAAG----G--CGAACAGCAAG-------------GAUA---CCUGCUGUUUU-CU-----G-AA--UCU-UGGAGA-U---A------------------UUCU--------------------U-A-UCAGAG-AUAGGUC-----------CAAAA-------------------GACU-UUCUGCCA--------------------------------------GGC-GA-UGUUAG-----------UCAAUGUAUUUC-------AGCGUAAGGCUUUUU----CUGAGCUGGCAA-GCAC--AAU---AAGU-U-GAU----------------------GUGAA----------------------A-AUCA-----GCUUGCA-----UCAG---GGUUUUUGACCUA-AUAUUAAG--GCGGAAAA----CUUAA-UUGGAACCUCAA----------------------------------------------UGUAA---------------------------------------------------------------------------------------------------------UGACCAA-------CAA-GCUUGU------UUGCUGUGAC-----GUAUGC---GAUCAAAA-----GCAUGC--UAUAA-CAGGUCAG-----AAAAGAACGAGUA----GCUUAAUC--GGCAAGAUUAAAUGAUACUAUUAGGUACAAUAUAUA--------------------------------------------------GAACGCACA---------------------UCAAGU----GAAAGUUUA-CGG-------UA-A--GCAAU-------CCG-UUUAGGACUUCGGUA------------------------GGUU-----------------------------CUUUG---------------------------------AACC---CAACGCAAG---------------------------------------AAAGAAGCAUAAAUAGCUAAUCUGUGGGCGGU----------------------CUUGU--UA-UCCUAUGGCU-GAAUA---AAGAAAA-----GAAAAGUA-UGAA---------------------------------------AAG-CAUAUUUUCCUAACGUU
>URS0000D6C6B5_748671_1-581
UAUAUUAUAGAAGACGCUGCUGAUACGGA-UGU--------AUA---ACGGA--CUGAUAA---UCCUU---UCCGUA--AAUU-ACCUGUAAGUC---------------AGA--UAAG----G--CGAACAGCAAG-------------GAUA---CCUGCUGUUUU-CU-----G-AA--UCU-UGGAGA-U---A------------------UUCU--------------------U-A-UCAGAG-AUAGGUC-----------CAAAA-------------------GACU-UUCUGCCA-------------------------------------GGCG-AU-GGUAGUCA---------AUGUAUUUC----------AGCGUAAGGCUUUUU----CUGAGCUGGCAA-GCAC--AAU---AAGU-U-GAU----------------------GUGAA----------------------A-AUCA-----GCUUGCA-----UCAG---GGUUUUUGACCUAAUAAUUAAG--GCGGAAAA----CUUA-AUUGGAACCUCAA----------------------------------------------UGUAA---------------------------------------------------------------------------------------------------------UGACCAA-------CAA-GCUUGU------UUGCUGUGAC-----GUAUGC---GAUCAAAA-----GCAUGC--UAUAA-CAGGUCAG-----AAAAGAACGAGUA----GCUUAAUC--GGCAAGAUUAAAUGAUACUAUUAGGUACAAUAUAUA--------------------------------------------------GAACGCACA---------------------UCAAGU----GAAAGUUUA-CGG-------UA-A--GCAAU-------CCG-UUUAGGACUUCGGUA------------------------GGUU-----------------------------CUUUG---------------------------------AACC---CAACGCAAG---------------------------------------AAAGAAGCAGAAAUAGCUAAUCUGUGGGCGGU----------------------CUUGU--UA-UCCUAUGGCU-GAAUA---AAGAAAA--------GAAAAGUAU---------GAA----------------------------AAG-CAUAUUUUUCUAACGUU
>URS0000D66891_12908_1-580
UAUAUUAUAGAAGACGCUGCUGAUACGGA-UGU--------AUA---ACGGA--CUGAUAA---UCCUU---UCCGUA--AAUU-GCCUGUAAGUC---------------AGA--UAAG----G--CGAACAGCAAG-------------GAUA---CCUGCUGUUUU-CU-----G-AA--UCU-UGGAGA-U---A------------------UUCU--------------------U-A-UCAGAG-AUAGGUC-----------CAAAA-------------------GACU-UUCUGCCAG-------------------------------------GCG-AU-GGUAGUCA---------AUGUAUUUC----------AGCGUAAGGCUUUUU----CUGAGCUGGCAA-GCAC--AAU---AAGU-U-GAU----------------------GUGAA----------------------A-AUCA-----GCUUGCA-----UCAG---GGUUUUUGACCUA-AUAUUAAG--GCGGAAAA----CUUAA-UUGGAACCUCAA----------------------------------------------UGUAA---------------------------------------------------------------------------------------------------------UGACCAA-------CAA-GCUUGU------UUGCUGUGAC-----GUAUGC---GAUCAAAA-----GCAUGC--UAUAA-CAGGUCAG-----AAAAGAACGAGUA----GCUUAAUC--GGCAAGAUUAAAUGAUACUAUUAGGUACAAUAUAUA--------------------------------------------------GAACGCACA---------------------UCAAGU----GAAAGUUUA-CGG-------UA-A--GCAAU-------CCG-UUUAGGACUUCGGUA------------------------GGUU-----------------------------CUUUG---------------------------------AACC---CAACGCAAG---------------------------------------AAAGAAGCAUAAAUAGCUAAUCUGUGGGCGGU----------------------CUUGU--UA-UCCUAUGGCU-GAAUA---AAGAAAA--------GAAAAGUAU---------GAA----------------------------AAG-CAUAUUUUCCUAACGUU
>URS0000D6A595_12908_1-556
AUCCUACUCCCCGAAUACACCAAAGGGCA-UAA--------UU----CCAC---UUAGCAA----GUGG---UGCCUGG-GUUA-UCUUGUUAAGACC-------------UGC--AAUU----G--UGGUA--UAGG-------------GAUA---CCUU--UACUA-UU-----G-UU--G---UUC---------------------------CAGA---------------------------GUG-G-AGACCG----------GUGAAA-----------------UGGUU-CAGGCUGA--------------------------------------GAU-AA-CUUGCGA----------GAC--GGUGC----GA---AAAACAAGGUGCUC-----UGCGAAUCGUCG-CAAC--AAG---UGUC-A-GUG-AACGGG---------------AUUCG-----------------UCCU-AUAGCU-----GGCCGCAAC---AGUGAA-UCU--------------GAG----GUGACA--------CUU-----AGGGAACCAAA-----------------------------------------GUUGUG-----------------------------------------------------------------------------------------------------------UGUCGAA------CAA-UGCGAU------UGUAGUUGAU-----GUUGCG---GUAA---------CGUAAC--UAUAA-GAUUUUCG------GAGGCAC-----UCAGGCAAAAU---CUACGUUGGAUAUAACGUUUACGUAUGGGUAAAAAAAUCUA------------------------------------------------UUAUGUGGU------------------GCUUGUUUGA----GUUGG-GGU-------UG----UUGAU-------ACU-UCCCACGCUUUAAAAA--------------------------------------------------------------------------------------------------------GGCUAG-----------------------------------------GUCAACCGGAGUUGCAAACCGGGG--------------------CCAUUC--CUAGUCAG--CGUG-UAACCUUAACA---GUUUGCA-------GCGCUAAGUCGA-------GUAGGAAAAAC---------------AUCC-UGG-UGUUUCACGGGUGGUAG
>URS0000D662C4_12908_1-471
ACAACCGCAUAUAUUGCCCUAAAACCAUU-UUG--------UAA---UCAGA--ACACCA----UCUGA---AAUGGA--CGUA-AA------------------------CGUGCUGAA----C--AAAAU--AACG-------------GAUA---CGUU--AUCUA-CA-----U-AAGCACG---------------------------------------------------------------------------------------------------------------------------------------------------------------UCU-GC-GGUACA-----------UC-AUAUUGU----UUG--UAGAAAAGGUACACA------CGACUACUCA-ACGC--AAU---AGCA-G-GAG------UU--------------CUAGG----------------AA------CUCU-G---AAAGACA-----AAACGG-CUA--------------UUC--CCGUGGAAC-------GAA-----AUGGGUACGC--------------------------------------------UGCCA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-GUUGAG------GUGCGGU--------------------------------------UAUCCAUAGUCUG------UGUG-GUC-----ACGAGCCUAAAUC-CGCACAAAAUUAAAAA--------------------------------------------------------------------CAAUUUUGCUGAAUG-----------------GUAGGUGAGU----G-UGA-AG--------GACA---------------CU-UCCGUAACUCGAC--------------------------------------------------------------------------------------------------------ACGGUACGG-AAGU-CAA--AUGGUAGCU----CCAU--UUG---------------------------------------------------GCUCAGC--CCGUACUA--UUAUGUGACU-GAAUA---UUCUGU--------GCAAUGUAGAUGU-------------UUGUAUAAGCCGUACACUA-----UCG-UGGCGGUGAAAACGUUA
>URS0000D6ABA7_362948_1-544
UUAGUAUAUAAGUGUACCGAUGAAGCUAG-UGG--------AU----GAGGU--GUGACAA---GCCGC---CUAGCCA-UACGACUCUUAAUAACUACU-----------AU---GACG----A--AA-UA--UACG-------------GAUA---CGUU--UA-UU-UU-----U-UCUA-AU-UUC-CA-C---UUGG---------------GUAGUA--------------C-UAA-U-UG-GGA-G-CAACGA----------AAAAAG-----------------UUGUG-UAGAGAGA--------------------------------------AGC-A--AGGGGA-----------CUCAUAUCU-----G----AAACUAAGACACUUGC-----CGUCAGGGAU-UCGC--AAU---AUGC------------------------------------------------------------C-------AUCUUC----A------GUUAAU-----------UAAGG--CUGAUUA-----CCUUA----GGAACCAAAA--------------------------------------------GAAGAA----------------------------------------------------------------------------------------------------------UAUCAAC------UAA-GAAUUC------GUGUCGUGAA-----GUUGUG---GUGA---------CGCAAC--UAUAA-CUGACGAG-----UAAGGUUUGAGUA----GCCAAAAUC-GACAAUCUUACAUUAACUGG----------------------------------------------------------------AACAUUGCACAUG-------------------UUUGGU----GAAAAUUGG-AUAG------GA-A--AAGAU------CUAUGCCCUGAACUUGAAAU------------------------------------------------------------------------------------------------------GCGGACUAG-GU---CGUG-GAAGUUGCU-----AGC-CAUG-----------------------------------------------------AUGUG--CUAGUCUGA-UUCAGUAGUC-UAAUA---AGUCC----------AGAUACAAGA-----------GUAUCCCACGUAAGCCA------AUACGCGU-CGGUUUACAUAAUUUUU
>URS0000D6ABA7_768728_1-544
UUAGUAUAUAAGUGUACCGAUGAAGCUAG-UGG--------AU----GAGGU--GUGACAA---GCCGC---CUAGCCA-UACGACUCUUAAUAACUACU-----------AU---GACG----A--AA-UA--UACG-------------GAUA---CGUU--UA-UU-UU-----U-UCUA-AU-UUC-CA-C---UUGG---------------GUAGUA--------------C-UAA-U-UG-GGA-G-CAACGA----------AAAAAG-----------------UUGUG-UAGAGAGA--------------------------------------AGC-A--AGGGGA-----------CUCAUAUCU-----G----AAACUAAGACACUUGC-----CGUCAGGGAU-UCGC--AAU---AUGC------------------------------------------------------------C-------AUCUUC----A------GUUAAU-----------UAAGG--CUGAUUA-----CCUUA----GGAACCAAAA--------------------------------------------GAAGAA----------------------------------------------------------------------------------------------------------UAUCAAC------UAA-GAAUUC------GUGUCGUGAA-----GUUGUG---GUGA---------CGCAAC--UAUAA-CUGACGAG-----UAAGGUUUGAGUA----GCCAAAAUC-GACAAUCUUACAUUAACUGG----------------------------------------------------------------AACAUUGCACAUG-------------------UUUGGU----GAAAAUUGG-AUAG------GA-A--AAGAU------CUAUGCCCUGAACUUGAAAU------------------------------------------------------------------------------------------------------GCGGACUAG-GU---CGUG-GAAGUUGCU-----AGC-CAUG-----------------------------------------------------AUGUG--CUAGUCUGA-UUCAGUAGUC-UAAUA---AGUCC----------AGAUACAAGA-----------GUAUCCCACGUAAGCCA------AUACGCGU-CGGUUUACAUAAUUUUU
>URS0000D6BA83_1423799_1-550
UUAGUAUAUAAGUGUACCGAUGAAGCUAG-UGG--------AUAA--GGU----GUGACAA-----GCC-GCCUAGCCAU-ACGUCUCUUAAUAACUACU-----------AU---GACG----A--AA-UA--UACG-------------GAUA---CGUU--UA-UU-UU-----U-UCUA-AUUUCC-A--C---UUGG---------------GUAGUA--------------C-UAA-U--U-GGGAG-CAACGA----------AAAAAAG----------------UUGUG-UAGAGAGA--------------------------------------AGC-A---AGGGG-----------ACUC--AUAUCU--G----AAACUAAGACACUU-----GCCGUCAGGGAU-UCGC--AAU---AUAC------------------------------------------------------------C-------AUCUUU----A------GUUAAU-----------UAAGG--CUGAUUA-----CCUUA----GGAACCAAC---------------------------------------------GAAGAA----------------------------------------------------------------------------------------------------------UAUCAAU------UAA-GAAUUC------GUGUCGUGAA-----GUUGUG---GUGA---------UGCAAC--UAUAA-CUGACGAG-----UAAGGUUUGAGUA----GCCAAAAUC-GACAAUCUUAUAUUAACAGAAAUA------------------------------------------------------------UGGACAUUACACAUG-----------------UUUGGU----GAAAAUUGG-AUAG------GA-A--AAGGU------CUAUGCCCUGAACUUGAAAU------------------------------------------------------------------------------------------------------GCGGACUAG-GU---CAUG-GAAGUUGCU----A-GC-CAUG-----------------------------------------------------AUGUG--CUAGUCUGA-UUCAGUAGUC-UAAUA---AGUCC-------AGAUACAAGAGUAUC---------------CCACGUAAGCCAAUACG-----CGU-CGGUUUACAUAAUUUUU
>URS0000D67A33_12908_1-558
UACGACUAACUUCUCAAAUACAAUGCUGG-UGG--------AGA---GCAG---CUAACAA----CUGU--GCCAGCG--GCGC-UCGGAAGACG------------------A--UGAG----CUGAACCG--CAAG-------------GAUA---CUUG--CGGCA-AG-----G-CG----------------------------------------------------------------------------------------------------------------------ACGGACUAAUCACCCCUGUGUCAA----------------------GAG-CG-UGCACU-----------CUCU--CUCAAUG-UA---AACCAAAUGCAACA-----UAUAGGUCGUGA-GCAG--AAU---AUGG-G-------GCGGU--------------UUAAUC---------------GCCGC-A----C-----CAAUCUGAG---UUAG---GUGGU------------AGC----CCGCAA--------GCG-----CCACAAAC--------------------------------------------CUUAGAA---------------------------------------------------------------------------------------------------------A-CGCAC-------CAA-GCUC-U------UAGCCGUGAC-----GGGCA----GAAA----------UGUCC--UAUAA-GACCUUAA-UGAUUUGGGUAA-----UCUCGCUUAA----GGCUAGCUCAAACUAGAAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC-----------------------------------UUUUAUACGGAAC------------------GUAGGUGAGA----UUUGC-GGG-------UA-AAGGUAAU-------CCC-GCCGCAGACCAG---------------------------UCC------------------------------GCAA-----------------------------------GGG---UGGGGCUUC-AAGC-UGU--CGAGUCGCU----CUCG--GCA---------------------------------------------------UCUCCGU--GGAGUCUC--CUGCGUGGCA-GAA-----CGGAG------CAUUGAAUAAGAGG--------GUACUCGGAAG---------------UCUG-AGA-GGACGACGAGUGGAAAG
>URS0000D6AC61_12908_1-559
ACUUGACUAACUUCUCAAUACAAUGCUGG-UGG--------AGA---GCAG---CUAACAA----CUGU--GCCAGCG--GCGC-UCGGAAGACG------------------A--UGAG----CUGAACCG--CAAG-------------GAUA---CUUG--CGGCA-AG-----G-CG----------------------------------------------------------------------------------------------------------------------ACGGACUAAUCACCCCUGUGUCAA----------------------GAG-CG-UGCACUUU---------CUC----UCAAUG-UA---AACCAAAUGCAACA-----UAUAGGUCGUGA-GCAG--AAU---AUGG-G-------GCGGU--------------UUAAUC---------------GCCGC-A----C-----CAAUCUGAG---UUAG---GUGGU------------AGC----CCGCAA--------GCG-----CCGCAAAC--------------------------------------------CUUAGAA---------------------------------------------------------------------------------------------------------A-UGCAC-------CAA-GCUC-U------UAGCCGUGAC-----GGGCA----GAAA----------UGUCC--UAUAA-GACCUUAA-UGAUUUGGGUAA-----UCUCGCUUAA----GGCUAGUCCAGACAAGAAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC-----------------------------------UUUUAUACGGAAC------------------GUAGGUGAGA----UUUGC-GGG-------UA-AAGGUAAU-------CCC-GCCGCAGACCAG---------------------------CCC------------------------------GCAA-----------------------------------GGG---UGGGGCUUC-AAGC-UGU--CGAGUCGCU----CUCG--GCA---------------------------------------------------UCUCCGU--GGAGUCUC--CUGCGUGGCA-GAA-----CGGAG------CAUUGAAUAAGAGG--------GUACUCGGAAGUC-------------UGAG-AGG-A-CGACGAGUGGGAAGG
>URS0000D6A23B_12908_1-558
ACUUGACUAACUUCUCAAUACAAUGCUGG-UGG--------AGA---GCAG---CUAACAA----CUGU--GCCAGCG--GCGC-UCGGAAGACG------------------A--UGAG----CUGAACUG--CAAG-------------GAUA---CUUG--CGGCA-AG-----G-CG----------------------------------------------------------------------------------------------------------------------ACGGACUAAUCACCCCUGUGUCAA----------------------GAG-CG-UGCACUUU---------CUC----UCAAUG-UA---AACCAAAUGCAACA-----UAUAGGUCGUGA-GCAG--AAU---AUGG-G-------GCGGU--------------UUAAUC---------------GCCGC-A----C-----CAAUCUGAG---UUAG---GUGGU------------AGC----CCGCAA--------GCG-----CCGCAAAC--------------------------------------------CUUAGAA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-GCUC-U------UAGCCGUGAC-----GGGCA----GAAA----------UGUCC--UAUAA-GACCUUAA-UGAUUUGGGUAA-----UCUCGCUUAA----GGCUAGUCCAGACAAGAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC------------------------------------UUUUAUACGGAAC------------------GUAGGUGAGA----UUUGC-GGG-------UA-AAGGUAAU-------CCC-GCCGCAGACCAG---------------------------CCC------------------------------GCAA-----------------------------------GGG---UGGGGCUUC-AAGC-UGU--CGAGUCGCU----CUCG--GCA---------------------------------------------------UCUCCGU--GGAGUCUC--CUGCGUGGCA-GAA-----CGGAG------CAUUGAAUAAGAGG--------GUACUCGGAAGUC-------------UGAG-AGG-A-CGACGAGUGGGAAGG
>URS0000D6B2FC_12908_1-559
ACUUGACUAACUUCUCAAUACAAUGCUGG-UGG--------AGA---GCAG---CUAACAA----CUGU--GCCAGCG--GCGC-UCGGAAGACGA--------------------UGAG----C--UGAACCACAAG-------------GAUA---CUUGCGG--CG-AG-----G-CG----------------------------------------------------------------------------------------------------------------------ACGGACUAAUCACCCCUGUGUCAA----------------------GAG-CG-UGCACU-----------CUCUC---UCAAUGUA---AACCAAAUGCAACA-----UAUAGGUCGUGA-GCAG--AAU---AUGG-G-------GCGGU--------------UUAAUC---------------GCCGC-A----C-----UAAUCUGAG---UUAG---GUGGU------------AGC----CCGCAA--------GCG-----CCGCAAAC--------------------------------------------CUUAGAA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-GCUC-U------UAGCCGUGAC-----GGGCA----GAAA----------UGUCC--UAUAA-GACCUUAA-UGAUUUGGGUAA-----UCUCGCUUAA----GGCUAGUCCAGACAAGAAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC-----------------------------------UUUUAUACGGAAC------------------GUAGGUGAGA----UUUGC-GGG-------UA-AAGGUAAU-------CCC-GCCGCAGACUAG---------------------------UCC------------------------------GCAA-----------------------------------GGA---UGGGGCUUC-AAGC-UGU--CGAGUCGCU----CUCG--GCA---------------------------------------------------UCUCCGU--GGGGUCUC--CUGCGUGGCA-GAA-----CGGAG-----CAUUGAAUAGGGGG---------GUACUCGGAAGUC-------------UGAG-AGG-A-CGACGAGUGGGAAGG
>URS0000D6B72B_12908_1-618
UAUAAAACCUAAUAGUAUUUUGAACCAGA-UGA--------AAAA--CUAGGG-GAGACA---CCCUAG--G-CUGGA--AUAC-UUCUCAAGGGAC--------------AGA-----GU---U--CCGUU--AGCA-------------GAGA---UGC---GACAG-GU------GAAGUCCU-UAC----G-AACUGU-G-------------GCAA---------------CA-CAG-C-GUAGUC-GGAGGCGA----------GCA--------------------UCGCC-AAGGGAG---------------------------------------AAG-UA-GGUGCA-----------GA-CUUAUC-----AGU--AUCAAAAACAACACCG---AACUACUCGGGA-CA----AAUC--GGGAGAC------CACA---------------CUGU------------------UGGG-C----G-----UACCUAGGU---AU-----UCUA-------------CGGG---GUGACA-------CCUG---UGAGGACAAU--------------------------------------------GCCUAAA----------------------------------------------------------------------------------------------------------UGUCAA-------GAA-AGUCCUUGAGA-GCGUAAUUGAG----GCUCG----GCAA----------CGAGC-GUAUAA-GAGUAGAA-----GGUGGUCCAAGUA----GCCCAAACU-UACGCUAUGAUUAACAAAUUAACUUUUGUUCUAGUGCGAUAGAAAAAAGAGCAAUUACUGCAUACG------------AGAGUAUGAAAAUGUCUAUU------------------GCGGGU----GAAAGGUGC-GAC-------GA----AGGAU-------GUC-GUAUGGGUUCUG---------------------------GAAC-----------------------------UUCG----------------------------------GUUC---UGGCUAAAC-GUGGAGGUG-CC--GGCG-------GG-UACC----------------------------------------------------AAGGGC--GGUUAGUC--CCCAUUGUGU-GAAUA---UUGGUUGG-------GGUAAGAUCU--------GUAUAAGGAGGA--------------CUUG-CAA-AAUACUUUUCUUAUUAU
>URS0000D67036_12908_1-612
UCUUUGAAAAGGGAAUAUUUAGAACCAGA-UGA--------AAAA--CAGUGUGUCGAC---CACACUG--G-CUGGA--AUAU-AACUCAAGGGAU--------------AGA--AUUC----C--GA-UC--AGCA-------------GAGA---UGC---GA-AC-AGG-UGAA-AU--CCU-UAG-CU-A---GUUA-G-------------GUAA---------------CU-AAC-C-CG-CUC-GGAGCUAC----------UCA--------------------GUGGC-AAGGGAG---------------------------------------UUA-UA-GGUGCA-----------GCUAUAUC------AGU--GUCAAAAAUAAUGCUA---AACUGUUCGGGG-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAUCGGGAGACCAACAUGGGCGUACCCACAUAUCCCACUACUGGAGACAGUGGUAAGGGCAAUGAGUGAAGAUCGCU---------------------------------AAA--GCCUUUG----CGUAAUUGAA-----GCAUC----GCAA----------GAUGU-GUAUAA-GAACAGAC-----GGCAGUCCAAGUA----GCCUAAAU--UUACGCUUCUAUUAACAAUUAUGAUUGCGUUUAGUGCGAAAAAAG------------------CAAUUUACUGUACACAAAAGGUGUAAAUGUCUAUC------------------GCAGGU----GAAAGGUGC-AAC-------GA----AAGAU-------GUU-GUCAGGGCAAGUCG-------------------------GAAGC----------------------------CUAUG--------------------------------GCUUU----GGCUAAAC-GUGGAGGUG-CA--GGCA-------UG-CACC----------------------------------------------------AAGGGC--GGUUAGUC--CCCUGUGUGU-GAAUA---UUGGCUGG--------GAUAUGGUGU-------GUAUAAGGAGGA--------------CUUA-CUA-AAUAUUCUUUUUUCAAA
>URS0000D6D35F_12908_1-613
UCUUUGAUAAGAGUAUAUUUUGAACCAGA-UGA--------AAAA--CAGUGUGUCGAC---CACACUG--G-CUGGAA-UAUA-ACCCAAGGGAU---------------AGA---GUUC---C--AA-UU--AGCA-------------GAGA---UGCA--AA-CA-GGU-GAA----AUCCU-UAG-CA-A---UUCA-A-------------GUAA---------------UU-GUC-U-UG-CUC-GUAGGCUC----------GCA--------------------GAGCC-AAGGGG----------------------------------------GUU-AUGGGUGCA-----------GCUAUAUC------AGU--GCCAAAAACAAUAUCA---AACUGUUCGGGA-C---A-AAU---CGGG-A-G----ACCCA---------------ACU-------------------UGGGG----CA-U---ACCCACGCA---AA-----UCA--------------CUGUC--AGAGAU------GAUAG----AGAGAUUAC--------------------------------------------UGUGUGA--------------------------------------------------------------------------------------------------------AUAUCGC--------UAA-AGUCCUUG----CGUAGUUGAA-----GCUUG----GUAA----------CAAGC--UAUAA-GAACAGAC-----GAUAGUCCAAGUA----GCCAAAA---UAAAGUCUACGCUUUAUUAACAAGUGCAAUUAUUUUGUUUAAGGUGAA-------ACAAACAAAUUACAGUUCCUAAAAAAG--GGAAAAUGUCUAUU------------------GCUGGU----GAAAGGUGC-GAC-------GA----GAGAU-------GUC-GUUAGGGUUUA----------------------------GGC------------------------------UUUA-----------------------------------GCU----GGGUAAGA-GUGGAGGUG-CA--GGCA-------UG-UGCC---------------------------------------------------A-AGGGC--UCUUAUUC--CCCUAUGUGU-GAAUA---UUGGUUGG--------GAUAUAGUGU-------GUAUGAGGAGGA--------------CUCA-CAA-AAUAUACUUUUAUCAAA
>URS0000D65A6B_12908_1-603
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACU-----UCGGU--GGCAGGG--CGUU-CCGGAAAGCCA---------------CGG--UACA----U--CU-UCAGGACA-------------GAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C---AAAC-A-------------GAGA---------------UG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACGGCAAA-------------------------------------GGG-AC-GGCGGGUUCAUA-----AAGAAU--------UGAAAAGCAAAAGGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------GCGG---------------AAGUU-----------------CCGC-A----G-----UAACCGUGC---GGGCC--C----------------UGG---UUUGAGAC-------CCA--------GAAGCA-------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAG-----ACCUU----GAAA----------AAGGU-GUAUAA-GCUUUACC-----CCCUGUUU------AACGGGCAAAC--CCUGGAAAUUUUAAAAAGAUGUCAUUUACACUUAU--------------------------------------------------UUAAAAUCUGAAUG-----------------UCGCCCGGA-----GAUGC-AGG-------UAAA-----UC-------CCU-GCACAUGCGUAG---------------------------CAACUCCAAGCAC--------------------UUGU-------------------------GUGCGAGGAGCUGG--UUGUCCAGG-AAGU-AUG--GAGGUAGCU----CCCC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-------------GUUCUUAUAUUGGGCUUAGGGGGAAG---------------CCCC-CGC-CUGAUGUCUUAAAUCUC
>URS0000D693EB_12908_1-604
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACU-----UCGGU--GGCAGGG--CGUU-CCGGAAAGCCA---------------CGG--UACA----U--CU-UCAGGACA-------------GAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C-AA--AC-A-------------GAGA---------------UG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACGGCAAA-------------------------------------GGG-AC-GGCGGGUUCAUA-----AAGAAU--------UGAAAAGCAAAAGGCAAGGGGAACGGGAGUGGCAUC-CGAC--AAC---AGAC-G-------GCGG---------------AAGUU-----------------CCGC-A----G-----UAACCGUGC---GG-----GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAG-----ACCUU----GAAA----------AAGGU-GUAAAA-GCUUUACC-----CCCUGUUU-------AACGGGC-AAACCCUGGAAAUUUUUUUAAUAUGUCAUUUACAUUUUAU-------------------------------------------------AAAAAAUCUGAAUG----------------UCGCCCGGA------GAUGC-AGG-------UA-A----AUU-------CCU-GCACAUGCGUAG---------------------------CAACUCCAAGCAC--------------------UUGU-------------------------GUGCGAGGAGCUGG--UUGUCCAGG-AAGU-AUG--GAGGUAGCU----CCCC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-------------GUUCUUAUAUUGGGCUUAGGGGGAAG---------------CCCC-CGC-CUGAUGUCUUAAAUCUC
>URS0000D6C52E_12908_1-604
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACC-----UCGGU--GGCAGGG--CGUC-CCGGAGCGCCG---------------CGG--UACA----U--CU-UCAGAACA-------------GAUA---AAC-U-GG-AG-AAU-GUAA-CAAACCG-UUG-UC-C---AAAC-A-------------GAGA---------------UG-GGA-G-GA-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACGGCAAA-------------------------------------GGG-AC-GGCGGG-----------UUCA--UAAAGAAUUGAAAAGCAAAAAGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------GCGG---------------AGGUU-----------------CCGC-A----G-----UAACCGUGC---G--G---GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAG-----ACCUU----GAAA----------AAGGU-GUAUAA-GCUUUACC-----CCCUGUUU-------AACGGGCAAAC-CCUGGAAAUUUUUUUAAUAUGUCAUUUACAUUUUAU-------------------------------------------------AAAAAAUCUGAAU----------------GUCGCCCGGA------GAUGC-AGG-------UA-A----AUU-------CCU-GCACAUGCGUA----------------------------GCAA-CUCCAAGCAU------------------UUGU-----------------------GUGCAAGGAGCAGGU----UGUCCAGG-AAGU-AUG--GAGGUAGCU----CCUC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-----GUUCUUAUAUUGGAC--------UUAGGGGGAAG---------------CCCC-CGC-UUGAUGUCUUUUAAAAU
>URS0000D6C582_12908_1-605
AUACACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACC-----UCGGU--GGCAGGG--CGUC-CCGGAACGCCG---------------CGG--UACA----U--CU-UC--AGGA-----------CAGAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C---AAAC-A-------------GAGA---------------UG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACAGCAAA-------------------------------------GGG-AC-GGCGGG-----------UUCA--UAAAGAAUUGAAAAGCAAAAGGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------GCGG---------------AGGUU-----------------CCGC-A----G-----UAACCGUGC---GG-----GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAG-----ACCUU----GAAA----------AAGGU-GUAUAA-GCUUUACC-----CCCUGUUU-------AACGGGCAAA-CCCUGGAAAUUUUAAAAAGAUGUCAUUUAAACACUUAU------------------------------------------------UUAAAAUCUGAAUG----------------UCGCCCGGA------GAUGC-AGG-------UA-A----AUC-------CCU-GCACAUGCGUAG---------------------------CAACUCCAAGCAC--------------------UUGU-------------------------GUGCGAGGAGCUGG--UUGUCCAGG-AAGU-AUG--GAGGUAGCU----CCCC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAACA---UUGCG-----GUUCUUAUAUUGGAC--------UUAGGGGGAAG---------------CCCC-CGC-UUGAUGUCUUUUAAAAU
>URS0000D67E3B_12908_1-603
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACU-----UCGGU--GGCAGGG--CGUU-CCGGAAAGCCA---------------CGG--UACA----U--CU-UCAGGACA-------------GAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C---AAAC-A-------------GAGA---------------UG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUUC-AACGGCAAA-------------------------------------GGG-AC-GGCGGG-----------UUCA--UAAAGAAUUGAAAAGCAAAAGGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------GCGG---------------AAGUU-----------------CCGC-A----G-----UAACCGUGC---GG-----GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAG-----ACCUU----GAAA----------AAGGU-GUAUAAGCU-UUACC-----CCCUGUUU-------AACGGGCAAAC-CCUGGAAAUUUUAAAAAGAUGUCAUUUACACUUAU--------------------------------------------------UUAAAAUCUGAAU----------------GUCGCCCGGA------GAUGC-AGG-------UAAA-----UC-------CCU-GCACAUGCGUAG---------------------------CAACUCCAAGCAC--------------------UUGU-------------------------GUGCGAAGAGCUGG--UUGUCCAGG-AAGU-AUG--GAGGUAGCU----CCUC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-----GUUCUUAUAUUGGAC--------UUAGGGGGAAG---------------CCCC-CGC-UUGAUGUCUAUUAAUUC
>URS0000D68AC4_12908_1-605
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACU-----UCGGU--GGCAGGG--CGUC-CCGGAACGCCA---------------CGG--UACA----U--CU-UC--AGGA-----------CAGAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C---AAAC-A-------------GAGA---------------CG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACGGCAAA-------------------------------------GGG-GC-GGCGGG-----------UUCA--UAAAGAAUUGAAAAGCAAAAGGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------UCGG---------------AGGUU-----------------CCGA-A----G-----UAACCGUGC---GG-----GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAA-----GCCUU----GAAA----------AAGGU-GUAUAA-GCUUUACC-----CCCUGUUC-------AACGGGCAAA-CCCUGGAAAUUUUUUUGAUAUGUCAUUUACAUUUUAUA------------------------------------------------AAAAAAUCUGAAUG----------------UCGCCCGGA------GAUGC-AGG-------UA-A----AUU-------CCU-GCACAUGCGUAGCA---------------------------ACUCCAAGCGC--------------------CUUU-------------------------GCGCAAGGAGCAGG--UUGUCCAGG-AAGU-AUG--AAGGUAGCU----CCUC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-----GUUCUUAUAUUGGAC--------UUAGGAAGAAG---------------UUCC-CGC-CUGAUGUCUUAAAUCUC
>URS0000D6BC32_12908_1-605
AUAUACUAGACAAUGUCAGGCGAACCUGC-UGA--------AGA---GCCGA--UGACC-----UCGGU--GGCAGGG--CGUC-CCGGAACGCCA---------------CGG--UACA----U--CU-UCAGGACA-------------GAUA---AACU--GG-AG-AAU-GUAA-CAAACCG-UUG-CC-C---AAAC-A-------------GAGA---------------UG-GGA-G-GG-CAG-A-AGGAUA----------UACA-------------------UUUCC-AACGGCAAA-------------------------------------GGG-GC-GGCGGG-----------UUCA--UAAAGAAUUGAAAAGCAAAAGGCAAGGGGAACGGGAGCGGCAUC-CGAC--AAC---AGAC-G-------UCGG---------------AGGUU-----------------CCGA-A----G-----UAACCGUGC---GG-----GCC--------------CUGG--UUUGAGAC------CCAG-----AAGCA-----------------------------------------------GCACGGC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-CGGAUGCA----UCAGGUUGAA-----GCCUU----GAAA----------AAGGU-GUAUAAGCU-UUACC-----CCCUGUUC-------AACGGGCAAAC-CCUGGAAAUUUUUUUGAUAUGUCAUUUACAUUUUAUA------------------------------------------------AAAAAAUCUGAAU----------------GUCGCCCGGA------GAUGC-AGG-------UA-A----AUU-------CCU-GCACAUGCGUAG---------------------------CAACUCCAAGCGC--------------------UUUU-------------------------GCGCAAGGAGCAGG--UUGUCCAGG-AAGU-AUG--AAGGUAGCU----CCUC--CAU---------------------------------------------------GCUCAGA--CCUGGGCA--CAUGUUGGCU-GAAUA---UUGCG-----GUUCUUAUAUUGGAC--------UUAGGGGGAAG---------------CCCC-CGC-UUGAUGUCUUAAUCCUU
>URS0000D6A431_12908_1-623
GCCAGCUGGGAGCCGUGCCGGGACCUCGG-UGA--------ACAA--AGAGA--ACACCA----UCCCU---CCGAGGA-CCGG-ACGCAUUCCG----------------UGG--UCUG----U--C--CG--UGCG-------------GAUA---CGCA--CG--G-GU-----A-CG--CCA-UCU-GC-G--ACAUG-C-------------GCGA---------------GC-AUGCC-GC-GGG-A-AGGACGG---------AGCAGGAACCGC----------CCGUCC-AACGGACG--------------------------------------GUC-CGGGUCGCC-----------CGG-GCACGGA---GA---AGGACAACGCACGGUG---AUGCCGUGCCCA-CCGC--AAU---ACGA-A-GGG---GUGCU--------------GAACA----------------GGCUC-C-CCCG-----AAACCC-GC---AAAC---CAG--------------GCCGC--AUGAGAAC----GCGGU-----GCUGUAAG--------------------------------------------GC-GGGA---------------------------------------------------------------------------------------------------------ACCUCACC------CAC-GGUGGG---CGGCGCACACGGC-----GCCCCG---GAAA---------CGGGAC-GUAUAA--ACGGCAA-----GCCGGUCCAAGUA----GCCAAAGC--GUGCGUACUUCAAACAUUUGAUAAGUGGUCCAUGUGAGAACAACAGGGAAACU--------------------------------UUCUUAGCUGAAUG-----------------GCUGGU----GAACGAUGC-GGG-------UAUGAAAAAUC-------CCC-GUCAGAGCAAG----------------------------GCAUCC---------------------------UCCG--------------------------------GGGUGC----GGCUCCCA-UAGU-C--GAGGGCGA-CG----GCCCG-AAG---------------------------------------------------GCUCAGG--UCGGAGUC--CUCUGUGGCG-GAAC----GUCCGCG------UCCAUGCACCGG--------GUAGGGCGAAG---------------GUCC-CCC-GGCACGGCUCCCAGCUG
>URS0000D6A833_12908_1-582
GUCCAUCAGUUUCCGUUUGUGCAUCUCGG-UUG--------AAG---CAAG---GUGAUA-----CUUG--UCCGAGA--GCCU-UCUAAGGGCGACCGAAAGUCCUAA--AGU--AGCUA---A-CAAGAGUUGAGG-----------U-GAUA--GCCUC--UU----UG----AG-AU--GUUACCU-GU-----GAGU-U-------------GUGA---------------AA-CGU-U-GC-AGG---ACUAGU----------AAAA-------------------GCUAG-UGUGAAGAU-------------------------------------GGA-GG-UGUGCC-----------GCAAUAACAU----A----AUCAUAGAGCAUAAGU-----CUUUUCGUUG-GAUAG-AAGU--AAGC-A-----CAUGCC---------------GACAG-----------------GGUG-A----U-GACUUUA-CCAGA---UAAG---GGCA-------------AGC----GUGAUAG-------CCU-----UGCCAAAC--------------------------------------------UCUGG-A--------C------------------------U-----------------------------------------------------------------------AAAUCAAA------CAA-UCCAAU------UUGCCGUGAA-----CAGAA----GAAA----------UUCUG-GUAUAA-GAAAAGCG-----CUUAGUAUGAGUA----GCACAA----GGCAAACAAACAGAUAAUUAUAUGAAAGCAUAUCAU-------------------------------------------------AACAAAUCUGUAU-------------------CGUGU----GAAAGUUGGUGGG-------UU----UCGUU-------CCCAGCCCUAACAUUAAAAG-------------------------------------------------------------------------------------------------------CAAUAGG-AG-C-UUAA-GGAGUUGCU----A-CU-UUAA---------------------------------------------------G--UAGAG-CCUAUUGGG-UUAG-UCGCU-UAAUA---AUGAGA--------GUGUUAUUGUG--------GUUGG----AGAAAA------------ACC-GCA-CAAUUAAGGGUUAUUCG
>URS0000D65ACD_12908_1-635
GAGUUCCUCCAAGCCAUUCUGCAACUCAG-UGC--------CAAA--GCGG---GAUGAAAA---CCGU--UCUGAGA--GGCG-UCGGCUUUCGGCAGUGGAAGCUGC--CGG--AACG----U--CC-GCAUUGGGGAAAAGCGCCGGGGAUA---CCCU--GC-GU-CA-----G-UG--CC--CUG-UG-A-AACCGG-U-------------GCGA---------------AC-CGG-C-GA-CGG-A-AUGUUG----------AGA---------------------GACA-GAAAAUGC--------------------------------------AGU-GC-UGUGCC-----------GG-AGGAAC-----GC---GAACCAAGGCGCAG-----UUUCUGCCGCCG-GCA---AAC---AGAC-GC------CCUCC--------------CGGAA----------------GGAGGGA----A-----UAACCCGG----AAUG---CC-G-------------CAGG---GUGGUG-------CCUG-----CAGGA-------------GAGCGAUCGGGAUCAUGAGCGCCCGAUC-CUUUA--CGGGA---------------------------------------------------------------------------------------------------------AGACCCU--------GC-GCCGGU------UUCCAGUGAA-----GCCCC----GAAA----------GGGGU-GUAUAA-GACGGAAC-----ACUGGCCCAUGUA----GCGGAA----UGGAGAAAGUCUCAUCUUCCAGCUUGCGACAUCUGAUCAACCAUCG---------------------------------------CUUAUUGCCGGAAG-----------------AUCCGU----GAAUGGCAG-AGG-------UA-A--CCAGU-------CCU-CUUUGGGAACA----------------------------GCGGU----------------------------GAAA---------------------------------ACCGC----AGGAUACG-CG---GACG-GGAGUCGCU----G-CC-CGUC---------------------------------------------------AACCGGC--CGUAUUCU--CCCAGUGGCU-GAACA---GGUUCGAA-------GUUCCGGUCG--------GUACCGUGAAA---------------GCGG-GCA-GGAUGGUUUGGAGGAAC
>URS0000D6696F_12908_1-547
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GAAAAUUAAAUAAAGUGUUUGCACCUCGG-UGA--------AGU---CACC---CUGCU------GGUG--GCCGAGG--CUCA-ACCAUAA-------------------GA---AUUA----U--UA-AU--GUGG-------------GAUA---CUGU--AU-UA-AU-----A-AUAA-GA-----------------------------------------------------------------------------------------------------------------CCACCGUGUAUUCGCCUUUAAUUAGACGCUAUG-------------GUU-GGUGUCGCA-----------AGCA--GUUCU---UC---GAUGUAAGCAAUUAG-----UGUGUGGGGGC-G-AC--AAG---AAGC-UC------UAUA---------------GAAA------------------UAUA------U-----CUCGCG------AUAA---GAUAUAA----------AGC----CUGAGAA-------ACU---UAUAUCUC-------------------------------------------------CGC-----------------------------------------------------------------------------------------------------------UCUCA-----AAGGAA---GCCU------UUGACUUGAU-----GUUAA----GCAA----------UUAAC--UAUAA-CCACAUU------CUAAGUGCGAGUA----GCGAAAU---GUCAACGUUCAGUUUAUGGAGUAUAAA----------------------------------------------------------AAGAUCGCUGAAG------------------CUUCGU----GAAAGUUGA-AAGA------UAAU--CGAGU------UCUU-UC-CACCGUUUC---------------------------GUUA-----------------------------CAUUG---------------------------------UAAC----CAUUCUAG-AAGC-AUA--GAGGUAGCU----CCUA--UAU---------------------------------------------------GCUCAGC--CUAGCGUG--AGUG-UGUGC-GAAUA---ACAAAUU------AGAAUAAUGCUU--------GUAGGGCGAAG---------------GCCC-GCG-AACACUUUGUUUAAAAU
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--UUUUGACAAAUAUAUCGUAUAACUCGG-UGC--------ACUAAAGGGU---UGUC-------ACCCCCUCCGAGA--AUAC-CGGAAGCUGU----------------GAC--CAGG----C--UG-CC-UGCGG-------------GAUA---CUGC--GA-CA-GU-----G-AG--GUU-UCU-AU-C---GCUC-C-------------GUGA---------------GG-ACU-G-AU-GGA-GAA-GCUC----------AAA--------------------AGGCA-ACACAGAA--------------------------------------CGG-UA-UGUGCG-----------GAUCU-UGGU----GU---CGAUUAAAGCUCGAA----GGAUUCUGGCAG-CGAC--AAU---AGAC-GC------UAGCU--------------CGAAA----------------GGCUAGA----A-----AAAUCCGU----GAAACC-UGCA-------------GCA-----GGGAUGC------UGC-----AGCGAACUUA-------------------------------------------GCGGAA---------------------------------------------------------------------------------------------------------ACUCCGAA------CCA-AGCUGU------UGGUAGUGAA-----GCGGA----GAAA----------UCCGU-GUAUAA-CAGAAUUC-----UGAGGAAAAAGUA----GCUCAA----UACCAAAAGUUAUACUGGUCUUGAAAACCAGAGAUAGAAAA--------------------------------------------CAUUUUUCUGAAAG-----------------AUGGGU----AAAAUUUGU-GGG-------UA-A--CCAUU-------CCC-GCGGCAGGCAAA---------------------------------------------------------------------------------------------------------AGGGGCAGG-AAGC-U--C-AGGGUCGCU----CCCG--AAG---------------------------------------------------GCUCAGA--CCUGUCUU--CUGUGUUGCU-GAAGA---AAUCGGAA------ACCGUAGAUUGC-------GUAAGGCGAAG---------------GUCU-AUA-UGAUAUAUUUGUCAAAG
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>URS0000D67C5D_12908_1-567
UGUUUUGACAAAUAUAUCGUAUAACUCGG-UGC--------ACUAAAGGGU---UAUCA------ACCC-AUCCGAGA--AUAC-CGGAAGCUGU----------------GAC--CAGG----C--UG-CC-UGCGG-------------GAUA---CUGC--GG-CA-GU-----G-AG--GUU-UCU-GU-U---GCUC-C-------------GCGA---------------GG-ACU-G-AU-GGA-GAA-GCC-----------CAAAA-------------------GGCA-ACACAGAA--------------------------------------CGG-UA-UGUGCG-----------GAUCU-UGGU----GC---CGAUUAAAGCACAAA----GGAUUCUGGCAG-CGAC--AAU---AGAC-GC------UAGCU--------------CGAAA----------------GGCUAGA----A-----AAAUCCGU----GAAAC--CUGC-------------AGC----AGGGAU--------GCU-----GCAGCGAACUUA-----------------------------------------GCGGAA---------------------------------------------------------------------------------------------------------ACUCCGAA----G-CAA--GCUGU------UGGUAGUGAA-----GCGGA----GAAA----------UCCGU-GUAUAA-CAGAAUUC-----UGAGGUAAAAGUA----GCUCAA----UACCAGAGUGUUGCUAGUUCUCGAAACUAGCUGGCU-------------------------------------------------CAAUUAUCUGAAAG-----------------AUGGGU----GAAAUUUGU-GGG-------UA-G--CCAUU-------CCC-GCGGCAGGCAAA---------------------------------------------------------------------------------------------------------AGGGGCAGG-AAGC-U--C-AGGGUCGCU----CCCG--AAG---------------------------------------------------GCUCAGA--CCUGUCUU--CUGCGUGGCU-GAAGA---AAUCGGAA------ACCGUAGAUCAC-------GUAAGGCGAAG---------------GUCU-AUA-UGAUAUAUUUGUCAAAG
>URS0000D679FA_12908_1-604
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>URS0000D6BF6C_12908_1-587
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>URS0000D6CFB2_12908_1-623
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>URS0000D6CE71_12908_1-580
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>URS0000D69DFE_12908_1-579
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>URS0000D6824D_12908_1-579
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>URS0000D6A2CD_12908_1-579
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>URS0000D6B0AB_12908_1-579
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>URS0000D6B83C_12908_1-583
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>URS0000D66547_12908_1-623
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>URS0000D6A7F3_12908_1-619
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>URS0000D68A40_12908_1-588
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>URS0000D6BEEB_12908_1-592
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>URS0000D695F5_12908_1-592
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>URS0000D6CE44_12908_1-594
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>URS0000D666A2_12908_1-578
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>URS0000D6A64E_12908_1-579
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----GCCAGCUUAAACAUGAUUACCUCGG-UGU--------AGA---GAGGUU-UUUC-----AGCCUU--GCCGAGA--UGUG-CAGUAACG------------------AGA--UAGA----U--AA-AU--UCGG-------------GAUA---CUGG--AU-UU-AU-----U-GA-UUCU-UUC-CU-C---AGAG-A-------------GUGA---------------UC--CU-G-CG-GAG-A-AGAUGG----------AAA--------------------CCGUC-AACAAUGC--------------------------------------UGU-GC-AGUGUA-----------UCAUCAUAGA----GAA--AAUCAAAAGCAGAAU-----CCUUGUGGUCG-GCGUAGAAA---AGAC-G-------CUUA---------------CGGUG-----------------UAAG-A----A-----UAAUCCAUU---GAUG---UCGGC------------AGU---GUGAGAG--------ACU-----ACGGACUA--------------------------------------------AAUGGAA----------------------------------------------------------------------------------------------------------CUCUAAA----A-GAA-GUCGAU------UUGCCUUGAA-----CCUGA----GAAA----------UCGGG-GUAUAA-CACAAGAA-----AUUCGUUAAAGUA----GCGGUAU---GGCAGCAAACAAAAAGUUUCCUCAAUAGAGUAUUGAGUUUUU-------------------------------------------AAAACAUCUGAAAG-----------------AACCGU----GAAAUUUGC-AGG-------UG-A----AAU-------CCU-GCAUGUGCUUUGACC-------------------------------------------------------------------------------------------------------GCGGCAAG-AAGC-A-U--AGGGUCGCU----CCCG--AAA---------------------------------------------------GCUCAGA--CUUGUCGU--CACAUUGGUU-GAAUA---UGAUUGCA------UCGUCGAUGA---------AUAAGGGGAAG---------------CCCU-AAU-CAUGUUUAUUUUGGAGU
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>URS0000D69945_12908_1-593
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>URS0000D6C942_12908_1-593
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>URS0000D6CC21_12908_1-591
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>URS0000D66B09_12908_1-549
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>URS0000D65F24_12908_1-549
AUAUGAAUUAUGCUUUAUGAUCAACUCGG-UUA--------GAAA--AGCGG--CUCCA-----CCGCU---CCGAGG--CACA-GGGUAGUACUC---------------AGU--UAAU----A--UG-CA--UAAG-------------GAUA---CUUU--UG-CA-AA-----A-AG--GCU-GUU-AA-U---CAUU-A-------------GCGA---------------UA-AUG-A-UU-AAG-A-AGAAGA----------AAA--------------------UCCUC-AACAGUAAA-------------------------------------CCU-GU-GGCGCAAA---------GUU-GAUCG-----U----AUUGAAAAGCACGGA-----ACUUCCGGGUG-CAAU--AAU---ACAC-G-------CUCG---------------CAGUG-----------------CGAG-A----A-----UAAACCUGA---AAGC---UUAU-------------CGG---CGUGGCAA-------CCG-----AUGAUUAC--------------------------------------------UCAGGUA---------------------------------------------------------------------------------------------------------AAGCCAU-------CAA-UGCACU------UUGCCUUGAC-----UUCGA----GAAA----------UCGGA--UAUAA-CGGAAGAC-----UCCGGUAAUGGUA----GCCGAAU---GGCAAUAAAUGAACUUU--------------------------------------------------------------------UACCUAAUUGAAUG-----------------GUCGGU----GACAUUUGC-AGG-------GA-A--CCUAU-------CCU-GUGUAAGAUGU----------------------------GGUU-----------------------------UUUAA---------------------------------AACC----GGGGUAAG-UAGU-U--A-GGGGUAGCU----CCCC--GAA---------------------------------------------------GCUCAAG--CUUAUCUC--CUUACUUGCU-GAAGA---UUAAUG---------CGUGAAAACAAU------GUACGGCGAAG---------------GUCG-GAC-CAUAAAGCAUAGUUGAU
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>URS0000D69518_12908_1-615
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>URS0000D6B6F1_12908_1-579
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>URS0000D6952A_12908_1-573
GAACAAUGUAUAAACUAUGACCAACUCAG-UGC--------AGAG--GGU----ACAC---------AC-UGCUGAGA--UGGG-CGAUUA--------------------AGG--AAUG----G--CG-AA--GAGG-------------GAUA---CCU---UU-AG-CAU----A-UG--CCU-UUU-GA-C---CGUA-G-------------GCGA---------------CU--CG-G-UC-UUG-A-AGAGAU----------UAAU-------------------UUCUC-AACAAU----------------------------------------CGU-UU-AGUGCA-----------AUAAUUGAAU----A----GGAAUAAGACAGUA-----AGUGAAAGGGCG-AGAC--AAU---AGAC-G-------CUCU---------------CUGUG-----------------AGAG-A----A-----UAACCCU-----AGAUGGUCGGC-------------UGA---UGUGGUAG-------UCA---GUGACGGACAA---------------------------------------------AGGGA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-CUCGUU------UAGCAGUGAU-----GCUGG----GUUU----------CCAGC--UAUAA-CUUUUGCU------UAUGUACCAGUA----GCCGAAUC--UGCUAUAGAUAAAGAAAAUAAUGGAGCAGAACUCCUUUUAAUUUA----------------------------------------AAUUUUUCUGAAAG------------------UCGGU----GAAAGUUGU-GGG-------UC----ACAGU-------CCC-AU-AUGGUUUUAGG-------------------------UCAAUGC--------------------------UUCG-------------------------------GUAUUGA---UGGUAUAAG-AAGC-CUA--GGAGUCGCU----CUCC--UUU---------------------------------------------------GCUCAGA--CUUGUAUCA-CUAU-UAGUC-UAAUA---AUUUG---------GUUCAAUUGUUU-------GUAAGGGGAAA---------------CCUU-GGU-CGUGAUUUAUAGUUCUU
>URS0000D66E57_12908_1-660
UGCUUUAAAAUGCACGCAUUAUAUCCUGG-UGA--------AGA---AUAG---CUAAUCA----CUAU--GCCAGGA--CAAUAUCUCAAUGC-----------------ACG--GACG----A--GA-CU--AAAG-------------GAUA---CUUU--GG-UC-GGU---AG-UUUACG--UUC-UC-A---AUGU-AUA-AGGC------UAU---------GCCGAAGU--CGG-A-GA-GUG-A-AGACGG----------GAAC-------------------CCGUC-AAGCAAGGA-------------------------------------GAG-UU-GGUGUGU----------AUUAUAUAC-----AA---CGAUUAGUGUGACA-----UGCUUUUGGUCA-GUGU--AAU---AGAC-G-------GCUC---------------CUGUG-----------------GAGC-A----A-----UAACCCUG----GGAA---CUG-G------------AUGAG-CUGGUAA------CUCAU----UACAGAUGG---------------------------------------------CAGGGA---------------------------------------------------------------------------------------------------------AUUACCAA----AACAA-GCUGAU------UUGCCGUGAUA----CCUGG----ACAA----------CCAGGAGUAUAA-CAAAAGCA----UAAGU-CGUAAGUA----GCCCAA----GGCAAUAAAAGAUUAUUUAUGAUAUUGAACAAUUAUCAAUGAAUA----------------------------------------AAACAAUCUGAAUG-----------------AUGGGU----GAAAGCUGG-AGG-------UG----AUAUU-------CCU-UCAUGGGUUUGAC--------------------------GCU-AAUUAAGG--ACGAACAUCACAAUCCAUCCGUAG---GGUGCGAGAGU-AUGUU-GUAGAAUUAAUUUAGC---UGGGGCAAG-AAGU-CAU--UAUCGA-CG----GAUA-UUUG---------------------------------------------------GCUCAGA--CUUGUCUC--CCCAUUCGCA-UAAUA---AAUUACA--------GUAUAUAAUUC-------AUAAGAUGAAUAAAA-----------GUCU-AUA-AUGUGUGUGUUUUAAAG
>URS0000D67FBE_12908_1-512
CCCUGUUCCCGGAAUCGCAUUGAAAAGUG-UAA--------CC-----CUCC--UGACU-----GGAG---GCACUUACUUUAA-CUCAUUAAAUCC--------------AAA--AGUC----G-UUU-AU--GAGG-------------GAUA---CCUU--AU-AAAUU-----C-CU--U---GUC---------------------------UCCG---------------------------GAC-U-ACUCU-----------UGAU--------------------UGAG-GAUUGGUAG-------------------------------------AGC-UAGAGUGCU-----------GCGU----GUUAU-G----AUACUAAGGUAACG-----AUAGAGUCGGUC-UCGC--AAG---AA-----------GGGU---------------UUU-------------------ACCC------U-------CGCCA-------AA---GUUAA------------CAGUU--GUGGCAU-----AACUG-----GAACCAAAG---------------------------------------------UGGUA----------------------------------------------------------------------------------------------------------UGCCAAA------UAA-GAGAU-------UUCUCGUGAU-----GUCCAA---GUGA---------UUGGGC--UAUAA-GAUUUUAU------CGGAUCU-----UUUUCCUUAA----GAGGCAGUUUACAAUAACU-------------------------------------------------------------------AUUGGUGUG---------------------UUAAGGAAAA----AGCGG-GUC-------UG----CCAAU-------GAC-GCCCGGGACUAGAAAU------------------------------------------------------------------------------------------------------GCGGUGAG-AGU--AACC-AGUGUCGCU----AACU-GGG-----------------------------------------------------G-CAUUCUCUCAUCAU--CCUG-UGACU-GAGUA---AGUAGCA----AUAACAAUGACGUG--------GUAGGGGUAAC---------------GCCC-CAA-UGCUUUUAUGGAGAGGU
>URS0000D65A76_12908_1-513
CCCUGUUCCCGGAAUCGCAUUGAAAAGUG-UAA--------CC-----CUCC--UGACU-----GGAG---GCACUUACUUUAA-CUCAUUAAAUCC--------------AAA--AGUC----G-UUU-AU--GAGG-------------GAUA---CCUU--AU-AAAUU-----C-CU--U---GUC---------------------------UCCG---------------------------GAC-U-ACUCU-----------UGAU--------------------UGAG-GAUUGGUAG-------------------------------------AGC-UAGAGUGCU-----------GCGU----GUUAU-G----AUACUAAGGUAACG-----AUAGAGUCGGUC-UCAC--AAG---AA-----------GGGU---------------UUU-------------------ACCC------U-------CGCCA-------AA---GUUAA------------CAGUU--GUGGCAU-----GACUG-----GAACCAAAG---------------------------------------------UGGUA----------------------------------------------------------------------------------------------------------UGCCAAA----A-AAA-GAGAU-------UUCUCGUGAU-----GUCCAA---GUGA---------UUGGGC--UAUAA-GAUUUUAU------CGGAUCU-----UUUUCCUUAA----GAGGCAGUUUACGAUAACU-------------------------------------------------------------------AUUGGUGUG---------------------UUAAGGAAAA----AGCGG-GUC-------UG----CCAAU-------GAC-GCCCGGGACUAGAAAU------------------------------------------------------------------------------------------------------GCGGUGAG-AGU--AACC-AGUGUCGCU----AACU-GGG-----------------------------------------------------G-CAUUCUCUCAUCAU--CCUG-UGACU-GAGUA---AGUAGCA----AUAACAAUGACGUG--------GUAGGGGUAAC---------------GCCC-CAA-UGCUUUUAUGGAGAGGU

Rfam family RF03087 maps to these 30 chains: 9ISV|1|A, 9J3R|1|A, 9J3R|1|B, 9J3R|1|C, 9J3R|1|D, 9J3T|1|A, 9J3T|1|B, 9J3T|1|C, 9J3T|1|D, 9J3T|1|E, 9J3T|1|F, 9J3T|1|G, 9J3T|1|H, 9MM6|1|A, 9MM6|1|E, 9MM6|1|I, 9MM6|1|M, 9MM6|1|Q, 9MM6|1|U, 9MM6|1|Y, 9MM6|1|c, 9MME|1|U, 9MME|1|Y, 9MME|1|c, 9MME|1|g, 9MME|1|k, 9MME|1|o, 9MME|1|s, 9MME|1|w, 9MMG|1|c 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: 29-44, 72-73
Loop 2IL Column numbers: 45-48, 69-71
Loop 3HL Column numbers: 52-65
Loop 4IL Column numbers: 78-81, 353-355
Loop 5IL Column numbers: 81-82, 351-353
Loop 6IL Column numbers: 83-84, 348-350
Loop 7IL Column numbers: 84-86, 347-348
Loop 8IL Column numbers: 87-88, 308-346
Loop 9J4 Column numbers: 88-112, 186-188, 251-256, 298-308
Loop 10IL Column numbers: 114-117, 181-184
Loop 11IL Column numbers: 118-119, 178-180
Loop 12IL Column numbers: 119-125, 171-178
Loop 13IL Column numbers: 125-128, 169-171
Loop 14IL Column numbers: 129-131, 166-168
Loop 15IL Column numbers: 132-135, 162-165
Loop 16HL Column numbers: 138-159
Loop 17IL Column numbers: 190-192, 247-249
Loop 18IL Column numbers: 193-195, 244-246
Loop 19IL Column numbers: 195-199, 242-244
Loop 20IL Column numbers: 201-202, 238-240
Loop 21IL Column numbers: 202-204, 237-238
Loop 22HL Column numbers: 204-237
Loop 23HL Column numbers: 260-294
Loop 24IL Column numbers: 419-421, 751-752
Loop 25J3 Column numbers: 422-446, 490-506, 625-750
Loop 26IL Column numbers: 449-465, 467-487
Loop 27HL Column numbers: 465-467
Loop 28HL Column numbers: 504-505
Loop 29IL Column numbers: 511-522, 571-620
Loop 30IL Column numbers: 525-539, 562-568
Loop 31HL Column numbers: 542-559
Loop 32HL Column numbers: 763-764
Loop 33IL Column numbers: 771-777, 804-806
Loop 34HL Column numbers: 782-799
Loop 35IL Column numbers: 833-843, 974-983
Loop 36IL Column numbers: 848-945, 951-969
Loop 37HL Column numbers: 855-856
Loop 38HL Column numbers: 945-951
Loop 39IL Column numbers: 987-989, 1019-1021
Loop 40HL Column numbers: 991-1017
Loop 41J3 Column numbers: 1027-1060, 1134-1139, 1247-1250
Loop 42HL Column numbers: 1064-1130
Loop 43IL Column numbers: 1146-1149, 1233-1240
Loop 44IL Column numbers: 1151-1153, 1179-1231
Loop 45IL Column numbers: 1155-1158, 1174-1177
Loop 46IL Column numbers: 1161-1162, 1166-1171
Loop 47HL Column numbers: 1162-1166
Loop 48HL Column numbers: 1164-1165
Loop 49HL Column numbers: 1308-1328

Loop 1 Internal loop

Column numbers: 29-44, 72-73 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-UGA--------AGA*GC  108

    
    G-UGC--------AGA*GC   32

    
    G-UGU--------AGA*GC   23

    
    G-UGU--------AUG*UC    8

    
    C-UGA--------AGA*GG    7

    
    G-UGC--------ACU*UC    5

    
    G-UGG--------AGA*GC    4

    
    G-UGA--------AGU*GC    3

    
    G-UGU--------AU-*UC    3

    
    U-UGG--------AAA*GG    2

    
    UCUGU--------AA-*GA    2

    
    C-UGU--------AA-*AG    2

    
    G-UAA--------CC-*GC    2

    
    G-UGU--------AG-*GC    2

    
    A-UGC--------ACA*UU    1

    
    A-UGU--------AUG*GU    1

    
    G-UGA--------AUA*AC    1

    
    G-UGA--------AUA*UC    1

    
    G-UGC--------AUA*UC    1

    
    G-UGC--------AUG*GC    1

    
    G-UGC--------CAA*UC    1

    
    G-UGG--------AUA*CC    1

    
    G-UGU--------AUA*GC    1

    
    G-UGU--------AUA*UC    1

    
    G-UGU--------AUG*GC    1

    
    G-UUA--------AGA*GC    1

    
    G-UUG--------AAG*UC    1

    
    UCUGU--------AA-*GG    1

    
    Omitted sequenced and counts

    
    A-UGA--------ACA*-U    8

    
    G-UGA--------AUA*-C    7

    
    G-UGUGAGAAAUCGAA*-C    5

    
    G-UGA--------AAA*-C    5

    
    G-UGC--------AUA*-C    4

    
    A-UGA--------AAA*G-    3

    
    A-UGU--------AUA*-U    3

    
    G-UGUGCGAAAGCGAA*-C    2

    
    G-UCA--------UAA*-C    2

    
    G-UGA--------ACA*-C    2

    
    G-UGA--------AUG*-C    2

    
    G-UGC--------AGA*-C    2

    
    G-UGU--------AGA*-C    2

    
    G-UGU--------AUA*-C    2

    
    G-UUA--------UAA*-C    2

    
    U-UGG--------AAA*-G    2

    
    A-UGA--------AA-*-U    2

    
    G-UGG--------AU-*-C    2

    
    A-UGA--------AAG*-U    1

    
    A-UGA--------CAG*-U    1

    
    A-UGC--------ACA*-U    1

    
    G-UGA--------AGA*-C    1

    
    G-UGC--------ACA*-C    1

    
    G-UGC--------ACU*-C    1

    
    G-UGC--------UAA*-C    1

    
    G-UGU--------AAA*-C    1

    
    G-UUA--------AAA*-C    1

    
    G-UUA--------GAA*-C    1

    
    G-UUA--------UUA*-C    1

    
    U-UGA--------UAA*-G    1

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

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

    
    G-UGA--------AG-*-C    1

    
    G-UGG--------AG-*-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_53596.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L	2.76	-24.77	5	3
2	Motif group IL_38186.6 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	1.38	-26.56	3	2
3	Motif group IL_46086.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	1.38	-35.40	7	4
4	Motif group IL_33711.1 View motif instance in 3D Basepair signature: cWW-cSH-cWW-L-L-R-L	0.46	-49.68	6	4	Minor groove platform
5	Motif group IL_27393.10 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L-R	0.46	-76.02	7	5

Loop 2 Internal loop

Column numbers: 45-48, 69-71 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--G*C-U   39

    
    U--A*U-U   26

    
    U--C*G-U    7

    
    U--U*A-U    4

    
    AAAG*C-C    3

    
    A--G*C-U    3

    
    U--G*U-U    3

    
    AAAG*CCC    1

    
    AAAG*C-A    1

    
    CA-C*G-U    1

    
    GG-G*C-U    1

    
    U--G*CCU    1

    
    A--A*U-U    1

    
    A--G*C-G    1

    
    G--G*C-U    1

    
    Omitted sequenced and counts

    
    ---A*U--   49

    
    ---G*U--   38

    
    A--A*U--   23

    
    ---C*G--   19

    
    ---U*G--   11

    
    A--C*G--    9

    
    ---C*G-G    8

    
    ---G*U-U    8

    
    ---G*C--    7

    
    ---U*A--    5

    
    ---G*U-A    3

    
    A--G*U--    3

    
    A--U*A--    3

    
    ---A*U-U    2

    
    ---G*C-U    2

    
    ----*---    2

    
    AA-A*U--    1

    
    AA-G*C--    1

    
    AA-U*A--    1

    
    ---A*U-G    1

    
    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 View motif instance in 3D Basepair signature: cWW-L-cWW	93.55	5.81	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	60.22	0.13	3	2	Multiple bulged bases
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	11.83	-5.19	3	1	Intercalated cWS
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	11.83	-6.97	3	1
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	10.75	-11.31	2	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	10.75	-18.45	4	1
7	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	7.53	-6.75	3	1	Multiple bulged bases
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	6.45	-17.95	2	1	Single stack bend
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	6.45	-19.01	2	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	6.45	-22.86	4	1

Loop 3 Hairpin loop

Column numbers: 52-65 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ---GUGACA-----   21

    
    ---UGCUC------   20

    
    A--AGAGCA----U   12

    
    U--UUUC------A   12

    
    A--AGACCA----U    9

    
    UU-UUUC-----AG    7

    
    U--UAGUC-----A    7

    
    ---GUGAUA-----    7

    
    AUUUCGCA---GAU    5

    
    U--GUCA------G    5

    
    ---CUAACAA----    4

    
    ---GUGUCAA----    4

    
    A--UGACU-----U    4

    
    C--UUGCU-----G    4

    
    U--UACUC-----A    4

    
    ---UGGUCA-----    4

    
    U--GCCA------G    4

    
    ---UAAUC------    4

    
    A--CUGAUAA---U    3

    
    AU-GCGAU----GU    3

    
    A--AUGCCA----U    3

    
    A--AUUCCA----U    3

    
    U--UUUUCA----G    3

    
    ---CUAACCA----    3

    
    A--UGACC-----U    3

    
    G--UGACA-----C    3

    
    ---AUAUCA-----    3

    
    ---UUAAUC-----    3

    
    C--GCCA------G    3

    
    U--GGUC------A    3

    
    ---UGUCA------    3

    
    GUGUCGAC---CAC    2

    
    UC-CUGACA---GG    2

    
    U--CUAAUCA---A    2

    
    U--GUGACAA---G    2

    
    UU-UAACA----AA    2

    
    A--ACACCA----U    2

    
    U--AUGACA----G    2

    
    UU-AAUC-----AA    2

    
    ---CUAAUCA----    2

    
    ---CUGACAA----    2

    
    ---CUUGUCA----    2

    
    ---GUGACGA----    2

    
    C--UGACU-----G    2

    
    G--CUCCA-----C    2

    
    U--UGUCA-----A    2

    
    ---CUGUCA-----    2

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

    
    ---UAGUC------    2

    
    ---UUGCU------    2

    
    ---ACAC-------    2

    
    ---GUCA-------    2

    
    ---UGCA-------    2

    
    GUCGCGCA---GAU    1

    
    AA-CCAACA---UU    1

    
    GG-AUACCG---CC    1

    
    GG-GAGACA---CC    1

    
    GUUUUCA----GAC    1

    
    ---CAUAACCAA--    1

    
    AU-UCGAU----GU    1

    
    AUUAAUC----AA-    1

    
    CU-UUUCA----AC    1

    
    G--UAAACUG---C    1

    
    GU-UGUCA----AC    1

    
    U--CUAACAA---A    1

    
    UC-UGGCA----GA    1

    
    ---GAUGAAAA---    1

    
    A--AGACAA----U    1

    
    A--AUGCAA----U    1

    
    A--UUGACA----A    1

    
    C--CUGACA----G    1

    
    G--AUACCA----C    1

    
    G--CAAUAU----C    1

    
    U--CUGAAC----A    1

    
    U--CUGGCA----G    1

    
    U--UUGACA----A    1

    
    UU--AAUC----AA    1

    
    ---CCAGUCA----    1

    
    ---CUAGUCC----    1

    
    ---GUAAGCA----    1

    
    ---GUAGUUA----    1

    
    ---GUGACAA----    1

    
    ---UUAACCA----    1

    
    ---UUAGCAA----    1

    
    ---UUGACAA----    1

    
    A--GCUAC-----U    1

    
    C--GGUCA-----G    1

    
    U--GAACC-----A    1

    
    U--UAACC-----A    1

    
    U--UAGUU-----A    1

    
    U--UGAAC-----A    1

    
    U--UGACC-----G    1

    
    U--UGAUA-----A    1

    
    ---AAGCCA-----    1

    
    ---ACACCA-----    1

    
    ---AGACCA-----    1

    
    ---AGAGCA-----    1

    
    ---AGGCUA-----    1

    
    ---AUGACA-----    1

    
    ---AUGCCA-----    1

    
    ---AUGUUA-----    1

    
    ---GUGAU-----A    1

    
    ---UGUCAA-----    1

    
    ---UGUUAC-----    1

    
    ---UUAGUC-----    1

    
    ---UUUGUC-----    1

    
    U--GAGA------A    1

    
    U--UUAC------A    1

    
    ---CUGCU------    1

    
    ---UAACA------    1

    
    ---UAUCA------    1

    
    ---UGCAA------    1

    
    ---UGUUA------    1

    
    ---UUACA------    1

    
    U---AAUC------    1

    
    U--GUC-------A    1

    
    ---GACA-------    1

    
    ---GCAA-------    1

    
    ---UGAC-------    1

    
    ---UGAU-------    1

    
    ---UGUC-------    1

    
    ---GUU--------    1

    
    ---UAC--------    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_70782.2 View motif instance in 3D Basepair signature: cWW-F	36.21	-48.58	3	3
2	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	18.97	-41.88	4	3
3	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	16.90	-152.00	4	3
4	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	15.86	-43.85	3	2
5	Motif group HL_64690.6 View motif instance in 3D Basepair signature: cWW-cSW-F-F-F-F	15.86	-142.32	4	3
6	Motif group HL_67667.2 View motif instance in 3D Basepair signature: cWW-F-F	12.07	-1770.71	4	3.5
7	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	11.72	-54.89	3	3
8	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	11.72	-557.28	3	2	Purine riboswitch
9	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	11.03	-1544.01	2	2	Pseudoknot geometry
10	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	10.69	-368.29	3	2	Mini UNCG

Loop 4 Internal loop

Column numbers: 78-81, 353-355 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    A--U*AGU   35

    
    A--A*UGU   31

    
    A--C*GGU   27

    
    A--U*GUA   26

    
    G--U*GGC   24

    
    G--C*GGC   19

    
    A--G*UGU   12

    
    GU-U*AAG   11

    
    A--G*CGU   11

    
    G--U*AGC    9

    
    G--A*UGC    8

    
    AA-C*GGU    7

    
    A--C*GUU    6

    
    A--A*GGU    5

    
    G--C*GUC    5

    
    CAUU*AAU    4

    
    AU-U*AGU    4

    
    G--G*UGC    4

    
    G--U*AUC    4

    
    ACUU*AGU    2

    
    CAUU*GAU    2

    
    AA-C*GUU    2

    
    CA-U*AGG    2

    
    GA-C*GGG    2

    
    A--U*GUU    2

    
    C--A*UGA    2

    
    GCCC*GGU    1

    
    UACU*GGU    1

    
    UGCG*CUG    1

    
    UGUU*AGC    1

    
    AA-A*UGU    1

    
    AA-U*GGU    1

    
    AA-U*GUU    1

    
    AC-C*GGU    1

    
    CA-U*GAU    1

    
    GA-C*GUC    1

    
    GG-C*GAA    1

    
    GG-G*CUU    1

    
    GU-A*UAC    1

    
    GU-G*UAU    1

    
    GU-U*AAC    1

    
    GU-U*AGC    1

    
    A--A*UUG    1

    
    A--U*GGC    1

    
    A--U*GGU    1

    
    CAU-*-AG    1

    
    G--A*GGC    1

    
    G--G*GGC    1

    
    AA--*-UU    1

    
    AU--*-GU    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 View motif instance in 3D Basepair signature: cWW-cWW	89.66	27.97	4	1	Multiple bulged bases
2	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	87.93	25.61	3	1	Stack and bulge
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.41	28.53	4	1	Intercalated cWS
4	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	81.72	51.36	3	0	Major groove platform
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	81.72	18.31	3	1
6	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	81.38	32.95	2	0	Single stack bend
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	81.38	25.66	3.5	1
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	81.03	49.83	2	0	Major groove intercalation
9	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	81.03	39.42	2	0	Major groove platform
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	80.34	7.29	3	1	Single stack bend

Loop 5 Internal loop

Column numbers: 81-82, 351-353 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UU*A-G   30

    
    UA*U-A   29

    
    CG*C-G   24

    
    UA*U-G   24

    
    CA*U-G   20

    
    UG*C-A   18

    
    AU*A-U   17

    
    AG*C-U   13

    
    GC*G-U   12

    
    UG*U-A   12

    
    CG*U-G   11

    
    UU*A-A    9

    
    GC*G-C    8

    
    AA*U-U    6

    
    CU*A-G    6

    
    AC*G-U    5

    
    GU*A-C    5

    
    GU*A-U    4

    
    CC*GUG    2

    
    UU*AGA    2

    
    AA*U-G    2

    
    AU*A-G    2

    
    AU*G-U    2

    
    CC*G-G    2

    
    UG*U-G    2

    
    CC*GAG    1

    
    CC*GGG    1

    
    CG*CAG    1

    
    CG*CGG    1

    
    CU*AUG    1

    
    CU*GUG    1

    
    UA*UAA    1

    
    UA*UAG    1

    
    UA*UGG    1

    
    AC*G-G    1

    
    AG*U-G    1

    
    AU*C-U    1

    
    CU*U-G    1

    
    GA*U-G    1

    
    GG*C-U    1

    
    UA*C-A    1

    
    UG*C-G    1

    
    UU*G-G    1

    
    Omitted sequenced and counts

    
    UA*--A    2

    
    -U*A--    2

    
    -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 View motif instance in 3D Basepair signature: cWW-L-cWW	97.89	19.90	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	95.79	19.24	2	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	94.74	21.26	3	2	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	88.77	16.70	3	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	70.18	3.80	1	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	69.82	14.88	3	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	69.82	10.91	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	69.82	2.88	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.40	8.88	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.40	6.50	2	1	Single stack bend

Loop 6 Internal loop

Column numbers: 83-84, 348-350 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CA*U-G   50

    
    UC*G-A   31

    
    UA*U-A   20

    
    AC*G-U   17

    
    GU*G-C   14

    
    AU*A-U   11

    
    CG*C-G   11

    
    GU*A-U   10

    
    UA*U-G    9

    
    AA*U-U    8

    
    GU*A-C    8

    
    UU*A-A    8

    
    UU*A-G    8

    
    GC*G-C    7

    
    GG*U-C    7

    
    UG*U-G    7

    
    CC*G-G    6

    
    UG*C-A    6

    
    UU*G-A    6

    
    CU*A-G    5

    
    CC*A-G    4

    
    CG*U-G    4

    
    CG*C-A    3

    
    GA*U-C    3

    
    GC*A-C    3

    
    GC*G-U    3

    
    GG*U-U    3

    
    UC*G-G    3

    
    AA*C-U    2

    
    AU*G-U    2

    
    CU*G-G    2

    
    CA*UAG    1

    
    CA*C-G    1

    
    GC*G-A    1

    
    GG*C-C    1

    
    GU*G-U    1

    
    UG*C-G    1

    
    UU*G-G    1

    
    Omitted sequenced and counts

    
    U-*--G    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	99.31	17.35	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	95.83	24.85	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	92.01	17.64	3	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	80.90	15.08	3	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	78.47	4.69	1	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	76.39	13.99	3	1
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	75.00	4.12	2	1
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	71.88	10.06	2	1	Major groove intercalation
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	67.01	7.86	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	67.01	4.86	2	1	Single stack bend

Loop 7 Internal loop

Column numbers: 84-86, 347-348 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    C-U*AG   41

    
    A-C*GU   28

    
    A-G*UU   20

    
    A-U*AU   16

    
    U-G*CA   16

    
    A-A*UU   15

    
    C-C*GG   13

    
    U-A*UG   13

    
    U-A*UA   11

    
    U-C*GA   11

    
    U-U*AA   10

    
    C-A*UG    8

    
    G-U*AU    8

    
    G-C*GC    7

    
    A-U*GU    6

    
    G-A*UC    6

    
    A-G*CU    4

    
    G-C*GU    4

    
    U-C*GG    4

    
    U-G*CG    4

    
    GAC*GC    3

    
    C-A*UA    3

    
    C-G*CG    3

    
    G-A*UU    3

    
    G-G*CU    3

    
    U-U*AG    3

    
    GUC*GC    2

    
    A-C*GC    2

    
    C-U*UA    2

    
    G-U*GC    2

    
    U-U*GA    2

    
    UAU*AG    1

    
    A-A*CU    1

    
    A-U*GC    1

    
    A-U*UU    1

    
    C-C*UG    1

    
    C-G*UG    1

    
    C-U*GG    1

    
    G-A*CU    1

    
    G-G*CC    1

    
    G-G*UU    1

    
    G-U*AC    1

    
    G-U*GU    1

    
    U-A*CG    1

    
    Omitted sequenced and counts

    
    C-U*-A    2

    
    --A*U-    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	98.25	18.08	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	96.15	19.06	3	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	95.80	24.71	3	2	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	86.71	16.36	4	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	85.31	5.39	1	1	Single bulged G
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	78.32	11.27	2	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	78.32	6.54	3	1
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	73.78	15.39	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	68.88	9.38	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	68.88	5.76	2	1	Single stack bend

Loop 8 Internal loop

Column numbers: 87-88, 308-346 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UA*UUGAGGGUGU----------------------------A   22

    
    CG*A-------------------------------------G   13

    
    CU*G-------------------------------------G    6

    
    UU*G-------------------------------------A    5

    
    CG*AUCACCCCUGUGUCAA----------------------G    4

    
    UA*UUGAGGGCGU----------------------------A    4

    
    GG*A-------------------------------------C    4

    
    CC*-------------------------------------GG    3

    
    UC*A-------------------------------------G    3

    
    UG*A-------------------------------------G    3

    
    AC*G------------------------------------GU    2

    
    GU*GG------------------------------------C    2

    
    CC*G-------------------------------------G    2

    
    CG*G-------------------------------------G    2

    
    CU*A-------------------------------------G    2

    
    UC*G-------------------------------------A    2

    
    UC*G-------------------------------------G    2

    
    UU*AGAUGAAGCUUAAAGGUUACGGAAAGUACCAAUAGUUAG    1

    
    CC*UAUUCGCCUUUAAUUAGACGCUAUG-------------G    1

    
    UA*UUGAGAGUGU----------------------------A    1

    
    UG*----------------------------UUGAGGGUGUA    1

    
    UG*UUGAGGGUGU----------------------------A    1

    
    AC*UUGAGAGUG-----------------------------U    1

    
    UC*GGAAAGAG------------------------------A    1

    
    CU*CAAG----------------------------------G    1

    
    AC*U-----------------------------------GGG    1

    
    UC*AC----------------------------------G-G    1

    
    AU*------------------------------------GGU    1

    
    CC*U------------------------------------GG    1

    
    AC*G-------------------------------------U    1

    
    AU*-------------------------------------UU    1

    
    CA*G-------------------------------------G    1

    
    CU*U-------------------------------------G    1

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

    
    GC*G-------------------------------------C    1

    
    GU*A-------------------------------------C    1

    
    GU*G-------------------------------------C    1

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

    
    UU*-------------------------------------AA    1

    
    UU*G-------------------------------------G    1

    
    Omitted sequenced and counts

    
    GG*--------------------------------------C   39

    
    UG*--------------------------------------G   38

    
    CG*--------------------------------------G   27

    
    UG*--------------------------------------C   13

    
    AG*--------------------------------------U   10

    
    UU*--------------------------------------A    7

    
    GC*--------------------------------------C    6

    
    UC*--------------------------------------A    6

    
    CU*--------------------------------------G    5

    
    UG*--------------------------------------A    5

    
    CC*--------------------------------------G    4

    
    UU*--------------------------------------G    4

    
    AA*--------------------------------------U    3

    
    AC*--------------------------------------U    3

    
    GA*--------------------------------------C    2

    
    GG*--------------------------------------U    2

    
    UC*--------------------------------------G    2

    
    -A*UUGAGGGUGU-----------------------------    1

    
    AU*--------------------------------------U    1

    
    CA*--------------------------------------G    1

    
    CG*--------------------------------------A    1

    
    GG*--------------------------------------A    1

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

    
    UA*--------------------------------------U    1

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

    
    CA*---------------------------------------    1

    
    -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 View motif instance in 3D Basepair signature: cWW-L-cWW	59.62	-2975.83	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	46.15	-3812.75	4	2	Multiple bulged bases
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.73	-3727.35	4	1	Intercalated cWS
4	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	31.73	-3829.73	3	1	Multiple bulged bases
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	29.81	-3847.42	2	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	27.88	-3619.34	4	1
7	Motif group IL_19852.1 View motif instance in 3D Basepair signature: cWW-tWH-cWW-cWH-cWH-cWH	22.12	-401.70	10.5	9	Part of G-quadruplex
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	19.23	-3731.36	2	1	Single stack bend
9	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	19.23	-3733.56	4	1
10	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	18.27	-824.92	3	1	Major groove intercalation

Loop 9 4-way junction loop

Column numbers: 88-112, 186-188, 251-256, 298-308 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAAUGAAGCU--------------C*G-C*G-A-AG*U-GAAAGUAA-   17

    
    GGAAAAUG----------------A*U-U*C-G-AG*C-AAGAUUAA-   11

    
    GAAUAAAGCU--------------C*G-C*G-A-AG*U-GAAAGUAA-    6

    
    GAAGCUGU----------------G*U-U*A-GAA-*A-ACACAGAA-    6

    
    GUGCUAAAUCGCU-----------C*G-G*G-A-AU*A-AAGACGUU-    5

    
    GAAUUG------------------A*U-U*G-A-AG*C-AACAAAGU-    4

    
    UAAA--------------------C*GAG*U-ACGA*U-GAAUU--A-    4

    
    GGAAAGCCA---------------C*G-U*G-A-AG*C-AACGGCAAA    3

    
    UGAAUGUAG---------------A*U-U*A-A-AG*C-AAAUACAAG    3

    
    GAAUGCAG----------------A*U-U*A-U-AG*C-AAGUGCAA-    3

    
    GUAAUUUC----------------C*G-G*G-G-AG*C-AACAAAAA-    3

    
    UGAAUG------------------A*UUG*U-U-CU*G-AGUAUCAAG    3

    
    GGUAACG-----------------A*U-U*G-A-AG*C-AACAAUGC-    3

    
    GGUGACG-----------------A*U-U*G-A-AG*C-AACAAUGC-    3

    
    CUUAAUAACUACU-----------A*U-U*A-G-CA*G-UAGAGAGA-    2

    
    GAAAAGUGCU--------------C*G-C*G-A-AU*A-GAAAGUAAA    2

    
    UGUGACGGAA--------------C*G-U*G-G-AG*C-AACUUCAGG    2

    
    ACCUCUAAUU--------------C*GA-*--UCAG*U-GCGUGGGU-    2

    
    GGAACGCCA---------------C*G-U*G-A-AG*C-AACGGCAAA    2

    
    GUAGUACUC---------------A*U-G*G-A-AG*C-AACAGUAAA    2

    
    GUGAUUCAG---------------A*U-U*G-G-AG*C-AACUGAAGG    2

    
    CUAAACAAGG--------------C*G-U*G-A-AU*A--AACUUAA-    2

    
    GAAUAUUC----------------A*U-G*G-A-AG*C-AACAACAAA    2

    
    GGAUGUCG----------------G*C-U*A-UACU*U-AAAGACAA-    2

    
    ACAUAAUUCC--------------C*-UU*G-U---*--UAAGAAGAU    2

    
    CAACCGGA----------------G*U-U*G-G-AG*C-AAUCGAAG-    2

    
    GAAUAGUG----------------G*U-U*G-UAAG*C--AAAACAU-    2

    
    GUACUUUC----------------A*U-G*G-G-AG*C-AACAAAAA-    2

    
    GUAGUUUC----------------U*A-G*G-G-AG*C-AACAAAAA-    2

    
    GAAAUGGU----------------C*G-U*G-A-A-*U-AAAUCAAA-    2

    
    GAAUAGUG----------------G*U-U*U-A-AG*C-AAAA-CAU-    2

    
    GGUGAUG-----------------A*U-U*G-A-AG*C-AACAACGC-    2

    
    CAAGG-------------------A*U-U*G-A-AG*C-AACCGAGCA    2

    
    GAAAUGGU----------------C*G-U*G-A-A-*--AAAUCAAA-    2

    
    GUAAUG------------------A*U-U*G-A-AG*C-AACAAUUC-    2

    
    UAAACCC------------------*A-G*U-ACGA*U-GAA--UUA-    2

    
    GCA---------------------C*G-U*G-GAUG*CAAAGCG--A-    2

    
    AUUA--------------------A*U-U*G-A-AG*C-AACAAU---    2

    
    CCUAUAAAUAAUACUCACAUUCCUG*U-G*G-A-AA*G-AAAAGGAUG    1

    
    CUAGUCACAUAUGACAAAUUAG--A*UUU*A-CAAG*C-AAGUAAGUG    1

    
    AGGGUUAAUCUCGUAAAGCGG---C*AAA*C-U-AC*G-UGCCGUGGG    1

    
    CUACCAUUGUUAUGGGAAGCAG--A*U-U*U-A-CG*C-AAGUGUGUG    1

    
    UAAGGGCGACCGAAAGUCCUAA--A*UAC*G---AC*G-UGUGAAGAU    1

    
    UCCUAAUCAAGACGCCCCCUG---C*G-C*C-AACG*C-GCCGGCCGG    1

    
    CUUCGCUUUCGAGCGUACUACG--C*GCU*U-U--G*C-UGUUAG-AG    1

    
    CCCACCUGCGGGUAAGAAU-----A*AAA*G-CCAC*A--AUGGUUCU    1

    
    CCGCUCGAAGAGAGUGGUCUAG--A*U-G*C-U-GC*U-----AGAGG    1

    
    UCUGCCUUAAGAC--------UCUC*G-G*G-A-AU*A-AAGAAGCA-    1

    
    CUUAAUAACUACU-----------A*UUU*GAG-CA*G-UAGAGAGA-    1

    
    GGACAUGAAAAGGU----------C*-GU*G-GAGA*C-AAACCUAA-    1

    
    CGUGCUAAAUCGCU----------C*G-G*G-A-AU*A-AAGACGUU-    1

    
    GGUAAUAAAUCCU-----------G*U-C*G-G-GG*C-UUGGGUAAA    1

    
    CCUAUCAAAGC-------------A*U-U*A-AACU*A-GUGUGUGUG    1

    
    GGAUAAGUCGAU------------A*U-G*G-ACUA*U-AAUCGCAA-    1

    
    GUACUAAAUCGCU-----------C*G-G*G-A-AU*A-AAGACGUU-    1

    
    ACAUAAUUCU--------------C*AAU*U-C-AU*G-AAAGAAGAU    1

    
    CAAAAAGACU--------------C*G-G*G-A-AU*A-AAGUCUAAA    1

    
    CUGUAAGUC---------------A*U-U*G-AUAG*U-UUCUGCCAG    1

    
    GAAAGACGCU--------------C*G-C*G-A-AC*G-GAAAGUAAA    1

    
    GAAUAGGCU---------------A*U-U*A-GGAG*C-AAAGCCUAA    1

    
    GGAACAGCUG--------------A*U-U*G-A-AG*C-AACAGAGAA    1

    
    GGAACUGCCU--------------A*U-A*--AAAG*C-AAUGGAGAA    1

    
    ACAUAAUUCC--------------U*AAU*U-C-A-*--UAAGAAUAU    1

    
    CUCAAGGGAC--------------A*U-U*C-GGAG*C-AAGGGAG--    1

    
    CUCAAGGGAU--------------A*U-U*C-GGAG*C-AAGGGAG--    1

    
    CUGUAAGUC---------------A*U-U*G-AUAG*U-UUCUGCCA-    1

    
    GAAUAAAGCU--------------C*-GC*G-A-AG*U-GAAAGUAA-    1

    
    GGAACGCCG---------------C*G-U*G-A-AG*C-AACAGCAAA    1

    
    GGAAUUCUU---------------A*U-G*G-G-AG*C-AACAGAAAA    1

    
    GGAGCGCCG---------------C*G-U*G-A-AG*C-AACGGCAAA    1

    
    GGAUAGGGCU--------------C*G-C*G-A-A-*A-GAAAGUAAA    1

    
    GGUAAGUC----------------A*UGU*G-G-AG*CAAAACGAGA-    1

    
    GUAAAUUG----------------U*AAC*G-GUAG*C-GAGAAUAA-    1

    
    UAGAUGUGU---------------A*U-U*A-U-AG*U-AAAUGCAAG    1

    
    UGAACGAUG---------------C*G-U*G-U-UC*G-AAUAUCAAG    1

    
    UGAACGUAG---------------A*U-U*A-A-AG*C-AAAUACAAG    1

    
    UGUGACGGAA--------------C*G-U*G-G-A-*A-ACUCCAGAG    1

    
    AGAAAACG----------------A*U-U*G-G-AG*C-AACAAUGCU    1

    
    CUAAACAAGG--------------C*G-U*G-A-AU*A-AACU-UAA-    1

    
    CUAGACAAGG--------------C*G-U*G-A-AU*A--AACUUAA-    1

    
    GAACAACA----------------G*C-C*G-AUAA*G-AAUGUUAA-    1

    
    GAAUAUCG----------------G*C-U*A-UAUU*U-AAAGAUAA-    1

    
    GAAUGUCG----------------G*C-U*A-UACU*U-AAGGACAA-    1

    
    GGAUAUCG----------------C*G-U*A-UACC*U-AAAGAUAA-    1

    
    GUAGUUCC----------------C*G-C*G-GAAG*C-AACGAAAA-    1

    
    GUAGUUCC----------------C*G-C*G-GGAG*C-AACGAAAA-    1

    
    GUAUAACG----------------A*U-U*G-AAAG*C-GAAGUCAC-    1

    
    GUAUAUCG----------------A*U-U*A-UAGU*U-AAAGAUAA-    1

    
    UCUAUAAAUCGAC------------*-AA*U-GACC*G-----UUGA-    1

    
    UGUAAGUC----------------A*U-U*G-AUAG*U-UUCUGCCA-    1

    
    AAAUGCAA----------------A*U-U*A-U-AG*C-AAAUGCAA-    1

    
    CCAAGGGAU---------------A*U-U*C-GUAG*C-AAGGGG---    1

    
    CUUGUU------------------C*G-U*A-AAAU*A-AAAUGUAGG    1

    
    GAACAUUU----------------A*U-A*G-A-AG*C-AACAAUAA-    1

    
    GAACGCUA----------------G*C-U*C-U-AG*C-GAAAGCAA-    1

    
    GAACGUUG----------------A*U-U*G-U-AG*C-AAUAACAA-    1

    
    GAAUAGUC----------------A*U-G*G-A-AG*C-GACACUAA-    1

    
    GAAUGCAA----------------A*U-U*G-U-AA*U-AAGUGCAA-    1

    
    GAAUGCAA----------------A*U-U*G-U-AG*C-AAGUGCAA-    1

    
    GAAUGCAG----------------A*U-U*A-U-AG*C-AAAUGCAA-    1

    
    GAAUGCAG----------------A*U-U*G-U-AG*C-AAGUGCAA-    1

    
    GAAUGUAG----------------A*U-U*A-U-AG*C-AAAUACAA-    1

    
    GAAUGUAU----------------C*G-U*G-A-AG*C-AACUACAA-    1

    
    GCAUUCCG----------------U*A-U*G-A-AG*C-AACGGACG-    1

    
    GGAAAAUG----------------A*U-U*C-A-AG*C-AAGAUUAA-    1

    
    GGAUAAAU----------------C*G-U*G-G-AG*C-AACUUUAA-    1

    
    GUAAGGUC----------------G*CGU*G-U-AG*C-AAAC-CAA-    1

    
    GUAAUUUC----------------C*G-G*--GGAG*C-AACAAAAA-    1

    
    GUACAGCG----------------A*U-U*A-U-AG*C-AAAGCUAA-    1

    
    GUACAUAG----------------C*G-U*A-G-AG*C-GAUUAUAA-    1

    
    GUAGAAUG----------------A*U-U*C-U-AG*C-AAGAUUAA-    1

    
    GUAUAUCA----------------A*U-U*G-A-AG*C-AACGAUAA-    1

    
    GUAUGUGG----------------C*G-U*A-A-AU*A-AAUCACAA-    1

    
    GUAUGUUG----------------A*U-U*G-G-AG*C-AACGACAA-    1

    
    UCACUUG-----------------A*U-U*G-A-AG*C-AACAGAAAA    1

    
    UCUAUAAAUCGAC-----------A*A-A*U-GACC*G------UU--    1

    
    UGAAUG------------------A*U-U*U-CUUC*G-AGUAUCAAG    1

    
    UGAAUG------------------A*UUG*U-U-CU*U-AGGAGUAUC    1

    
    AAAGAGAA-----------------*A-C*G-U-AU*A-AACCGCUU-    1

    
    ACAUAAUUCC--------------C*-UU*G-U---*--UAAGAAGA-    1

    
    CAAGAAA------------------*A-C*G-U-AU*A-AACCGCUUU    1

    
    CUCGUU------------------C*GUG*A-AGAU*A-GAAAGAG--    1

    
    GGUAAUG-----------------A*U-U*G-G-AG*C-AACAAUAC-    1

    
    GGUAAUG-----------------A*U-U*G-G-AG*C-AACAAUGC-    1

    
    GGUGACG-----------------A*C-U*G-G-AG*C-AACAAUGC-    1

    
    GGUGACG-----------------A*U-U*G-G-AG*C-AACAAUGC-    1

    
    GGUGAUG-----------------A*U-U*G-A-AU*C-AACAACGC-    1

    
    GUUAUAUG----------------A*U-U*G-G-AG*C-AAUACA-C-    1

    
    CAGAAG------------------A*U-U*A-G-AG*C-AAUUAAAG-    1

    
    CCAUAAUAAU---------------*-AG*U-U-CC*G-----CUAGG    1

    
    CGAGG-------------------A*U-U*G-A-AG*C-AACCGAGCA    1

    
    GAAGUG------------------A*U-U*G-G-AG*C-AACAAAAU-    1

    
    GGGAACU-----------------C*G-U*G-A-AG*C-AAAA-GAA-    1

    
    GUAACG------------------A*U-U*G-A-AG*C-AACAAUGC-    1

    
    UAAGUA------------------A*U-U*G-A-AG*C-AACAAAGA-    1

    
    UAGAGU------------------A*U-U*G-A-AG*C-AAUAGUUA-    1

    
    UUUAAAUAC---------------C*GA-*--UCAG*U-----GCGUA    1

    
    CGAACG------------------A*U-U*G-A-AG*C-AACGGUG--    1

    
    UAAACCC------------------*-AG*U-ACGA*U-GAA--UUA-    1

    
    UAUAA-------------------U*A-A*A-UAAG*C-AAAU-UUA-    1

    
    CAAUA-------------------A*U-U*G-A-AG*C-AAUAAUG--    1

    
    CGCA--------------------C*G-U*G-G-AU*A-AAGCGAGU-    1

    
    GAAUUU------------------G*U-U*A-G-G-*--AGAUAAGU-    1

    
    UAUAA-------------------U*A-A*--UGAG*C-AAAU-UUA-    1

    
    ACA---------------------C*G-U*G-G-AU*A-AAGCGAGU-    1

    
    CAUG--------------------C*G-U*G-AUAU*U-AAAUGA---    1

    
    UUAAAAUC-----------------*-GU*C---AG*U--ACGGU---    1

    
    Omitted sequenced and counts

    
    ACAUAAUUCC--------------C*--U*U-----*--UAAGAAGAU   13

    
    ACAUAAUUCC--------------C*--U*G-U---*--AAAGAAGAU    3

    
    GGAAGACG-----------------*---*------*--ACGGACUAA    3

    
    CAUUAAAUCC--------------A*--G*C-U-AC*G-GAUUGGUAG    2

    
    GAAUAGUG----------------A*--C*G-AAAG*C-AAAACUAA-    2

    
    ACAUAAUUCC--------------C*--U*G-U---*--UAAGAAGAU    2

    
    AUAUAAUUCC--------------C*--U*G-U---*--AAAGAAGAU    2

    
    GUACCUCU----------------G*C--*--GAAG*C-AACGGGAA-    2

    
    UGUGCUCUCAAAAGGAGUUAUGUGA*U--*--AGAG*CUUACAGUUC-    1

    
    GGCUUUCGGCAGUGGAAGCUGC--C*--C*G-A-AU*A-GAAAAUGC-    1

    
    ACCUAAUCAAGACGCCCCCU----G*C--*C-A-AC*G-CCGGCCG-G    1

    
    UCUAAAUCGAU--------------*--A*--GCAG*U-UUGUGCGUG    1

    
    UUAUAAAUAC--------------A*--G*U-GUGG*C-UCUGGAUA-    1

    
    UUGUUAAGACC-------------U*--U*G-G-AG*U-CAGGCUGA-    1

    
    ACAUAAUUCC--------------C*--U*C-C-A-*--UAAGAAGAU    1

    
    ACAUAAUUCC--------------C*--U*U-C-A-*--UAAGAAUAU    1

    
    CGUAAAUCU---------------C*--U*U-UGCG*C-AAGAGUG--    1

    
    GUAUAAUG----------------C*--C*A-AUAA*A-AAAAUUAA-    1

    
    ACAUAAAUCC--------------C*--U*G-U---*--UAAGAAGAU    1

    
    CUUGAUGA----------------A*--A*C-UCUC*G--AGCGGAG-    1

    
    GAAGAGCA----------------U*G--*--UAGC*A-AAUGCUAA-    1

    
    GAAUAACA----------------G*C--*--UAGC*A-AAUGUUAA-    1

    
    GAAUGUUG----------------A*--U*G-U-AG*C-AAUAACAA-    1

    
    GCAUAAAUCC--------------C*--U*G-U---*--AAAGAAGAU    1

    
    GUAUUUUC----------------A*--C*G-A-AG*C-AACAAAAA-    1

    
    UCAAUGC-----------------A*--U*G-A-AG*C-AAGCAAGGA    1

    
    ACAUAAAUCC--------------C*--U*U-----*--UAAGAAGAU    1

    
    CGUAAUUCU---------------C*--U*G-U---*--UAAGAAGAU    1

    
    GCAUAAUUCC--------------C*--U*G-U---*--UAAGAAGA-    1

    
    AAGAGA-------------------*--A*U-CCGG*C-ACCGCUUU-    1

    
    CAAAUAA------------------*--G*UUACGG*C-GCUU-UG--    1

    
    UAGAGC------------------A*U--*--U-AA*U-UAUUAAAAA    1

    
    CAAAUAAGG----------------*---*--G-A-*A-ACCGCUUU-    1

    
    UGAAUGAUG----------------*--C*G----C*G-UAUCAAG--    1

    
    GGAAGACGA----------------*---*------*--ACGGACUAA    1

    
    CACAAGA------------------*--G*A-U-UC*G-----CUGU-    1

    
    CAUAA-------------------G*A--*------*--CCACCGUGU    1

    
    ------------------------C*G--*------*-----------    1

No Matches Found View All Results for this Loop

Loop 10 Internal loop

Column numbers: 114-117, 181-184 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--U*G--G   35

    
    U--U*A--A   32

    
    G--G*UGGC   21

    
    A--U*A-UU   13

    
    U--U*A--G   12

    
    C--C*G--G    8

    
    U--A*U--G    8

    
    G--U*AAAC    7

    
    A--U*A--U    7

    
    U--C*G--G    6

    
    G--U*AC-C    5

    
    G--A*G--C    5

    
    G--U*A--C    5

    
    A--C*AGAU    4

    
    C--G*CA-G    4

    
    A--A*U--U    4

    
    A--U*G--U    4

    
    G--A*C--C    4

    
    G--G*UGAC    3

    
    A--U*G--A    3

    
    C--U*A--U    3

    
    U--A*U--A    3

    
    C--C*AGAG    2

    
    C--U*AAUG    2

    
    G--A*UGAC    2

    
    A--A*AG-U    2

    
    U--C*GG-A    2

    
    U--U*AA-G    2

    
    C--A*U--G    2

    
    C--G*C--G    2

    
    C--G*G--G    2

    
    C--U*A--G    2

    
    G--U*G--U    2

    
    U--C*G--A    2

    
    UGCU*AGCA    1

    
    C--U*AGUG    1

    
    G--C*AGAC    1

    
    G--G*ACAA    1

    
    G--G*CGUC    1

    
    G--G*UUAC    1

    
    G--G*UUGC    1

    
    U--G*CUAG    1

    
    U--G*UGAA    1

    
    A--A*A-GU    1

    
    A--U*AA-U    1

    
    C--C*G-AG    1

    
    G--C*UA-C    1

    
    G--G*CA-C    1

    
    G-UG*A--A    1

    
    U--A*AA-A    1

    
    U--A*AC-U    1

    
    U--A*UU-G    1

    
    U--C*GG-G    1

    
    U--U*AG-A    1

    
    U--U*UA-G    1

    
    A--A*G--C    1

    
    A--A*U--C    1

    
    A--A*U--G    1

    
    A--G*A--U    1

    
    A--G*U--U    1

    
    C--A*C--G    1

    
    C--G*A--U    1

    
    C--G*C--U    1

    
    C--U*A--A    1

    
    G--C*G--C    1

    
    G--G*C--C    1

    
    G--U*A--A    1

    
    G--U*G--C    1

    
    U--A*A--G    1

    
    U--C*A--G    1

    
    U--G*A--G    1

    
    U--G*C--G    1

    
    U--U*C--G    1

    
    U--U*G--A    1

    
    U--U*G--U    1

    
    U--U*U--G    1

    
    Omitted sequenced and counts

    
    U--A*---A    4

    
    ---G*CUA-    3

    
    A--U*G---    3

    
    ---G*CAGA    2

    
    ---A*CAGA    1

    
    ---U*ACAA    1

    
    A---*AGUC    1

    
    ---A*UAA-    1

    
    ---C*AGA-    1

    
    ---C*GGU-    1

    
    ---G*C-AA    1

    
    ---G*CAA-    1

    
    ---G*UGA-    1

    
    A---*-AGG    1

    
    A---*-AUC    1

    
    G---*-CAA    1

    
    ---G*CA--    1

    
    ---U*G---    1

    
    --AA*----    1

    
    ----*--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 View motif instance in 3D Basepair signature: cWW-L-cWW	84.73	15.46	3	1	Major groove platform
2	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	62.21	14.65	3	1	Intercalated cWS
3	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	61.45	14.64	3	1	Major groove intercalation
4	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	61.45	8.29	4	1
5	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	59.54	0.24	4	2	Multiple bulged bases
6	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	57.63	2.97	3	1	Multiple bulged bases
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	54.20	12.86	4	1
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	45.04	-0.76	2	1	Single stack bend
9	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	42.75	-8.39	1	1	Single bulged G
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	41.22	-6.68	2	1	Single stack bend

Loop 11 Internal loop

Column numbers: 118-119, 178-180 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AC*G-U   30

    
    GC*G-C   30

    
    AG*U-G   12

    
    UU*A-A   12

    
    GA*U-A   11

    
    AC*A-C    9

    
    AA*U-U    8

    
    AC*A-U    7

    
    CG*G-G    7

    
    GU*A-U    7

    
    AA*U-A    6

    
    AG*G-A    6

    
    AU*G-U    6

    
    GC*G-U    6

    
    GG*C-C    6

    
    UU*A-G    6

    
    UU*G-A    6

    
    AG*C-U    5

    
    GG*C-A    5

    
    GU*A-C    5

    
    GU*G-C    5

    
    AU*A-U    4

    
    CA*U-U    4

    
    GA*G-C    4

    
    UG*U-A    4

    
    UG*U-G    4

    
    AA*A-U    3

    
    AA*G-A    3

    
    AC*U-U    3

    
    CC*U-A    3

    
    UC*G-G    3

    
    UG*C-A    3

    
    UU*G-G    3

    
    AA*A-A    2

    
    AG*C-G    2

    
    AG*G-U    2

    
    AG*U-U    2

    
    CU*A-C    2

    
    CU*A-G    2

    
    GA*U-C    2

    
    GA*U-U    2

    
    GC*A-C    2

    
    GU*C-C    2

    
    GU*G-U    2

    
    UC*G-A    2

    
    UG*A-G    2

    
    AA*A-G    1

    
    AA*G-G    1

    
    AA*G-U    1

    
    AA*U-G    1

    
    AC*C-A    1

    
    AG*C-A    1

    
    AG*G-G    1

    
    AU*A-G    1

    
    AU*G-G    1

    
    CG*U-A    1

    
    CU*A-A    1

    
    GA*A-C    1

    
    GA*G-A    1

    
    GC*A-A    1

    
    GC*G-A    1

    
    GG*G-A    1

    
    GG*U-A    1

    
    UA*U-A    1

    
    UA*U-G    1

    
    UG*A-A    1

    
    UU*U-G    1

    
    Omitted sequenced and counts

    
    -G*U-A    1

    
    -G*U-C    1

    
    A-*A-U    1

    
    AA*--U    1

    
    UA*G--    1

    
    --*-GA    1

    
    GU*---    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	77.74	7.46	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	68.20	9.66	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	55.83	1.73	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	47.70	-10.16	2	1	Single bulged G
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	46.64	-0.13	3	1	Intercalated cWS
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	43.82	-0.86	3	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	42.76	-4.88	2	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	42.76	-8.67	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	38.87	-8.20	2	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	38.87	-11.25	4	1

Loop 12 Internal loop

Column numbers: 119-125, 171-178 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CU----A*CG-----G   15

    
    AA----U*UG-----U   12

    
    CGC---U*AGA-UAAG   10

    
    CG----C*GGA-UAAG   10

    
    CU----A*CA-----G    9

    
    CA----U*AAU-GUAA    7

    
    UA----A*UU-----A    7

    
    GG----C*GC-----U    6

    
    GG----C*GU-----G    6

    
    GG----U*AU-----U    6

    
    GA----A*UAU---AG    5

    
    GC----U*GU-----C    5

    
    AA----G*UG-----U    4

    
    AG----C*AG-----G    4

    
    AU----G*UG-----U    4

    
    GG----U*AC-----U    4

    
    UU----A*UG-----G    4

    
    CAC---U*AGA-UAAG    3

    
    CGC---U*GGA-UAAG    3

    
    CG----U*GAC-GUAA    3

    
    AG----C*GUG----A    3

    
    AGA---G*CG-----U    3

    
    AG----G*CU-----G    3

    
    CG----A*UU-----U    3

    
    CU----U*AG-----G    3

    
    UA----U*UU-----A    3

    
    UG----C*GA-----A    3

    
    CGC----*-GA-UAAG    2

    
    GA----U*UGU----C    2

    
    GUA---U*AA-----C    2

    
    GUA---U*AA-----U    2

    
    UC----U*GGC----A    2

    
    UG----G*CAU----A    2

    
    AA----A*UU-----U    2

    
    AC----G*UU-----U    2

    
    CA----C*GG-----U    2

    
    CG----G*CU-----G    2

    
    GA----U*UG-----A    2

    
    GG----C*GC-----C    2

    
    GU----A*UA-----U    2

    
    GU----U*AG-----C    2

    
    GU----U*AG-----G    2

    
    UA----G*CG-----G    2

    
    UC----A*AG-----G    2

    
    UC----G*UU-----C    2

    
    UG----A*UU-----A    2

    
    UG----G*CU-----G    2

    
    UG----U*UU-----A    2

    
    U-----U*AU-----A    2

    
    GUA-CAC*GAA---AC    1

    
    UGU---U*GGA-UAAG    1

    
    AUAUUAU*AU-----A    1

    
    CA----C*GGA-UAAG    1

    
    CC----U*AAG-GCAA    1

    
    CC----U*AAG-GUAA    1

    
    CG----U*AAC-GUAA    1

    
    CU----G*AGG-UAAC    1

    
    CU--UGA*ACAA---G    1

    
    UC----A*UGG-GCAA    1

    
    UC----C*AGG-UGAA    1

    
    UUC---C*GGU-GAA-    1

    
    CG----G*AAG-UA-A    1

    
    CC----U*AGA---AG    1

    
    CG----A*GGU---AG    1

    
    CG----C*GUA---AG    1

    
    CUA---A*UG----AG    1

    
    GA----A*UAC---AG    1

    
    GA----C*GAU---AC    1

    
    GA----G*UCA---AC    1

    
    GG----A*UAU---AG    1

    
    GUA---G*CG----GC    1

    
    UC----C*ACU---GA    1

    
    UU----C*ACU---GA    1

    
    UUA---A*UG----GA    1

    
    AA----G*UAA----G    1

    
    ACA---C*-A----GU    1

    
    ACG---G*UC-----G    1

    
    AG----A*UUC----U    1

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

    
    CAA---U*AC-----G    1

    
    CAC---U*AA-----G    1

    
    GAU---A*UU-----U    1

    
    GG----U*UU----CU    1

    
    UAA---U*AC-----G    1

    
    -G----G*CU----AA    1

    
    AA----A*UU-----A    1

    
    AA----C*CA-----U    1

    
    AA----C*GG-----U    1

    
    AC----A*UG-----G    1

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

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

    
    AG----G*CG-----U    1

    
    AG----U*AA-----U    1

    
    AU----A*AA-----A    1

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

    
    AU----U*AG-----U    1

    
    AU----U*GG-----U    1

    
    CA----A*CG-----A    1

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

    
    CA----A*UG-----A    1

    
    CA----C*GA-----A    1

    
    CC----G*UU-----G    1

    
    CG----A*GA-----A    1

    
    CG----C*GG-----A    1

    
    CG----U*CA-----G    1

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

    
    CU----C*GA-----G    1

    
    CU----U*AA-----G    1

    
    GA----A*AA-----C    1

    
    GA----A*CA-----C    1

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

    
    GA----C*GU-----U    1

    
    GA----G*CU-----U    1

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

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

    
    GC----A*GA-----G    1

    
    GG----A*UU-----G    1

    
    GG----U*GC-----U    1

    
    GU----C*GG-----C    1

    
    GU----G*UG-----C    1

    
    UA----A*AA-----A    1

    
    UA----A*CA-----A    1

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

    
    UA----C*GG-----G    1

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

    
    UA----G*UG-----G    1

    
    UA----U*AU-----A    1

    
    UC----G*CG-----G    1

    
    UC----U*AG-----A    1

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

    
    UG----A*CU-----G    1

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

    
    UG----C*GU-----A    1

    
    UG----U*AA-----U    1

    
    UG----U*GU-----A    1

    
    UU----A*UA-----A    1

    
    UU----A*UG-----A    1

    
    UU----C*AU-----G    1

    
    UU----C*GU-----G    1

    
    UU----G*UA-----G    1

    
    UU----G*UU-----G    1

    
    -GU---U*GU------    1

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

    
    U-----G*CA-----G    1

    
    UCA----*-C-----A    1

    
    CA-----*-G-----U    1

    
    UA-----*-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_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	62.07	-33.65	4	1	Isolated non-canonical cWW pair
2	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	61.72	-25.35	4	1
3	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	59.66	-40.80	3	1	Stack and bulge
4	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	58.28	-49.32	3	1	Isolated cWS basepair
5	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	57.24	-44.86	3	1	Isolated non-canonical cWW pair
6	Motif group IL_44465.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	54.83	-57.32	3	1	Isolated non-canonical cWW contact
7	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	47.24	-67.98	2	1	Isolated non-canonical cWW pair
8	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	42.07	-1671.65	4	2	Multiple bulged bases
9	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	41.03	-47.06	3	1	Isolated non-canonical cWW pair
10	Motif group IL_10167.6 View motif instance in 3D Basepair signature: cWW-cHW-cWW	33.45	-79.50	2	1	Isolated cWH basepair

Loop 13 Internal loop

Column numbers: 125-128, 169-171 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--U*A-A   25

    
    A--A*A-C   24

    
    U--U*A-U   19

    
    C--U*A-G   18

    
    A--C*G-U   17

    
    G--U*A-U   10

    
    C-UC*G-G    9

    
    A--U*A-U    9

    
    U--C*G-A    9

    
    U--A*U-A    7

    
    U--U*A-G    7

    
    U--U*G-A    6

    
    G--C*G-C    5

    
    G--U*A-C    5

    
    U--C*G-G    5

    
    A--A*U-U    4

    
    C--C*G-G    4

    
    C--U*G-G    4

    
    G--A*U-C    4

    
    G--C*G-U    4

    
    G--C*U-C    4

    
    U--A*A-A    4

    
    CUGA*A-A    3

    
    A--G*C-U    3

    
    A--U*A-A    3

    
    A--U*G-U    3

    
    C--C*U-G    3

    
    U--A*G-A    3

    
    G-UU*AAU    2

    
    U-GU*A-A    2

    
    A--C*G-C    2

    
    C--C*G-A    2

    
    G--A*G-A    2

    
    G--U*G-U    2

    
    U--U*U-U    2

    
    C-CU*AGG    1

    
    G-UC*GAU    1

    
    A-CA*A-U    1

    
    U-GA*U-A    1

    
    A--A*A-A    1

    
    A--A*A-U    1

    
    A--A*C-C    1

    
    A--A*U-A    1

    
    A--C*G-G    1

    
    A--C*U-U    1

    
    A--G*A-A    1

    
    A--G*C-G    1

    
    A--U*A-G    1

    
    C--A*A-A    1

    
    C--A*A-C    1

    
    C--A*A-G    1

    
    C--A*U-G    1

    
    C--G*C-A    1

    
    C--G*C-G    1

    
    C--U*C-A    1

    
    C--U*G-A    1

    
    G--A*C-C    1

    
    G--A*U-U    1

    
    G--U*A-A    1

    
    G--U*C-A    1

    
    G--U*G-C    1

    
    U--A*G-U    1

    
    U--A*U-G    1

    
    U--C*G-U    1

    
    U--C*U-A    1

    
    U--C*U-C    1

    
    Omitted sequenced and counts

    
    U-CA*--G    5

    
    C---*--G    3

    
    A-CA*--U    2

    
    ---G*U--    2

    
    ---U*A--    2

    
    A-AA*--U    1

    
    C-AC*--G    1

    
    C-AG*--G    1

    
    U-AA*--A    1

    
    A---*A-U    1

    
    A--A*--A    1

    
    A--A*--C    1

    
    C--G*--G    1

    
    C-UA*---    1

    
    ---C*G--    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	76.69	11.69	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	69.17	9.69	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	63.91	6.11	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	58.65	-6.56	2	1	Single bulged G
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	54.14	-0.48	3	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	53.01	-3.50	3	1
7	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	52.26	6.10	4	1	Intercalated cWS
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	48.87	5.54	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	46.99	-2.92	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	46.99	-6.23	2	1	Single stack bend

Loop 14 Internal loop

Column numbers: 129-131, 166-168 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-A*U-A   35

    
    G-A*U-U   24

    
    U-U*A-A   20

    
    A-U*A-U   17

    
    U-C*G-A   16

    
    A-A*U-U   15

    
    G-C*G-C    8

    
    U-U*G-A    8

    
    C-U*U-U    7

    
    C-G*G-G    6

    
    G-A*U-C    6

    
    U-G*U-A    6

    
    C-C*G-G    5

    
    G-U*A-C    5

    
    G-G*U-C    4

    
    G-U*G-G    4

    
    U-G*C-A    4

    
    GAA*UUU    3

    
    GUC*GAU    3

    
    UCC*G-A    3

    
    A-C*G-U    3

    
    A-G*C-U    3

    
    A-U*A-A    3

    
    U-A*U-G    3

    
    U-A*U-U    3

    
    ACC*GGC    2

    
    A-G*U-U    2

    
    A-U*A-C    2

    
    G-C*G-U    2

    
    G-U*A-U    2

    
    G-U*G-C    2

    
    U-G*G-A    2

    
    U-U*A-G    2

    
    AAA*UCU    1

    
    ACU*GGC    1

    
    CGU*ACA    1

    
    GGU*ACU    1

    
    UCU*AGA    1

    
    ACG*G-G    1

    
    CGG*C-A    1

    
    A-A*A-A    1

    
    A-A*U-A    1

    
    A-C*G-C    1

    
    A-G*C-G    1

    
    A-U*G-U    1

    
    C-A*C-A    1

    
    C-A*U-C    1

    
    C-C*G-A    1

    
    C-G*C-G    1

    
    C-G*U-G    1

    
    C-U*A-G    1

    
    G-A*C-C    1

    
    G-A*U-A    1

    
    G-A*U-G    1

    
    G-C*A-C    1

    
    U-C*G-U    1

    
    U-G*U-G    1

    
    U-U*C-U    1

    
    U-U*G-G    1

    
    Omitted sequenced and counts

    
    --A*U--   13

    
    GCU*A--    6

    
    A--*A-A    3

    
    AAC*G--    1

    
    AGA*U--    1

    
    GAA*--C    1

    
    GAA*G--    1

    
    GGC*G--    1

    
    GUU*A--    1

    
    A--*G-U    1

    
    A-A*--G    1

    
    C-G*--G    1

    
    U--*A-A    1

    
    --C*G--    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 View motif instance in 3D Basepair signature: cWW-L-cWW	86.33	12.24	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	80.86	12.00	3	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	79.69	10.17	3	2	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.27	7.03	3	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	69.53	-4.78	1	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	59.38	5.81	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	58.20	-0.26	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	58.20	-4.54	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	56.25	-0.09	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	56.25	-4.20	2	1	Single stack bend

Loop 15 Internal loop

Column numbers: 132-135, 162-165 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--A*U--A   28

    
    U--U*G--A   28

    
    G--A*U--C   25

    
    U--G*C--A   19

    
    C--G*C--G   15

    
    A--A*U--U   13

    
    U--G*U--A   12

    
    U--U*A--A   12

    
    A--U*U--U   11

    
    A--G*U--U    9

    
    AAAC*G--U    6

    
    C-UG*C--G    6

    
    A--U*G--U    6

    
    C--A*U--G    6

    
    C--G*U--G    6

    
    --UG*CA--    5

    
    CAGG*U--G    4

    
    A--U*A--U    4

    
    G--C*G--C    4

    
    CAGC*GCUG    3

    
    A--C*G--U    3

    
    C--G*U--U    3

    
    G--C*G--U    3

    
    G--U*U--C    3

    
    U--C*G--A    3

    
    AGUG*UACU    2

    
    AUGA*UA-U    2

    
    U-UG*CA-G    2

    
    C--U*A--G    2

    
    G--C*G--A    2

    
    G--G*U--U    2

    
    G--U*A--C    2

    
    G--U*A--U    2

    
    U--G*C--G    2

    
    CCAC*GCGG    1

    
    CGUG*UACG    1

    
    UAUA*UAUA    1

    
    AAUU*GU-U    1

    
    AUGA*U-AU    1

    
    UUUA*UA-A    1

    
    -CAG*CA-A    1

    
    A-AU*GG-U    1

    
    A-UC*GA-U    1

    
    AAAG*C--U    1

    
    AAGC*GC--    1

    
    CAGA*-U-G    1

    
    CAUU*U--G    1

    
    GUUG*C--U    1

    
    U-UG*CA-A    1

    
    U-GA*U--A    1

    
    U-UA*U--G    1

    
    --GC*GU--    1

    
    --UG*UU--    1

    
    A--C*U--U    1

    
    A--U*A--A    1

    
    C--C*G--G    1

    
    C--U*U--G    1

    
    G--A*U--U    1

    
    G--G*C--C    1

    
    G--G*U--C    1

    
    U--A*A--A    1

    
    U--A*U--G    1

    
    U--U*G--G    1

    
    Omitted sequenced and counts

    
    A--G*---U    2

    
    A--U*---U    1

    
    C--A*---G    1

    
    U--A*---G    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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	83.45	14.55	3	2	Multiple bulged bases
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	83.10	9.08	3	1	Multiple bulged bases
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	82.75	6.07	2	1	Major groove platform
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	70.07	10.26	3	1	Intercalated cWS
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	60.56	7.52	3	1
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	57.04	0.39	3	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	57.04	-6.07	3	1
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	56.34	-5.31	2	1	Single stack bend
9	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	54.93	-16.18	2	1	Single bulged G
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	53.17	-5.99	2	1	Single stack bend

Loop 16 Hairpin loop

Column numbers: 138-159 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-------------GAUA---C  196

    
    A-------------GAUA---U   43

    
    C-------------GAUA---G   14

    
    U-------------GAUA---G    9

    
    A-------------GAUA---A    5

    
    A-------------GAGA---U    4

    
    G-------------GAUG---C    4

    
    A-----------CAGAUA---A    2

    
    G-----------G-GAUA--CC    2

    
    GGAAAAGCGCCGGGGAUA---C    1

    
    -------CGUCCGUGUCU----    1

    
    G-----------U-GAUA--GC    1

    
    --------------AGAGCGG-    1

    
    C-------------GAUAU--G    1

    
    G-------------GAUUG--C    1

    
    A-------------AAUA---U    1

    
    C-------------GAUG---G    1

    
    G-------------AAUA---C    1

    
    G-------------GAUA---U    1

    
    U-------------GCGA---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_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	96.90	21.98	3	1
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	96.90	12.60	3	1
3	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	96.90	10.39	3	1
4	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	96.90	-9.04	3	1
5	Motif group HL_62934.1 View motif instance in 3D Basepair signature: cWW-tSH-F	96.55	20.34	3	1
6	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	96.55	13.65	1	1	Pseudoknot geometry
7	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	96.55	2.22	1	1
8	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	96.55	-13.64	1	1
9	Motif group HL_66103.1 View motif instance in 3D Basepair signature: cWW-F-F	96.21	-6.56	3	1
10	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	95.17	14.29	1	1

Loop 17 Internal loop

Column numbers: 190-192, 247-249 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-C*G-A   46

    
    C-U*A-G   35

    
    U-U*A-A   26

    
    U-G*C-A   20

    
    U-A*U-A   19

    
    C-C*G-G   17

    
    G-C*G-C   13

    
    A-C*G-U   11

    
    C-A*U-G    6

    
    C-U*G-G    5

    
    G-A*U-C    5

    
    U-G*U-G    5

    
    G-G*C-C    4

    
    G-U*A-C    4

    
    U-G*C-G    4

    
    GAG*CAG    3

    
    A-U*A-U    3

    
    G-U*G-C    3

    
    C-A*UAG    2

    
    C-G*UAG    2

    
    A-A*U-U    2

    
    C-G*C-G    2

    
    C-G*U-G    2

    
    U-A*U-G    2

    
    U-C*A-C    2

    
    U-C*G-G    2

    
    U-G*C-U    2

    
    U-U*A-G    2

    
    C-A*UCG    1

    
    C-G*CAG    1

    
    UCC*G-A    1

    
    A-G*C-U    1

    
    A-G*U-U    1

    
    C-A*A-G    1

    
    C-A*U-A    1

    
    C-U*A-A    1

    
    G-A*A-C    1

    
    G-C*G-A    1

    
    G-U*C-C    1

    
    U-C*G-U    1

    
    U-C*U-A    1

    
    U-G*U-A    1

    
    U-U*G-A    1

    
    U-U*G-C    1

    
    U-U*G-G    1

    
    Omitted sequenced and counts

    
    ---*---    9

    
    C--*--G    3

    
    C--*UAG    2

    
    C-U*--G    2

    
    C--*UUG    1

    
    --A*AG-    1

    
    C-G*--G    1

    
    U-G*--G    1

    
    --U*A--    1

    
    A--*--U    1

    
    G--*--U    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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	93.98	25.64	3	2	Multiple bulged bases
2	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	93.98	16.06	2	1	Major groove platform
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	92.11	21.64	3	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	90.23	17.73	3	1	Intercalated cWS
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	88.72	17.06	3	1
6	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	87.59	2.68	1	1	Single bulged G
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	85.34	5.65	3	1
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	84.21	13.02	2	1	Major groove intercalation
9	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	83.46	1.49	2	1	Stack and bulge
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.71	11.39	2	1	Single stack bend

Loop 18 Internal loop

Column numbers: 193-195, 244-246 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    A-U*A-U   36

    
    C-U*A-G   24

    
    G-A*U-A   15

    
    U-U*A-A   12

    
    A-C*G-U   10

    
    G-U*A-U    9

    
    GAA*U-A    8

    
    C-C*G-G    8

    
    A-A*U-U    7

    
    U-G*C-G    6

    
    A-C*U-U    5

    
    U-U*G-A    5

    
    A-U*A-C    4

    
    G-C*G-C    4

    
    G-U*A-C    4

    
    U-A*U-A    4

    
    C-U*G-G    3

    
    G-G*C-U    3

    
    U-C*G-A    3

    
    AAA*UUU    2

    
    GGG*CUU    2

    
    AAA*U-A    2

    
    A-A*A-U    2

    
    A-A*C-U    2

    
    A-A*U-C    2

    
    A-G*U-U    2

    
    A-U*G-U    2

    
    C-A*A-G    2

    
    C-A*U-G    2

    
    C-G*A-G    2

    
    G-A*U-U    2

    
    G-G*C-C    2

    
    U-G*A-A    2

    
    U-G*C-A    2

    
    AUG*CAU    1

    
    GGA*UUU    1

    
    -UC*GAG    1

    
    A-C*GUU    1

    
    AAC*A-U    1

    
    CAG*-AG    1

    
    CGA*A-G    1

    
    GAU*A-U    1

    
    UGC*G-C    1

    
    -AG*U-C    1

    
    -UU*AA-    1

    
    A-G*C-C    1

    
    A-U*U-U    1

    
    AA-*A-U    1

    
    C-A*C-G    1

    
    C-G*C-G    1

    
    C-U*A-U    1

    
    C-U*U-G    1

    
    CA-*G-G    1

    
    G-A*C-G    1

    
    G-A*U-C    1

    
    G-C*G-U    1

    
    G-G*A-C    1

    
    G-G*U-U    1

    
    G-U*G-C    1

    
    U-A*C-C    1

    
    U-A*U-U    1

    
    U-C*G-C    1

    
    U-G*A-G    1

    
    U-G*U-A    1

    
    U-U*A-G    1

    
    UA-*-CA    1

    
    Omitted sequenced and counts

    
    ---*---   17

    
    --U*A--    8

    
    G--*U-A    7

    
    --C*G--    4

    
    A-G*--U    2

    
    C--*--G    2

    
    G--*UAC    1

    
    UUA*U--    1

    
    --G*C-G    1

    
    --G*C-U    1

    
    -UA*U--    1

    
    A-U*U--    1

    
    AG-*--U    1

    
    C--*A-G    1

    
    CG-*--G    1

    
    U--*U-A    1

    
    U--*U-G    1

    
    UU-*--A    1

    
    --C*U--    1

    
    A--*--U    1

    
    U--*--A    1

    
    U--*--G    1

    
    U--*U--    1

    
    --G*---    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	88.79	14.86	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	81.03	16.79	3	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	79.74	13.63	3	2	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	65.52	9.92	4	1	Intercalated cWS
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	63.36	9.47	4	1
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	62.93	0.65	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	62.50	5.70	3	1	Major groove intercalation
8	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	62.50	-3.68	1	1	Single bulged G
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	59.91	4.96	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	59.91	1.33	2	1	Single stack bend

Loop 19 Internal loop

Column numbers: 195-199, 242-244 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U---U*A-A   40

    
    U---A*U-A   20

    
    U-AA-*A-A   11

    
    C---U*A-G   11

    
    U---U*U-A    9

    
    A---A*U-U    8

    
    A---U*A-U    6

    
    C---A*A-G    6

    
    C---U*A-U    6

    
    U---G*U-G    6

    
    G---U*G-C    5

    
    U---C*G-A    5

    
    U--AC*G-A    4

    
    C---C*G-G    4

    
    G---C*G-C    4

    
    G---G*C-C    4

    
    A---A*U-A    3

    
    A---A*U-C    3

    
    A---G*C-U    3

    
    A---G*U-U    3

    
    C---A*U-G    3

    
    U---G*U-A    3

    
    U---U*A-G    3

    
    U---U*G-A    3

    
    G-GAA*U-A    2

    
    G-A-A*U-A    2

    
    A---A*G-A    2

    
    A---C*G-U    2

    
    C---G*C-G    2

    
    C---U*G-G    2

    
    C-U--*-AG    2

    
    G---U*A-C    2

    
    G---U*A-U    2

    
    C-AAA*GAG    1

    
    A-AAC*G-C    1

    
    G--AC*GCC    1

    
    G-AAA*U-A    1

    
    G-AAA*U-C    1

    
    G-AAC*G-C    1

    
    U-A-A*UAA    1

    
    U-GAU*A-A    1

    
    U-GUG*C-A    1

    
    --AAA*U-A    1

    
    --UAC*G-U    1

    
    --UAC*GA-    1

    
    --UAG*C-U    1

    
    C-AA-*A-G    1

    
    G--AG*U-C    1

    
    G-U-A*G-C    1

    
    U-GA-*A-A    1

    
    A---G*C-C    1

    
    A---U*C-U    1

    
    A---U*G-U    1

    
    C---G*U-G    1

    
    C---U*U-G    1

    
    G---C*G-U    1

    
    G---G*U-U    1

    
    G---U*G-U    1

    
    G-A--*G-A    1

    
    U---C*G-U    1

    
    U---G*C-A    1

    
    U---G*C-G    1

    
    U---U*U-U    1

    
    Omitted sequenced and counts

    
    A----*--U   25

    
    -----*---   19

    
    ----C*G-U    7

    
    ----A*U--    2

    
    G-CUG*U--    1

    
    G-UAA*U--    1

    
    G-UGA*U--    1

    
    ----A*U-A    1

    
    ----G*U-G    1

    
    ----G*U-U    1

    
    ----U*G-U    1

    
    ---AA*U--    1

    
    -AUA-*---    1

    
    C----*U-A    1

    
    G---A*A--    1

    
    U----*A-G    1

    
    ----U*A--    1

    
    U----*--A    1

    
    U----*--U    1

    
    -----*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 View motif instance in 3D Basepair signature: cWW-L-cWW	89.59	16.62	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	79.19	16.62	3	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	76.92	13.67	3	2	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.85	17.84	3	1	Intercalated cWS
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	71.49	15.25	4	1
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	70.14	4.64	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	9.33	3	1	Major groove intercalation
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	65.16	2.62	2	1	Single stack bend
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	64.25	6.56	2	1	Single stack bend
10	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	57.47	-8.57	1	1	Single bulged G

Loop 20 Internal loop

Column numbers: 201-202, 238-240 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AU*A-U   29

    
    GU*A-C   27

    
    GU*A-U   22

    
    UC*G-A   16

    
    UU*A-A   15

    
    UG*U-G   14

    
    GA*U-C   10

    
    GG*U-C    8

    
    AC*G-G    7

    
    AC*G-U    7

    
    AU*U-G    7

    
    GC*G-U    7

    
    UG*C-A    7

    
    AA*U-U    6

    
    AG*U-G    6

    
    GA*U-U    5

    
    UG*C-G    5

    
    AU*G-U    4

    
    CG*C-A    4

    
    CU*A-G    4

    
    UA*U-A    4

    
    CG*C-G    3

    
    GC*G-C    3

    
    GG*C-U    3

    
    AA*G-A    2

    
    AG*C-U    2

    
    UA*U-G    2

    
    UC*G-G    2

    
    UC*G-U    2

    
    UU*A-G    2

    
    GU*GAU    1

    
    AA*G-C    1

    
    AC*A-U    1

    
    AU*A-C    1

    
    CA*U-G    1

    
    CC*G-G    1

    
    CU*U-U    1

    
    GA*C-C    1

    
    GG*C-C    1

    
    GG*U-U    1

    
    UA*C-A    1

    
    UG*C-C    1

    
    UG*U-A    1

    
    UU*G-G    1

    
    UU*U-A    1

    
    UU*U-U    1

    
    Omitted sequenced and counts

    
    --*---   26

    
    UA*U--    3

    
    --*A-G    3

    
    CG*C--    2

    
    --*U-G    2

    
    AG*C--    1

    
    GU*--C    1

    
    --*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 View motif instance in 3D Basepair signature: cWW-L-cWW	94.42	14.63	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	85.66	17.73	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	80.88	10.89	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	73.31	-0.81	1	1	Single bulged G
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	62.55	8.51	4	1	Intercalated cWS
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	60.16	7.31	3	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	58.96	3.70	2	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	58.96	-1.93	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	54.58	0.85	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	54.58	-2.75	2	1	Single stack bend

Loop 21 Internal loop

Column numbers: 202-204, 237-238 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-A*UA   60

    
    C-A*UG   30

    
    G-A*UU   26

    
    U-G*CA   21

    
    A-A*UU   19

    
    G-A*UC   17

    
    U-C*GA    8

    
    A-G*CU    6

    
    C-C*GG    6

    
    U-A*UU    6

    
    U-U*GA    6

    
    C-U*GG    5

    
    G-G*UC    5

    
    U-C*GG    5

    
    A-U*AU    3

    
    A-U*GU    3

    
    U-C*GU    3

    
    A-G*CG    2

    
    C-G*CG    2

    
    G-G*CC    2

    
    G-G*CU    2

    
    U-U*AA    2

    
    CUA*UG    1

    
    UAG*CA    1

    
    A-A*UC    1

    
    A-A*UG    1

    
    A-G*CC    1

    
    C-A*CG    1

    
    C-C*GA    1

    
    G-C*GC    1

    
    G-U*AC    1

    
    U-G*CG    1

    
    U-G*CU    1

    
    Omitted sequenced and counts

    
    ---*--   26

    
    G--*-C    3

    
    --G*UA    2

    
    G--*-U    2

    
    U--*-A    2

    
    --G*CU    1

    
    U-A*U-    1

    
    ---*AA    1

    
    ---*AU    1

    
    ---*-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 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	16.76	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	97.20	25.49	4	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	94.00	19.87	2	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	87.60	16.57	2	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	86.00	5.81	1	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	75.20	15.64	3	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	74.80	9.58	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	74.80	3.20	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.00	9.02	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.00	5.90	2	1	Single stack bend

Loop 22 Hairpin loop

Column numbers: 204-237 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    A-------------GUAA---------------U   61

    
    A-------------GUGA---------------U   56

    
    C-------------GUGA---------------G   17

    
    G-------------GCGA---------------C   16

    
    A-------------GCGA---------------U   14

    
    A-------------GCAA---------------U   13

    
    G-------------GUAA---------------C   10

    
    U-------------GUGA---------------G    9

    
    A-------------GAGA---------------U    8

    
    G-------------GUGA---------------C    8

    
    AUA-----------UUGA-----------AGUGU    5

    
    C-------------GCGA---------------G    4

    
    --------------GUAGUA--------------    3

    
    G-------------GCAA---------------C    3

    
    G-------------GCAA---------------U    3

    
    U-------------GUGA---------------A    3

    
    --------------AGAA----------------    3

    
    --------------GAAA----------------    3

    
    --------------UUCU----------------    3

    
    C-------------GAAA---------------G    2

    
    G-------------GCGA---------------U    2

    
    G-------------GUAA---------------U    2

    
    --------------GUAA----------------    2

    
    --------------GUGA----------------    2

    
    --------------UCCG----------------    2

    
    UAUAAUUGAUAAGUCCACU-ACUUAUUAAGAA-G    1

    
    U--AUAAUGACUGGGUAAG-UCACCCGUAAGAAG    1

    
    U---------GUAUAAAA--GUACUCAGUGAAGA    1

    
    ---GAUGC-AG---GUAA-----CUGGCAUCUAA    1

    
    AUA-AGGC------UAU---------GCCGAAGU    1

    
    AUAUA---------UCGA-------------AGU    1

    
    A-------------UUAAG--------------U    1

    
    A-------------AUAA---------------U    1

    
    A-------------GAGA---------------C    1

    
    A-------------UCGC---------------U    1

    
    C-------------GAGA---------------G    1

    
    G-------------AUGA---------------C    1

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

    
    G-------------GAGA---------------C    1

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

    
    U-------------GAAA---------------G    1

    
    U-------------GCGA---------------A    1

    
    U-------------GCGA---------------G    1

    
    U-------------GGAA---------------G    1

    
    --------------AGACA---------------    1

    
    --------------AGAUA---------------    1

    
    --------------GUGA---------------A    1

    
    --------------GUGAC---------------    1

    
    --------------UAUAU---------------    1

    
    --------------CAGA----------------    1

    
    --------------GCGA----------------    1

    
    --------------UUAU----------------    1

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

    
    --------------UUU-----------------    1

    
    --------------GU------------------    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_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	87.68	-127.73	0	0	GNRA
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	87.68	-192.24	2	1
3	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	87.32	-163.35	2	1
4	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	87.32	-664.32	2	1
5	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	86.97	-501.77	3	1
6	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	85.92	-209.77	3	2
7	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	85.56	-196.46	3	1
8	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	85.21	-267.12	3	1
9	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	84.86	-480.57	3	1	Pseudoknot geometry
10	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	83.10	-255.03	3	1

Loop 23 Hairpin loop

Column numbers: 260-294 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G----------AAA--------------------C   49

    
    U----------GAA--------------------G   26

    
    G----------CAA--------------------U   24

    
    A----------UACA-------------------U   19

    
    C----------AGAU-------------------G    8

    
    G----------AUAAG------------------C    7

    
    A----------AAA--------------------U    7

    
    GU---------AAGUAGUCAAC-----------AC    6

    
    -----------CAAAA-------------------    6

    
    U----------AAA--------------------A    6

    
    A----------AGAU-------------------U    4

    
    C-UC-------AAAACG--------------GAGG    3

    
    G----------CAAAG------------------C    3

    
    U----------GGAAA------------------A    3

    
    A----------ACA--------------------U    3

    
    C----------AAA--------------------A    3

    
    U----------GAC--------------------G    3

    
    ACC--------GAAAAGGAAAUA---------GGU    2

    
    C----------GUAAGACACUUG-----------G    2

    
    GUA--------GACAAAGA-------------UGC    2

    
    GUG--------GAAG-----------------CAC    2

    
    GUG--------GAAG-----------------CAU    2

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

    
    U----------UAAU-------------------U    2

    
    -----------UCAAU-------------------    2

    
    C----------AAA--------------------G    2

    
    G----------GAA--------------------C    2

    
    U----------GGA--------------------G    2

    
    -----------GAAC--------------------    2

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

    
    -----------UGAU--------------------    2

    
    G----------C-A--------------------U    2

    
    GUAGAGGCCGUGAAACCGCAUA--ACGGUC---GC    1

    
    UUCGCUC----GAAACA-----------GAG-GUG    1

    
    CUC--------AAAACGGAGGUGG-----------    1

    
    GG---------AGCAGGAACCGC----------CC    1

    
    G----------UAAGUAGUCAACA----------C    1

    
    GU---------AGAUAAAGAC------------GC    1

    
    GUA--------GAUAAAGA-------------UAC    1

    
    -----------GAGGCUGAACCAA-----------    1

    
    -----------GUAACACACUUG------------    1

    
    -----------GUAAGACACUUG------------    1

    
    -----------GUAAUACACUUG------------    1

    
    CUC--------GAAACA---------------GAG    1

    
    A----------AAUAAAGC---------------U    1

    
    AG---------CUACGA----------------UU    1

    
    CU---------UAAAUG----------------AG    1

    
    -----------AUUAAAAGA---------------    1

    
    A----------AAAAAAG----------------U    1

    
    AC---------GGAAA-----------------GU    1

    
    U----------AAAGGUG----------------U    1

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

    
    AU---------GGAAA-----------------A-    1

    
    C----------UAAAUG-----------------G    1

    
    G----------AUAAAA-----------------C    1

    
    G----------GUGAAA-----------------U    1

    
    G----------UAAAAG-----------------C    1

    
    G----------UAAGUU-----------------U    1

    
    U----------GAGAGA-----------------G    1

    
    U----------GGUAGA-----------------G    1

    
    U----------UAAAUG-----------------A    1

    
    U----------UUAAUU-----------------A    1

    
    A----------UACCA------------------U    1

    
    C----------GAAAG------------------U    1

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

    
    GC---------AAA-------------------GC    1

    
    U----------AAACA------------------A    1

    
    U----------AAAUU------------------U    1

    
    -----------AAUAAA------------------    1

    
    -----------GGCUGA------------------    1

    
    -----------GUAAAA------------------    1

    
    -----------UUGAGU------------------    1

    
    A----------GAAC-------------------U    1

    
    C----------AAGA-------------------G    1

    
    C----------AGAA-------------------G    1

    
    C----------AGAG-------------------G    1

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

    
    G----------GAAC-------------------C    1

    
    G----------GAAU-------------------C    1

    
    G----------UAAA-------------------A    1

    
    U----------AAAA-------------------G    1

    
    U----------AAUA-------------------A    1

    
    A----------AAC--------------------U    1

    
    A----------GCA--------------------U    1

    
    C----------AGU--------------------G    1

    
    C----------GCA--------------------G    1

    
    C----------UCA--------------------G    1

    
    G----------AAA--------------------U    1

    
    G----------ACA--------------------C    1

    
    G----------AGA--------------------C    1

    
    G----------GAC--------------------U    1

    
    G----------GGA--------------------A    1

    
    G----------UGU--------------------U    1

    
    U----------GGA--------------------A    1

    
    U----------GUCA--------------------    1

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

    
    -----------UAGU--------------------    1

    
    -----------UGAA--------------------    1

    
    -----------UGUC--------------------    1

    
    -----------UGUU--------------------    1

    
    A----------ACA---------------------    1

    
    G----------AAA---------------------    1

    
    G----------AGA---------------------    1

    
    -----------AAG---------------------    1

    
    -----------AGU---------------------    1

    
    Omitted sequenced and counts

    
    -----------------------------------    7

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 View motif instance in 3D Basepair signature: cWW-F	70.32	-1082.44	2	1
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	66.43	-186.84	2	1
3	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	62.54	-111.54	3	2
4	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	57.95	-1039.30	4	2
5	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	56.89	-1048.80	3	2	Mini UNCG
6	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	54.06	-741.17	3	2
7	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	53.71	-1089.57	3	2
8	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	53.00	-893.32	3	2	tRNA D-loop
9	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	51.94	-758.28	3	2
10	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	50.18	-278.47	3	2

Loop 24 Internal loop

Column numbers: 419-421, 751-752 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-G*CC   46

    
    G-U*AC   45

    
    G-C*GC   38

    
    G-A*UC   35

    
    A-G*CU   27

    
    A-U*GU   13

    
    C-C*GG   10

    
    U-C*GA   10

    
    A-A*UU    7

    
    A-U*AU    7

    
    G-U*GC    7

    
    G-G*CU    5

    
    G-G*UC    5

    
    A-C*GU    4

    
    C-G*CG    3

    
    C-U*AG    3

    
    U-U*AA    3

    
    C-A*UG    2

    
    C-C*GA    2

    
    U-G*CA    2

    
    AUC*GU    1

    
    G-A*CC    1

    
    G-A*UU    1

    
    U-C*GG    1

    
    Omitted sequenced and counts

    
    C-G*-G    8

    
    A-G*-U    3

    
    C-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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	31.85	2	2	Multiple bulged bases
2	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	99.64	15.35	3	1	Major groove platform
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	98.92	21.34	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	96.40	8.25	1	1	Single bulged G
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	93.53	20.15	3	1
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	91.73	19.99	3	1	Intercalated cWS
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	89.21	12.52	2	1
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	88.49	16.14	2	1	Major groove intercalation
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	87.41	13.56	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	87.41	12.09	1	1	Single stack bend

Loop 25 3-way junction loop

Column numbers: 422-446, 490-506, 625-750 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UUC--AAU---AGAC-G-------U*A-A----A-----UA*AC*GA--------------------------------------------------------------------------------------------------------AUAAUCA---------AA-A   11

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UAA--   10

    
    AAC--AAU---AGAC-G-------G*C-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------A-UCCAA-------UAA-U    7

    
    AAC--AAU---AGAG---GGU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    5

    
    AAG--AAU---AGAG---GGU-U-A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    5

    
    GAC--AAC---AGAC-G-------G*C-A----G-----UA*AC*GC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-C    5

    
    GAC--AAU---UGAU-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    4

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA--    4

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    4

    
    AAG--AAU---AGAG---GGU-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    3

    
    CAC--AAU---AAGU-U-GAU----*--A-AUCA-----GC*UU*AA---------------------------------------------------------------------------------------------------------UGACCAA-------CAA-G    3

    
    CGU--AAU---AGAG-A-G-----U*A-U--GCU-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA------UAA-G    3

    
    CGUAGAAU---AGAC-G-------C*G-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA----G-CAA--    3

    
    UGAU-AAU---AGAU-G-------G*C-A----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA----A-UAA-G    3

    
    UGAUUAAU---AGAC-A-------U*A-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    UGAUUAAU---AGAC-G-------U*A-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    AAU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AAGCCAAA------CAA-U    3

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UA--A    3

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA--    3

    
    GAU--AAU---AGAU-G-------G*C-A----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA----A-UAA--    3

    
    AAC--AAU---AGAC-G-------U*A-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------GGCCAA-------CAA-U    3

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------GGCCAA-------CAA-U    3

    
    CGC--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCA--------UAA-G    3

    
    -AC--AAG---AGGC-UC------U*A------U-----CC*CA*U-----------------------------------------------------------------------------------------------------------UCUCAAA----A-GAA--    3

    
    CGU--AAU---UGAA---AGG-U-A*UGC-CCUA-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    2

    
    AAG--AAU---AGAG-G-G-U-U-A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    2

    
    AAG--AAU---AGAG-G-GUU---A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    2

    
    CGC--AAU---AGAU---AUG---A*U---CAUU-----GA*AC*GA---------------------------------------------------------------------------------------------------------GUGCCA--------UAA-G    2

    
    CGUAGAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA------UAA-G    2

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA-----CCAA--    2

    
    AAU--AAU---AGAC-G-------G*C-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAAA----A-CAA-U    2

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AACUCAU-------UAA-G    2

    
    CAU--AAU---AGAC-G-------A*U-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    2

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    2

    
    UGC--AAU---AAAA-AG-----U-*--U----C-----CU*CU*AA---------------------------------------------------------------------------------------------------------AUACCCAA------CAA-A    2

    
    -AU--AAG---UAUC-U-------A*U-A----G-----GU*CA*UG---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    2

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCAA-------UAA-U    2

    
    AAU--AAU---ACAC-G-------C*G-A----A-----UA*AA*UA---------------------------------------------------------------------------------------------------------AAGCCAU-------CAA-U    2

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAA-------CAA-U    2

    
    CAC--AAU---AGAC-G-------G*C-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAACCAA-------UAA-G    2

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------A-GCCAA-------GAA-U    2

    
    GAC--AAC---AGAC-G-------U*A-A----G-----UA*AC*GC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-C    2

    
    CGC--AAU---AGAG-A-------C*G-C----C-----GA*AU*AA--------CUUGAAUUGUCGGAGUGAGUCGCAGUUGCUGCGUCAGAAAACUCCCAGAGGUUAAUCUCUGCUGACAGUUC--------------------------UUCCCAA-------UAA-G    1

    
    UGAAGAAU---AGAC-G-------A*U-A----A-----UA*AG*CAGAUUGUUGACAUUGUUGCCGCAAGGUGCAAUCUU--------------------------------------------------------------CAGUAAUC-GUGUUAG-------UAA-G    1

    
    AAU--AAU---UGAA-GAAGUGUAC*GGAUACUAAC---AC*GG*UA---------------------------------------------------------------------------------------------------------AUAUCCAAA---A-CAA--    1

    
    GAC--AAU---UGAACAGGUA-UAC*GGA-UACUGAC--AC*GG*UA--------------------------------------------------------------------------------------------------------AUAUCCA-----AAACAA--    1

    
    GAC--AAUU-GAGCA-G-GUA-UAC*GGA-UACUGAC--AC*GA*UA--------------------------------------------------------------------------------------------------------AUAUCCAAA----A-CAA--    1

    
    GAC--AAUU-GAGCA-G-GUA-UAC*GGA-UACUGAC--AC*GG*UA--------------------------------------------------------------------------------------------------------AUAUCCAAA----A-CAA--    1

    
    GAU--AAU---UGAG-GAGAU-U-C*G-A-AUCAAU---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    CGC--AAU---AGAA-A-GCU-AGG*U-A-AGCC-----GA*AU*AA--------------------------------------------------------------------------------------------------------AAGACCAA-------UAA-G    1

    
    AAC--AAG---UGUC-A-GUG-AAC*U-AUAGCU-----GG*CC*G-----------------------------------------------------------------------------------------------------------UGUCGAA------CAA-U    1

    
    CAU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------GUUCGAA-----U-CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---G*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    AAU--AAU---AGAA---GAC-AAG*U-A-GUCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-U    1

    
    AGC--AAU---AGAA---GGU-GGG*U-G-ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AGACCAA-------CAA-U    1

    
    CAC--AAU---AGAA---GCU-AAG*U-A-AGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------GUGCCAC-------UAA-G    1

    
    CAC--AAU---AGAA-A-GGA-U-A*G-A-UCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------ACUCGAA-------CAA-G    1

    
    CAU--AAU---AGAA---GUC-AAG*U-A-GACU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AGACCAA-------UAA-G    1

    
    CGC--AAU---ACGA-A-GGG---G*C-C-CCCG-----AA*AC*GA---------------------------------------------------------------------------------------------------------ACCUCACC------CAC-G    1

    
    CGC--AAU---AGAA---GGC-AAG*U-A-GCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-G    1

    
    CGC--AAU---AGAA---GGC-AAG*U-A-GCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------UAA-G    1

    
    CGC--AAU---AGAA---GUU-GAG*U-G-AACU-----GA*AG*UA---------------------------------------------------------------------------------------------------------AAGCCAA-------UAA-G    1

    
    GGU--AAU---AGAA-A-GCA-U-U*A-A-UGCC-----GA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    UGU--AAU---AGAG-A-GUU-AC-*----UGCU-----UA*AC*GA---------------------------------------------------------------------------------------------------------GUACCAAA----A-UAA-G    1

    
    CAUA-AAG---AGAA---GCA---C*G---UGCU-U---AC*UC*AA---------------------------------------------------------------------------------------------------------AAUCCAA-------UAA-G    1

    
    CGC--AAU---AGGA-A-GCC-A-G*C-A-GGCC-----AA*AU*AA---------------------------------------------------------------------------------------------------------AAACCA--------CAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAU-ACCAAUAA-C    1

    
    UGUAUAAU---AGAC-GA------C*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AUAUGCAG-------GCG-G    1

    
    UGUAUAAU---AGAC-GA------C*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AUAUGCAG-------GUG-G    1

    
    AAG--AAU---AGAG---GGU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG---GGU-UA-*--C-ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G--GU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-G-U-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-GUU---A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-GUU---G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    CGC--AAU---AGCA-G-GAG----*----CUCU-G---AA*AG*CA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    1

    
    GAC--AAU---AGAA-A-GCC---U*A---GGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------ACACCAA-------CAA-C    1

    
    GGC--AAU---AGAC-A-GCC---U*A---GGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-C    1

    
    U----AAUC--ACAA---AGC-AAC*G-A-GAUA-----AA*AG*GA----------------------------------------------------------------------------------------------------------UACCAA-------UAA-A    1

    
    UGC--AAU---AGAC-A-GCU---U*A---AGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-A    1

    
    UGUAAAAU---AGAC-G------AC*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AAAUGCAG-----G-C---A    1

    
    -AU--AAU---AGAA---GCG-G-U*U-C-CGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA--    1

    
    AAC--AAU---AGAA-A-GUU---A*U---AGCC-----U-*CU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-U    1

    
    AAU--AAU---AGAG-A-G-----C*G-U--GCU-----GA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAAC----A-UAA--    1

    
    AG---AAU---AGAG---GGU-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    CAC--AAU---AGAG-A---G-CUG*C------U-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA----A-UAA-G    1

    
    CGC--AAU---AGAU-A-GCA---G*U---UGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCA--------UAA-G    1

    
    UGAUUAAU---AGAC-A-------U*A-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCUCAA----A-UAA-G    1

    
    CAU--AAU---UGAA-A-------C*GGA----G-----UA*GU*AA--------------------------------------------------------------------------------------------------------AUCUUCAA-----C-CAA-G    1

    
    CCUACAAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUGCAG-------GAAGG    1

    
    CCUACAAU---AGAC-G-------C*G-A----A-----UA*AC*GA--------------------------------------------------------------------------------------------------------AUUGCAG--------AAAGG    1

    
    CG---AAUA--AUAA-AC-----GC*G-A-A--U-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AAUCUCAA-------UAA-G    1

    
    CGUAGAAA---AGAC-G-------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------CUCUAAA----A-GAA-G    1

    
    GAAU-AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCUCAA----ACUAA--    1

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA------CCA-A    1

    
    GAC--AAU---UGAG-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    GAU--AAU---AGAU-G---G---U*A---C--A-U---GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAAA-----UAA--    1

    
    GAU--AAU---UGAG-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    GAU--AAU---UGAG-GA------G*CGA----U-----GC*GG*UA----------------------------------------------------------------------------------------------------------AUUCCAAA---A-CAA--    1

    
    GAU--AAU---UGAG-U------AA*UAA----U-----GC*GG*UA---------------------------------------------------------------------------------------------------------AAUCCAAA----A-CAA--    1

    
    UGC--AAU---AAAA-A-----GUC*G-U----C-----CU*CU*AA--------------------------------------------------------------------------------------------------------AUACCCAA-------CAA-A    1

    
    UGU--AAU---AGAC-G-------G*C-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUACCAA----AACAA-G    1

    
    ---A-AAU---CGGG-A-G----AC*GG----CA-U---AC*CC*GA--------------------------------------------------------------------------------------------------------AUAUCGC--------UAA-A    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------A-UGCAAA----AGCAA-U    1

    
    AAU--AAU---AGAC-G-------G*C-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUGUCAAA----A-CAA-U    1

    
    AUA--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA------------------------------------------------------------------------------------------------------C-UAAACCAA-------GUA-U    1

    
    CAC--AAU---AGAG-A-------G*CGC----U-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCUAAU------UAA-G    1

    
    CAU--AAU---AGAC-CG------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------GUUCUAAA------UAA-G    1

    
    CAU--AAU---AGAC-G-------A*U-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA-G    1

    
    CG---AAUA--AUAA-AC-----GC*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGA--AUA---AUAA-AC-----GC*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGAAUAAU---AAAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCUAA----A-UAA-G    1

    
    CGC--AAU---AGAC-GC------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------ACGCACAA-----UAA-G    1

    
    CGU--AAU---AGAC-G-------U*A-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUCCCAAA----A-CAA-G    1

    
    GAC--AAG---AAGC-UC-----UA*U-A----U-----CU*CA*UA---------------------------------------------------------------------------------------------------------A-CUCAC-----AGGAA--    1

    
    UGUAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAU-------UAA-G    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AAGCCAAA------CAA-U    1

    
    AAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-U    1

    
    AAU--AAU---AGAC-G-------G*C-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA------CAA-U    1

    
    AAU--AAU---AUAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCCAAA------UAA-U    1

    
    AAUA-AAU---AGAC-G-------C*G-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-U    1

    
    AGU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------UUCCAAA----A-UAA-U    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAAC------CAA-G    1

    
    CAU--AAU---AGAC-GC------C*G-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-G    1

    
    CGC--AAU---AGAC-G-------U*A-A----A-----GA*AA*UA---------------------------------------------------------------------------------------------------------AUACCA------AAUAA-G    1

    
    GAC--AAG---AAGC-UC------U*A-A----C-----UC*AC*G----------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*AA---------------------------------------------------------------------------------------------------------ACGCUAUA----A-UAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AACUCAAA----C-CAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------ACGCUAAA----A-UAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAAA----U-UAA--    1

    
    GAG--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUGCUAAA----G-CAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------UAGCUAAA----A-UAA--    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------A-UCCAAA----U-UAA-C    1

    
    GGU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------A-UCCAAA----C-UAA-C    1

    
    U----AAU---CAAAAC--CG---C*G-A-CG-A-----UA*AC*GA----------------------------------------------------------------------------------------------------------UACCA--------UAA-A    1

    
    UAU--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    1

    
    UGC--AAU---AAAA-AG-----U-*--U----C-----CU*CU*AA---------------------------------------------------------------------------------------------------------AUACCCAG------CAA-A    1

    
    UGU--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-A    1

    
    A----AAUC--GGGAGAC------C*G-C----G-----UA*CC*AA----------------------------------------------------------------------------------------------------------UGUCAA-------GAA-A    1

    
    AAC--AAU---AGAC-G-------C*A-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCUC-------UAA-U    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCUC-------UAA-U    1

    
    AGU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------AGCCAAA------UAA-U    1

    
    CA---AAC---AGAC-GC------C*GGA----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AGACCCU--------GC-G    1

    
    CAA--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-G    1

    
    CAC--AAU---AGAC-G-------G*C-A----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-G    1

    
    CAC--AAU---AGAC-G-------G*C-A----G-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAACCAA-------UAA-G    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAC-------UAA-G    1

    
    CAU--AAU---AGAC-GC------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------UGCCAA-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AGCCAAA-------CAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------AUCCAAA------CAA-C    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    UAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAA-------UAA-G    1

    
    UGC--AAU---AGAG-G-------U*G-C----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------CGGUUCA-------UAA-G    1

    
    -AC--AAG---AAGC-UC------U*A------U-----CU*CA*G----------------------------------------------------------------------------------------------------------UUCUCAA-----AGUAA--    1

    
    AAG--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-CUCAA-------UAA-U    1

    
    AGC--AAU---AGAC-G--------*--A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAC------CAA-U    1

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------UGCCAA-------UAA-U    1

    
    AGU--AAU---AGAC-G--------*--A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAC------CAA-U    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------CAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-UGCAC-------CAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-G    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------UACCAA-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCA--------UAA-G    1

    
    CGC--AAU---AGAU-A-------U*A-U----U-----GA*AC*GA---------------------------------------------------------------------------------------------------------GUGCCA--------UAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------CAUCAA-------UAA-C    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-GCCAC-------UAA-C    1

    
    UUC--AAU---AGAC-G-------U*A-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUAAUC--------AAA-A    1

    
    -AC--AAG---AAGC-UC------U*A------U-----CU*CG*C-----------------------------------------------------------------------------------------------------------UCUCA-----AAGGAA--    1

    
    -AC--AAG---AGGC-UC------U*A------U-----CC*CA*U-----------------------------------------------------------------------------------------------------------CCUCAA-----AGGAA--    1

    
    -AC--AAG---UAU--U-------U*A-A----A-----U-*CA*UA---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    1

    
    -AU--AAG---AGGC-UC------U*A------U-----CC*CG*U-----------------------------------------------------------------------------------------------------------UCCUAAA-----GGAA--    1

    
    CAC--AAG---AA-----------G*C------U-------*CG*UA----------------------------------------------------------------------------------------------------------UGCCAAA----A-AAA-G    1

    
    CGC--AAG---AA-----------G*C------U-------*CG*UA----------------------------------------------------------------------------------------------------------UGCCAAA------UAA-G    1

    
    Omitted sequenced and counts

    
    AUUACAAU-----------------*---------------*--*----------UGCCGGCGGAGAUUUAGGCGCUCCGUGUAAAGCAGUCUCACGCUAAUCUGGCAGACAUGUCAGGGAACCACGAGAUAAAUGUAAGUUA-----------------------AAA-U    2

    
    CGC--AAU---AUGC----------*-------C-------*AU*AA----------------------------------------------------------------------------------------------------------UAUCAAC------UAA-G    2

    
    GAC--AAUCGCAUAA-G-------U*A-A------------*--*----------GCGGGGACUGACGCGGCUCUUUCGCGCCACAUAGGGAUAUGUGGGGAACGCUAAGAGAAUUCCAAAA--------------------------------------------CAA--    1

    
    -AU--AAG-----------------*---------------*--*-----------UAUCUAAUGCGUGUCAUUAGGUCACCUCGGUAUGACUAGGGUGAGAGCUAGGAACCGUAGAGGUGUUCUCAAGG------------------------------------GAA--    1

    
    -------------------------*---------------*--*----------AAAUCGGGAGACCAACAUGGGCGUACCCACAUAUCCCACUACUGGAGACAGUGGUAAGGGCAAUGAGUGAAGAUCGCU---------------------------------AAA--    1

    
    AUAG-AAGU--AAGC-A-----CAU*G-A----U-GACUUU*A-*-A--------C------------------------U-----------------------------------------------------------------------AAAUCAAA------CAA-U    1

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*A-*AA---------------------------------------------------------------------------------------------------------AUCUCAU-------AAA-G    1

    
    -AC--AAG---------UACC-UA-*-UA-GGUC-------*-G*UA----------------------------------------------------------------------------------------------------------UCUCAAA----AACAA--    1

    
    GAC--AAU---AGAC-GC------U*A-A----U-----G-*A-*-A---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    1

    
    CGC--AAU---AUAC----------*-------C-------*AU*AA----------------------------------------------------------------------------------------------------------UAUCAAU------UAA-G    1

No Matches Found View All Results for this Loop

Loop 26 Internal loop

Column numbers: 449-465, 467-487 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U---------------C*GUG-----------------A   34

    
    C---------------U*U-------------------G   33

    
    G---------------C*GUG-----------------C   24

    
    C---------------C*GUG-----------------G   18

    
    U---------------G*AUA-----------------G   14

    
    U---------------G*AUA-----------------A   13

    
    A---------------G*AA------------------U    9

    
    C---------------A*U-------------------G    9

    
    G---------------A*GUU-----------------C    7

    
    U---------------U*AAA-----------------G    7

    
    CU--------------C*AAA----------------GG    6

    
    GU--------------C*AAA----------------GC    6

    
    GU--------------G*AUA----------------GC    6

    
    A---------------C*GUG-----------------U    6

    
    C---------------G*U-------------------G    6

    
    UCACA-----------G*AA--------------UGGGG    5

    
    GU--------------U*AAUC---------------GC    4

    
    C---------------G*G-------------------G    4

    
    UG--------------G*AA-----------------CA    3

    
    U---------------G*GAA-----------------G    3

    
    U---------------U*U-------------------A    3

    
    G---------------C*GUG-----------------U    2

    
    G---------------C*UGU-----------------C    2

    
    U---------------C*AAA-----------------G    2

    
    U---------------U*CUA-----------------A    2

    
    C---------------A*AC------------------G    2

    
    C---------------G*AA------------------G    2

    
    U---------------A*GC------------------A    2

    
    AGUUUUGAGUUGACUCU*AA---GAGUUGAGGAGAAAAC    1

    
    AAGGGGAUUU------A*GGA--------AAA---CC-U    1

    
    UCACA-----------G*CAAA------------UGGGA    1

    
    UGGCA-----------G*AAUA------------UGUUG    1

    
    CCACA-----------G*AA--------------UGGGG    1

    
    UCU-------------C*AAA---------------GGA    1

    
    C---------------U*GAGAU--------------AG    1

    
    AU--------------G*AAU----------------AU    1

    
    CC--------------C*GAA----------------GG    1

    
    CU--------------G*ACA----------------GG    1

    
    U---------------G*AUAAG---------------A    1

    
    UU--------------C*AGG----------------AA    1

    
    UU--------------U*UAU----------------AG    1

    
    C---------------U*UUG----------------AG    1

    
    UG--------------U*GG-----------------UA    1

    
    UU--------------G*GA-----------------UA    1

    
    A---------------C*CGG-----------------U    1

    
    A---------------C*GUA----------------A-    1

    
    C---------------A*CUU-----------------G    1

    
    C---------------G*CAG-----------------G    1

    
    C---------------G*UGA-----------------G    1

    
    C---------------U*AUA-----------------C    1

    
    C---------------U*GCA-----------------G    1

    
    G---------------A*UCG-----------------U    1

    
    G---------------G*AUA-----------------C    1

    
    U---------------C*GUG-----------------C    1

    
    U---------------G*AAA-----------------G    1

    
    U---------------G*UAA-----------------G    1

    
    U---------------U*ACA-----------------G    1

    
    U---------------U*AUA-----------------A    1

    
    U---------------U*AUA-----------------G    1

    
    U---------------U*UUA-----------------A    1

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

    
    C---------------A*A------------------UG    1

    
    C---------------A*AU------------------G    1

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

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

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

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

    
    U---------------U*U-------------------G    1

    
    Omitted sequenced and counts

    
    -----------------*---------------------    7

    
    ----------------G*GAA------------------    3

    
    ----------------U*UG-------------------    2

    
    ----------------C*CUG------------------    1

    
    ----------------C*GUG------------------    1

    
    ----------------A*GU-------------------    1

    
    ----------------A*UU-------------------    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_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	67.15	-388.51	3	1	Intercalated cWS
2	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	65.69	-379.69	3	1
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	65.33	-185.40	3	1	Multiple bulged bases
4	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	65.33	-382.72	2	0	Major groove intercalation
5	Motif group IL_82107.4 View motif instance in 3D Basepair signature: cWW-cWW	59.49	-183.39	3	1	Multiple bulged bases
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	58.76	-414.16	4	1
7	Motif group IL_42626.2 View motif instance in 3D Basepair signature: cWW-cWW	52.92	-445.45	3	1
8	Motif group IL_56987.1 View motif instance in 3D Basepair signature: cWW-L-cWW	51.82	-411.11	3	1
9	Motif group IL_79895.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	51.82	-412.27	5	1
10	Motif group IL_15052.4 View motif instance in 3D Basepair signature: cWW-L-cWW-L	51.46	-485.59	3	1	Minor groove platform

Loop 27 Hairpin loop

Column numbers: 465-467 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAA   45

    
    CGG   39

    
    UGU   37

    
    CUG   26

    
    CAG   24

    
    UAA   10

    
    GCA    9

    
    AGU    8

    
    CAA    8

    
    GGU    8

    
    CGA    7

    
    GUG    7

    
    UUA    6

    
    AAG    4

    
    ACG    4

    
    AGA    4

    
    AGG    4

    
    GAG    4

    
    GUA    4

    
    UUU    4

    
    ACU    3

    
    UUG    3

    
    CGU    2

    
    GGA    2

    
    UAC    2

    
    AAC    1

    
    AUU    1

    
    CAC    1

    
    CUA    1

    
    CUC    1

    
    GAC    1

    
    GAU    1

    
    GUC    1

    
    UCU    1

    
    Omitted sequenced and counts

    
    ---    7

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 View motif instance in 3D Basepair signature: cWW-F-F	17.67	-14.35	3	2
2	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	17.67	-28.96	1	1	Mini UNCG
3	Motif group HL_32346.4 View motif instance in 3D Basepair signature: cWW-F	14.13	-20.31	2	1
4	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	12.01	-28.48	3	2

Loop 28 Hairpin loop

Column numbers: 504-505 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AA  239

    
    CG   13

    
    UC    9

    
    CC    6

    
    CU    4

    
    AC    1

    
    AG    1

    
    CA    1

    
    GC    1

    
    UA    1

    
    Omitted sequenced and counts

    
    --    6

    
    -A    4

    
    -C    4

No Matches Found View All Results for this Loop

Loop 29 Internal loop

Column numbers: 511-522, 571-620 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G---UUAG---G*CAAAC--------------------------------------------C   23

    
    G---UUAG---G*UAAAC--------------------------------------------C   11

    
    ----AAAG---A*AAACUA--------------------------------------------   10

    
    U---GAU----G*CUA----------------------------------------------A    9

    
    U---AA-----G*UUACU--------------------------------------------G    8

    
    ----GUA----G*CGAA----------------------------------------------    8

    
    G---UUAG---G*CAGUC--------------------------------------------C    7

    
    C---GG-----G*CA-----------------------------------------------G    5

    
    U---AAGU---U*AUUACU-------------------------------------------A    4

    
    ----AAGGG--G*UGACAG--------------------------------------------    4

    
    G---UUAG---G*CACAC--------------------------------------------C    4

    
    G---UUAG---G*CAGAC--------------------------------------------C    4

    
    U---AGAC---C*GUUAG--------------------------------------------G    4

    
    ----AAAC---C*GUAAG---------------------------------------------    4

    
    G---GUA----G*CGAA---------------------------------------------C    4

    
    ----AAGGGA-U*ACGACAG-------------------------------------------    3

    
    U---AGAG---G*CAAUC--------------------------------------------G    3

    
    U---AUU----G*CUUCC--------------------------------------------G    3

    
    ----UCAG---G*CUCAA---------------------------------------------    3

    
    U---UGU----G*CAA----------------------------------------------A    3

    
    ----GAU----G*CU------------------------------------------------    3

    
    C---AAGCG--A*UAAAGCCAAU---------------------------------------G    2

    
    ----GAAAC--C*GCGAACUUA-----------------------------------------    2

    
    ----GAUG---C*GAGGUAAGUA----------------------------------------    2

    
    U---AGAC---C*GAGCCAAU-----------------------------------------G    2

    
    ----AAGGGA-U*ACAAUAG-------------------------------------------    2

    
    ----GAAACC-U*GAACUUA-------------------------------------------    2

    
    A---AAGC---U*AUUAC--------------------------------------------U    2

    
    A---UAAG---G*CAAAC--------------------------------------------U    2

    
    A---UAAG---G*CAGAC--------------------------------------------U    2

    
    G---UUAG---A*UAAAC--------------------------------------------C    2

    
    U---AAAC---C*GUUAG--------------------------------------------G    2

    
    ----UGAU---G*CUAUAU--------------------------------------------    2

    
    G---AAUA---U*GGAU---------------------------------------------A    2

    
    ----AAAC---C*GUUAG---------------------------------------------    2

    
    ----AAGG---G*GACAG---------------------------------------------    2

    
    A---GU-----C*GCAGC--------------------------------------------U    2

    
    G---CGA----G*CAAA---------------------------------------------C    2

    
    G---GGA----G*CGAA---------------------------------------------C    2

    
    U---A--A---G*CCAAU--------------------------------------------G    2

    
    U---AA-----G*CCAAU--------------------------------------------G    2

    
    U---AU-----G*CCUCU--------------------------------------------A    2

    
    ------AA---G*CCAAAG--------------------------------------------    2

    
    ----GCAA---G*CAAA----------------------------------------------    2

    
    ----UGAU---G*CUAA----------------------------------------------    2

    
    U---GAU----G*CUA----------------------------------------------G    2

    
    ----A------G*CCAAAA--------------------------------------------    2

    
    ----CAA----G*CAAA----------------------------------------------    2

    
    ----CGA----G*CAAA----------------------------------------------    2

    
    ----CUA----G*CAAA----------------------------------------------    2

    
    ----C------G*CGUAG---------------------------------------------    2

    
    A---UAAG---G*CAGUCUCUAAAGUAAAUAUUUCUAUC------AGAGGAUAGGAAUAU--U    1

    
    ----AAUG---C*GA-------------GAGCGAUCGGGAUCAUGAGCGCCCGAUC-CUUUA-    1

    
    C---AGACA--G*GUGUGAAAACUU-------------------------------------G    1

    
    UA--GACA---G*UGUGAAAAACUU-------------------------------------G    1

    
    A---UG-----C*GAAUUGUAUAAG-------------------------------------U    1

    
    C---AGUGAA-U*GAACCAAA-----------------------------------------G    1

    
    G---CAAGGC-C*GAACCAAC-----------------------------------------C    1

    
    G---GUAGGC-C*GAACUGAA-----------------------------------------C    1

    
    G---GUAUGA-U*GGAACCGU-----------------------------------------A    1

    
    ----GAUG---C*GAGUUAAGUA----------------------------------------    1

    
    ----GAUG---C*GAGUUAGGUA----------------------------------------    1

    
    ----GUAGGC-C*GAACUGAA------------------------------------------    1

    
    C---AGA----C*GAAAAACUU----------------------------------------G    1

    
    G---AAAGUG-U*AAAUAC-------------------------------------------C    1

    
    U---AGA----C*GAAAAACUU----------------------------------------G    1

    
    ----AAACGG-C*GGUACGC-------------------------------------------    1

    
    ----AAGGGG-U*AUGACGG-------------------------------------------    1

    
    ----AGAUGGUC*GGACAA--------------------------------------------    1

    
    ----GAAACC-U*GAACUU-------------------------------------------A    1

    
    A---ACAC---C*GGAGAAA------------------------------------------G    1

    
    C---GGGCC--C*GAAGCA-------------------------------------------G    1

    
    ----AAAGA--C*GAAACUA-------------------------------------------    1

    
    ----AGAUG--G*CGGACAA-------------------------------------------    1

    
    ----UGAAG--U*ACAAAUC-------------------------------------------    1

    
    A---AGGA---U*ACAACC-------------------------------------------G    1

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

    
    A---UG-----C*GAGAUAAG-----------------------------------------U    1

    
    A---UG-----C*GAGGUAAG-----------------------------------------U    1

    
    C----------U*AAUGCUGAUU---------------------------------------G    1

    
    C---AGAC---U*AUUAAG-------------------------------------------G    1

    
    ----AAGGG--G*UGACGG--------------------------------------------    1

    
    ----AAUG---U*AGAAACG-------------------------------------------    1

    
    ----GAAUA--U*GGGAUA--------------------------------------------    1

    
    A---U--G--CC*GAUAAG-------------------------------------------U    1

    
    C---AAAC---C*GUAAG--------------------------------------------G    1

    
    C---AAAC---C*GUUAG--------------------------------------------G    1

    
    G---AAAC---C*AACUU--------------------------------------------A    1

    
    G---AAGA---U*AAGCC--------------------------------------------C    1

    
    G---AAUA---U*AGGAU--------------------------------------------A    1

    
    G---AAUA---U*GGGAU--------------------------------------------A    1

    
    G---UAAG---G*UAAAC--------------------------------------------C    1

    
    G---UUAG---A*UAGAC--------------------------------------------C    1

    
    G---UUAG---U*AAAAC--------------------------------------------C    1

    
    G---UUAG---U*GAAGG--------------------------------------------C    1

    
    U---AAGU---G*UUACU--------------------------------------------A    1

    
    U---AUG----C*GACACA-------------------------------------------G    1

    
    U---GAUG---U*GACUA--------------------------------------------A    1

    
    U---UGC----C*GAUACA-------------------------------------------A    1

    
    ----AAGG---G*CAACCG--------------------------------------------    1

    
    ----AGGGC--U*AAGUA---------------------------------------------    1

    
    A---A-AG---A*AAACU--------------------------------------------A    1

    
    A---AAC----C*GUUUA--------------------------------------------G    1

    
    A---AAU----C*GCAAA--------------------------------------------U    1

    
    A---AGC----C*GAAAC--------------------------------------------U    1

    
    U---A-UU---G*CUUCU--------------------------------------------G    1

    
    U---AGUA---A*UGAA---------------------------------------------A    1

    
    U---UCAA---U*AGAA---------------------------------------------G    1

    
    ----AAAC---C*GUCAG---------------------------------------------    1

    
    ----CGAG---G*CUGAC---------------------------------------------    1

    
    ----GAAA---U*AGGA---------------------------------------------A    1

    
    ----GGAA---C*GAUGG---------------------------------------------    1

    
    ----UUAG---G*CAGAC---------------------------------------------    1

    
    A---AA-----C*GUAAA--------------------------------------------U    1

    
    A---AA-----U*AUUAC--------------------------------------------U    1

    
    A---AAC----C*G-UAA--------------------------------------------G    1

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

    
    A---GG-----C*GAUUG--------------------------------------------U    1

    
    A---UA-----C*GUCAC--------------------------------------------U    1

    
    A---UA-----C*GUCCC--------------------------------------------U    1

    
    A---UG-----C*GAUUG--------------------------------------------U    1

    
    AUGCC------U*AA---------G-------------------------------------U    1

    
    C---AA-----G*CCAAU--------------------------------------------G    1

    
    C---CAAU---G*UAU----------------------------------------------G    1

    
    G---AUA----G*CAAC---------------------------------------------C    1

    
    G---CAA----G*CAAC---------------------------------------------C    1

    
    G---UA-----G*CAAGC--------------------------------------------C    1

    
    U---AU-----U*ACAAU--------------------------------------------G    1

    
    ----GGUA---G*CAAA----------------------------------------------    1

    
    ----UGAU---U*AUAU----------------------------------------------    1

    
    A---UGGG---U*AU-----------------------------------------------U    1

    
    G---G------A*AACAA--------------------------------------------U    1

    
    U---UG-----G*CAGC---------------------------------------------G    1

    
    ----AG-----A*UUAAU---------------------------------------------    1

    
    ----AGA----G*CAAA----------------------------------------------    1

    
    ----AUAA---G*CUC-----------------------------------------------    1

    
    ----AUAU---G*CUA-----------------------------------------------    1

    
    ----CAA----G*CAAC----------------------------------------------    1

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

    
    ----A------G*CCAAC---------------------------------------------    1

    
    ----U------G*CGUAG---------------------------------------------    1

    
    C---G--G---G*CA-----------------------------------------------G    1

    
    U---A------A*UAG----------------------------------------------G    1

    
    U---UG-----U*A---A--------------------------------------------A    1

    
    ----GAA----G*CU------------------------------------------------    1

    
    U---AA-----G*U------------------------------------------------G    1

    
    Omitted sequenced and counts

    
    ------------*--------------------------------------------------    5

    
    ----UUA----G*C-------------------------------------------------    1

    
    ----AU-----G*C-------------------------------------------------    1

    
    ----UG-----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_18487.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-cWW	18.09	-142.83	8	6
2	Motif group IL_90346.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L-L	7.80	-157.73	6	5
3	Motif group IL_11344.2 View motif instance in 3D Basepair signature: cWW-cSS-L-cWW	7.09	-188.78	6	5	180 degree turn
4	Motif group IL_89021.2 View motif instance in 3D Basepair signature: cWW-L-R-L-R-tHS-cWW	7.09	-263.83	6	5	UAA/GAN
5	Motif group IL_38507.2 View motif instance in 3D Basepair signature: cWW-tWH-L-tHS-cWW	6.74	-268.20	6	4	UAA/GAN
6	Motif group IL_61440.1 View motif instance in 3D Basepair signature: cWW-tSH-tHS-tWS-cWW	5.67	-289.66	7	5	Triple sheared
7	Motif group IL_38862.4 View motif instance in 3D Basepair signature: cWW-cSH-R-tWH-tHS-cWW	5.67	-419.46	5	4.5	5x5 Sarcin-Ricin with intercalated A; G-bulge
8	Motif group IL_17136.7 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tHS-cWW	5.32	-353.50	5	4	tSH-tWH-tHS
9	Motif group IL_99498.1 View motif instance in 3D Basepair signature: cWW-L-R-tHW-cWW	4.96	-139.31	7	5
10	Motif group IL_82292.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	4.61	-136.02	7	5

Loop 30 Internal loop

Column numbers: 525-539, 562-568 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-------------A*U-----A   25

    
    U-------------G*C-----A   12

    
    A-------------G*C-----G    9

    
    A-------------U*A-----U    9

    
    U-------------U*A-----A    8

    
    CUA-----------U*A---UAG    6

    
    A-------------U*A----UG    5

    
    GU------------A*G-----C    4

    
    U-------------U*G-----U    4

    
    AAU-----------U*A----GG    3

    
    UAA-----------G*U----UA    3

    
    AU------------G*U----AU    3

    
    AU------------U*A----AU    3

    
    GU------------A*U----AU    3

    
    UA------------U*A----UA    3

    
    C-------------G*C-----A    3

    
    G-------------C*G-----C    3

    
    UUUUGACCUA-AUAU*A-UUGGA    2

    
    AAGA----------U*A----CA    2

    
    AUGA----------C*G----GA    2

    
    UA------------A*U----UA    2

    
    A-------------C*G----CA    2

    
    AA------------C*G-----G    2

    
    A-------------C*G-----U    2

    
    A-------------G*C-----A    2

    
    A-------------G*U-----U    2

    
    A-------------U*G-----U    2

    
    C-------------U*A-----G    2

    
    U-------------C*G-----A    2

    
    UUUUGACCUAAUAAU*-AUUGGA    1

    
    GUUGGG-----AU-G*GC----U    1

    
    AUG-----------C*ACUCACU    1

    
    AUA-----------U*A-UAUAA    1

    
    AUAA----------A*U---UAU    1

    
    CU------------G*C-UUUAU    1

    
    UAAU----------A*G---UUA    1

    
    AUGA----------U*G----GA    1

    
    CUAA----------C*G----AG    1

    
    GAAU----------G*U----UU    1

    
    GUAA----------C*G----AC    1

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

    
    UGC-----------G*C---ACA    1

    
    UGC-----------G*C---ACG    1

    
    A-------------C*G--UAAA    1

    
    AGA-----------C*G----CA    1

    
    AUA-----------A*U----AU    1

    
    C-------------U*AUAU--A    1

    
    CA------------G*U---AUG    1

    
    CAAA----------G*C-----C    1

    
    CCU-----------U*A----UU    1

    
    GAAA----------C*G-----U    1

    
    GC------------U*G---UGC    1

    
    GG------------C*G---UGC    1

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

    
    UUG-----------C*G----AA    1

    
    A-------------C*G---UGA    1

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

    
    AA------------G*C----UU    1

    
    AC------------C*G----AG    1

    
    AG------------A*U----UU    1

    
    AG------------U*A----CG    1

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

    
    AU------------A*U----GU    1

    
    AU------------U*A----AC    1

    
    AU------------U*G----AU    1

    
    C-------------U*A---GUG    1

    
    CA------------G*C----AG    1

    
    CA------------U*A----UG    1

    
    CC------------A*U----GG    1

    
    GU------------C*G----GC    1

    
    GU------------G*C----AU    1

    
    GU------------G*G----CA    1

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

    
    UAU-----------C*G-----A    1

    
    UAU-----------U*A-----A    1

    
    UC------------G*C----AA    1

    
    UG------------U*A----UG    1

    
    UU------------G*C----AA    1

    
    UU------------U*A----UC    1

    
    UU------------U*G----UG    1

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

    
    A-------------C*G----AU    1

    
    CA------------G*U-----G    1

    
    CU------------G*U-----A    1

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

    
    G-------------U*A----UG    1

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

    
    GC------------A*U-----A    1

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

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

    
    U-------------U*G----GU    1

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

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

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

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

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

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

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

    
    G-------------G*U-----U    1

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

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

    
    G-------------U*G-----U    1

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

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

    
    Omitted sequenced and counts

    
    --------------C*G-----A   36

    
    --------------U*A------   14

    
    --------------C*G------    7

    
    ---------------*-------    5

    
    U-------------G*A------    4

    
    --------------U*A----UG    2

    
    --------------G*U-----A    2

    
    --------------U*G------    2

    
    --------------A*UAU----    1

    
    --------------C*G----AG    1

    
    --------------U*A----UU    1

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

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

    
    --------------G*C-----G    1

    
    --------------G*U-----G    1

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

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

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

    
    --------------G*C------    1

    
    C--------------*------A    1

    
    ---------------*------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_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	56.59	-224.85	3	1	Stack and bulge
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	56.10	-277.13	3	1	Multiple bulged bases
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	47.32	-243.28	3	2	Multiple bulged bases
4	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	45.85	-201.36	3	1	Major groove platform
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	45.37	-254.06	4	1	Intercalated cWS
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	40.98	-253.83	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	40.49	-262.42	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	39.02	-267.19	4	1
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	39.02	-269.17	2	1	Single stack bend
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	37.56	-273.72	3	1	Single stack bend

Loop 31 Hairpin loop

Column numbers: 542-559 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ----UUGGCGU-------   20

    
    AU--GUAGCA------GU   13

    
    GC--GUAGCA------GU   12

    
    ---GGUGAUAG-------   11

    
    ----GUGAGAA-------    8

    
    GU--GUGAGAG-----AC    7

    
    U---GUGGCA-------A    7

    
    G--UUUGAGAC------C    6

    
    ----GGGGAC--------    6

    
    G--CGUGAGAAA-----C    5

    
    ----CUGGUAA-------    5

    
    ----GUGGUA--------    5

    
    ----GUGGUG--------    5

    
    GU--GUGAAAG-----AC    4

    
    ---CGUCGAAAA------    4

    
    ----CUGGUGA-------    4

    
    ----GUGGAAG-------    4

    
    ----CCGCAA--------    4

    
    ----GUGGAA--------    4

    
    AG--GCGGAAAA----CU    3

    
    GG--CUGAUUA-----CC    3

    
    UU--AGGGAU------AA    3

    
    C--UGUGGUG-------G    3

    
    ---GGUGGAAG-------    3

    
    U---GUGGCA-------G    3

    
    -----GGGAUGC------    3

    
    ----GUAGCA--------    3

    
    G--CCUGAGAAA-----C    2

    
    G--CGUGAGAGA-----C    2

    
    GC--GUAGCA------GC    2

    
    GC--GUAGCG------GU    2

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

    
    ---CUUGGCCG-------    2

    
    ---UGUGGCAA-------    2

    
    ---UGUGGCAG-------    2

    
    C---UUGGCC-------G    2

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

    
    ----CUGGUUA-------    2

    
    ----GUGAGAG-------    2

    
    ----UUGGCAU-------    2

    
    ----UUGGCUU-------    2

    
    ----UUGGUGA-------    2

    
    ----UUGGUUA-------    2

    
    ---UGUGGUG--------    2

    
    ---UUUGCGG--------    2

    
    ----AGGGAU--------    2

    
    ----GUGGCA--------    2

    
    ----UGGGAG--------    2

    
    ----UUGGCA--------    2

    
    ----GUGGAAUGUUACAG    1

    
    GU-UAUGGGAAUA---GC    1

    
    UG-GGAGAUGAA----CG    1

    
    GC--AUGAGAAC----GC    1

    
    UCUAGGGAUA------GA    1

    
    ----GUGGAAUGU---UA    1

    
    A--CCUGAAGAA-----U    1

    
    AG--CUGGUGC-----UU    1

    
    AG-CUGGUAA------CU    1

    
    AU-UAUGGUG------AU    1

    
    G--CGUAGGAAA-----C    1

    
    G--CGUCGAAAA-----C    1

    
    GU--GUGAGAA-----GC    1

    
    GU--GUGAGAG-----GC    1

    
    GU-GUGAGAG------AC    1

    
    UU--GUGGCAU-----AA    1

    
    UU--GUGGCAU-----GA    1

    
    ----UUGGUACCCU----    1

    
    A---GUGGGAGC-----U    1

    
    AU--GGGGAC------AU    1

    
    AU--GGGGGC------AU    1

    
    AU--GUGGUA------GU    1

    
    G--GGUGAGAG------C    1

    
    GC--GUGGUU------GU    1

    
    GG--GUGGAA------CC    1

    
    GU--GUAGCA------AC    1

    
    GU--GUGAGA------GC    1

    
    UC--AGAGAU------GA    1

    
    ---CCUGAGAAA------    1

    
    ---CGUAGAAAA------    1

    
    ---CGUCGAAA------A    1

    
    ---CGUCGAAAC------    1

    
    ---CGUGAGAGA------    1

    
    --AAUGAGAGA-------    1

    
    --CCGUGGAAC-------    1

    
    --UAGAGGUAU-------    1

    
    A---UUGGUAA------C    1

    
    U---GUGAGAGA------    1

    
    ----UGUGGCAG------    1

    
    ---CGUGGCAA-------    1

    
    ---CUUGAUAA-------    1

    
    ---GGUGGUAG-------    1

    
    ---UGUGGUAG-------    1

    
    ---UUUGAGAC-------    1

    
    ---UUUGGUAC-------    1

    
    --GGUGAUAG--------    1

    
    -U--GUGGCA------G-    1

    
    C---GUAGCU-------G    1

    
    C---GUGGCA-------G    1

    
    G---GUGACA-------C    1

    
    G---GUGGAA-------C    1

    
    G---GUGGUG-------C    1

    
    U---AGGGAU-------A    1

    
    U---GUGACA-------A    1

    
    U---GUGGAA-------A    1

    
    U---UUGGCG-------A    1

    
    -----GGGGUGC------    1

    
    ----CCGCAAG-------    1

    
    ----CUAACGA-------    1

    
    ----CUGAGAA-------    1

    
    ----CUGCAAA-------    1

    
    ----CUGGUGC-------    1

    
    ----GUAGCAA-------    1

    
    ----GUGAUAG-------    1

    
    ----GUGGAAU-------    1

    
    ----GUGGGAA-------    1

    
    ----GUUGCAG-------    1

    
    ----UUGGUAA-------    1

    
    ----UUGGUAC-------    1

    
    ----UUGGUCG-------    1

    
    ---GUGAGAG--------    1

    
    ---GUUGCAG--------    1

    
    ---UUUGCAG--------    1

    
    ---UUUGGCA--------    1

    
    G---GUGGUG--------    1

    
    -----GGGAUA-------    1

    
    ----AUGGGG--------    1

    
    ----AUGGUG--------    1

    
    ----GUGACA--------    1

    
    ----GUGAGA--------    1

    
    ----GUGGCU--------    1

    
    ----UGGGUG--------    1

    
    -----GGGAU--------    1

    
    Omitted sequenced and counts

    
    ------------------    5

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_25061.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	23.16	-41.18	4	3
2	Motif group HL_75293.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	15.44	-60.25	5	3
3	Motif group HL_81538.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F	10.88	-87.36	3	3	GNRA with tandem sheared
4	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	7.72	-67.31	5	4	tRNA anticodon loop with synthetase
5	Motif group HL_78197.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	7.37	-140.77	4	3
6	Motif group HL_41543.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	7.02	-77.63	6	5
7	Motif group HL_85367.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	6.67	-102.86	4	3
8	Motif group HL_36684.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F-F	6.67	-4446.19	5	4
9	Motif group HL_33983.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	5.26	-61.70	5	4
10	Motif group HL_29129.3 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F	4.91	-83.43	5	4

Loop 32 Hairpin loop

Column numbers: 763-764 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UG  107

    
    GC   61

    
    GU   35

    
    CG   27

    
    CC   13

    
    CA   11

    
    GG   11

    
    AG    9

    
    UC    8

    
    AC    6

    
    GA    1

    
    UA    1

No Matches Found View All Results for this Loop

Loop 33 Internal loop

Column numbers: 771-777, 804-806 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    A-----G*U-G   44

    
    G-----G*C-C   30

    
    A-----U*A-G   27

    
    G-----A*U-G    8

    
    A-----C*G-G    7

    
    AAAC--G*CGA    6

    
    A-----A*U-G    4

    
    U-----G*C-G    4

    
    UG----C*G-A    3

    
    A-----G*C-G    3

    
    C-----C*G-C    3

    
    G-----U*A-C    3

    
    U-----C*A-G    3

    
    U-----C*G-G    3

    
    GA----C*GGG    2

    
    UA----C*GAG    2

    
    UC----G*CAG    2

    
    AA----G*C-A    2

    
    A-----C*G-C    2

    
    GAAAACG*CGA    1

    
    GA----U*AAG    1

    
    GC----C*GUG    1

    
    AA----A*U-A    1

    
    AG----C*G-A    1

    
    AG----C*G-C    1

    
    AG----G*C-G    1

    
    CG----C*G-A    1

    
    U-----A*UGC    1

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

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

    
    C-----G*C-G    1

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

    
    G-----C*G-G    1

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

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

    
    U-----G*U-G    1

    
    Omitted sequenced and counts

    
    U-----G*C--   55

    
    C-----G*C--   18

    
    A-----G*C--   16

    
    UA----G*C--    6

    
    ------G*C--    3

    
    -------*---    3

    
    C-----U*A--    2

    
    ------U*G--    2

    
    AAACUAA*U--    1

    
    AGG---C*G--    1

    
    CU----A*U--    1

    
    UC----C*G--    1

    
    UU----G*C--    1

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

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

    
    G-----G*C--    1

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

    
    ------G*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 View motif instance in 3D Basepair signature: cWW-L-cWW	86.29	2.56	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	49.71	-16.14	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	32.57	-69.45	3	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	30.86	-13.40	4	1	Intercalated cWS
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	30.29	-17.33	2	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	30.29	-24.66	3	1
7	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	29.71	-33.82	2	1	Single bulged G
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	29.14	-13.56	3	1
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	26.29	-26.89	2	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	26.29	-30.96	3	1

Loop 34 Hairpin loop

Column numbers: 782-799 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ----GAAA----------  132

    
    A---GAAA---------U   28

    
    ----GGGA----------   16

    
    CU--GAAU--------AA   11

    
    ----GCAA----------    9

    
    ----GUAA----------    9

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

    
    G---GAAA---------U    6

    
    ----GACA----------    6

    
    UA--GAAA--------UG    4

    
    C---GUAA---------G    4

    
    C---GAUCAAAA-----G    3

    
    A---GUAA---------U    3

    
    G---GUGA---------C    3

    
    ----GUAAU---------    3

    
    ----UAAA----------    3

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

    
    A---GAAA---------C    2

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

    
    G---GUAA---------C    2

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

    
    ----GAGA----------    2

    
    ----GUGA----------    2

    
    ----GUUU----------    2

    
    AAUCAGCAGUUAA-GGUU    1

    
    ----GAAUUGAAAA----    1

    
    CU--GAAUA-------AG    1

    
    ----GAAUAAAA------    1

    
    UA--GAAA--------UA    1

    
    A---UAAAA--------U    1

    
    CU--AUCA---------G    1

    
    GC--GAAA---------G    1

    
    U---UAAAA--------G    1

    
    ----CUAAA--------G    1

    
    A---GACA---------U    1

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

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

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

    
    G---GACA---------C    1

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

    
    G---UAAA---------A    1

    
    U---GAAA---------G    1

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

    
    ----AGGAA---------    1

    
    ----ACAA----------    1

    
    ----GAUA----------    1

    
    ----GGAA----------    1

    
    Omitted sequenced and counts

    
    ------------------    3

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	85.71	-8.03	2	0	GNRA
2	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	83.28	-50.68	2	1	Mini UNCG
3	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	78.05	-58.72	2	0
4	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	75.26	4.93	2	0
5	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	72.47	-36.06	2	0
6	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	71.08	-65.84	2	0
7	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	71.08	-187.24	2	0
8	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	70.38	-208.02	2	0	Pseudoknot geometry
9	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	70.03	-61.13	2	0	tRNA D-loop
10	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	68.99	-45.08	2	0

Loop 35 Internal loop

Column numbers: 833-843, 974-983 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CAAGUA----G*U----GAAAG   56

    
    CGAGUA----G*U----GAAAG   45

    
    AAAGUA----G*U----GAAAU   39

    
    UUAGUA----G*U----GAAAA   24

    
    C-----AACGG*UUGUU----G   11

    
    CGAGUA----C*G----GAAAG    8

    
    UAAGUA----G*U----GAAAG    7

    
    UAAGUA----G*U----GAACA    7

    
    UGAGUA----G*U----GAAAG    7

    
    AGAGUA----G*U----GAAAU    6

    
    CAAGUA----G*U----GAACG    5

    
    GGAGUA----G*U----GAAAC    5

    
    CAAGUA----C*G----GAAAG    4

    
    UGAGUA----G*U----GAAAA    4

    
    A-----UCUCG*UGAGA----U    4

    
    U-------AAC*GGA------G    4

    
    AAAGUA----G*U----AAAAU    3

    
    CGAGUA----G*C----GAAAG    3

    
    UUAGUA----G*U----GAAAG    3

    
    AGAGUA----G*U----GAAUU    2

    
    AUAGUA----G*U----GAAGU    2

    
    AUGGUA----G*U----GACAU    2

    
    CCAGUA----G*U----GAAAG    2

    
    GUAGUA----G*C----GAGGC    2

    
    AAAGUA----G*U----GAA-U    2

    
    C-----ACUGG*CUGGU----G    2

    
    U-----UUUUC*GAAAA----A    2

    
    C-------AAC*GGA------G    2

    
    AUAGUA----G*U----GAGGU    1

    
    C----UCGCAG*UCGGA----G    1

    
    CAAGUA----C*G----GAACG    1

    
    CAAGUA----G*C----GAAAG    1

    
    CAUGUA----G*U----GAAUG    1

    
    CCAGUA----G*U----GAGGG    1

    
    CCUGUA----G*U----GAAAG    1

    
    CCUGUA----G*U----GAAGG    1

    
    CGAGUA----A*U----GAAAG    1

    
    CGAGUA----G*U----GGAAG    1

    
    CGAUUA----G*U----GAAAG    1

    
    CUGGUA----G*U----GAAAG    1

    
    GUAGUA----G*C----GAAGC    1

    
    UGAGUA----C*G----GAAAA    1

    
    UUAGUA----G*U----GAACG    1

    
    A-----GAUAG*UUAUU----U    1

    
    C-----AACUG*UUGUU----G    1

    
    C-----ACGAG*UGAGU----G    1

    
    C-----UCAGG*UUUGA----G    1

    
    GUAGUA----G*U----GAA-U    1

    
    U-----ACUGG*CUGGU----G    1

    
    U-----GCUGG*CUGGC----A    1

    
    U-----GGUGG*UCGCC----A    1

    
    C-----AUA-G*UAAAU----G    1

    
    C-----AUA-G*UCAAU----G    1

    
    C-----GUC-G*UUGAU----G    1

    
    U------AACG*CGGA-----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_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	86.21	51.60	2	1	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	85.52	12.21	6	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	82.41	2.49	5	2	8x6 Sarcin-Ricin with inserted A; G-bulge
4	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	81.72	9.93	4	2	8x6 Sarcin-Ricin with inserted Y; G-bulge
5	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	79.66	-13.46	4	2	8x7 Sarcin-Ricin; G-bulge
6	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	77.93	-8.48	5	2	tSH-tSH-tHH-tHS
7	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	64.48	-11.69	5	3	7x7 Sarcin-Ricin with intercalated A; G-bulge
8	Motif group IL_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	44.14	-12.89	3	3	6x5 Sarcin-Ricin; G-bulge
9	Motif group IL_32016.1 View motif instance in 3D Basepair signature: cWW-tSH-tSH-tSS-tHS-L-R-cWW	37.59	-16.45	5	4	Kink-turn
10	Motif group IL_88116.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-L-R-L-R-cWW-cWW	32.76	-20.06	5	4

Loop 36 Internal loop

Column numbers: 848-945, 951-969 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AAU--CCA*CCAGAUUAAAUUAUGAAUA---------------------------------------------------------------CCAAAUUC*G-----------------C   12

    
    AAAU-GUG*CAGAUAAAACAUUUGGAUAUGUUUAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    6

    
    AAUC-UUG*GUUUACAAGAAUAUUCUUAAUUAUUUACUAGAAGA-----------------------------------------------AAAUAAUC*G-----------------A    5

    
    GA---GAC*AGGUUCUGAGUCAGGAAAAAUAAGAUCACAGA--------------------------------------------------ACAAAUGC*AG----------------U    5

    
    GA---GUG*CGUAGAGGAACGAUUUCUACAGAUAACGAAGCUAACAGGAAAUU--------------------------------------AUUAGAUC*G-----------------A    4

    
    GA---GAC*AGGUUCUGAGUCAGAAAAAGGAAGAUCACAGA--------------------------------------------------ACAAAUGC*AG----------------U    4

    
    GA---GAC*AGUUCUAUAAUGACAAGAAGAUCGUCAGG-----------------------------------------------------AAAACUGC*AG----------------U    4

    
    A-----GG*CGAUUUUACAAAUCAAGAAUAAUUGGUAAU----------------------------------------------------UCUAAUGC*G-----------------A    4

    
    AU---GAC*GGGUUUGAAGAUGAUCUUUUCUAUAUCAAAUAUGGAUUUUGUAAAAG-----------------------------------AAAAUUUC*G-----------------A    3

    
    A----UAC*CAAAAGUUAUACUGGUCUUGAAAACCAGAGAUAGAAAA--------------------------------------------CAUUUUUC*G-----------------A    3

    
    AAU--GUG*CAGAUGAACGAUACUGAUAUUGUUAUGCUAAAAC------------------------------------------------AAAUAUUC*G-----------------U    3

    
    AU---GGC*AGUUUUAAAAAGCAAUCUUUCGAUACGAGCAUAUGAGAAUAAGGAAAUGCAAAUAGGCGAAA--------------------GCAUAAUC*G-----------------A    2

    
    AG---GAC*AGUUUUGGUGUUUGAUCUUUAAUACGAUAUGAUGAAAAAGAAAUUGUAUGAAACUAUC------------------------AAAUUUUC*G-----------------A    2

    
    AGC--GUG*UUCAGUUCUAAACUAGACUGGAAAGAUCCGCACAAGUAGAAUGCGAAAAACUCUA---------------------------UUUUUGAC*G-----------------G    2

    
    A----GGU*AGUCAUAAUAGAAUGUAUAUUUUAAUUAAAACUACAUAUGAAAUUACAGUAUAUU---------------------------AAUGAUUC*G-----------------A    2

    
    AG---CUA*CAGCAUAUUGACUAAUUAAUGGCUCGUGAAAGAGCGAAAUGAAAAGA-----------------------------------AAAUUUGC*G-----------------A    2

    
    AU---GGC*AAGUUGAUGAAAAUAAAGCGAAUAGGUGUAAGAUGCAACUA-----------------------------------------UGAUAUUC*G-----------------A    2

    
    AAUC-UUG*GUUUACAAGAAUAUUCUUAAUUAUUUGAUAGAAGA-----------------------------------------------AAAUAAUC*G-----------------A    2

    
    AA---GUG*UGCAGAGGAUUUACAAGAUAUAUUGUGCUAAAA-------------------------------------------------UAUUAAUC*G-----------------U    2

    
    AAUU-GUG*CAGAGAAUUUACAAGAUAUAUUGUGCUAAAA---------------------------------------------------UAUUAAUC*G-----------------U    2

    
    GA---GAC*AGGUUCUGAGUCAGAAAAAGGAAGAUCACAGA--------------------------------------------------ACAAGUGC*AG----------------U    2

    
    GA---GAC*AGGUUCUGAGUCAGGAGAAAUAAGAUCACAGA--------------------------------------------------ACAAAUGC*AG----------------U    2

    
    GA---GAC*AGGUUCUGAGUCAGGAGAAAUAAGAUCACAGA--------------------------------------------------ACAAGUGC*AG----------------U    2

    
    A----UAC*CAGAGUGUUGCUAGUUCUCGAAACUAGCUGGCU-------------------------------------------------CAAUUAUC*G-----------------A    2

    
    AAA--CGU*GGAAAUUACAAUACAGGUUUUUGCAUAA-----------------------------------------------------CCAUCAAUC*G-----------------U    2

    
    AU---GGC*AAAACAAAAUUUUUUUUGCAAAUCAAA-------------------------------------------------------AAAAAUUC*G-----------------A    2

    
    AU---GGC*AGUUACUACUCUACA-------------------------------------------------------------------ACCAUUUC*G-----------------G    2

    
    AU---GGC*AAUAAAUGAACUUU--------------------------------------------------------------------UACCUAAU*G-----------------G    2

    
    AU---GGC*AAUUCUACAA------------------------------------------------------------------------UCAAAUUC*G-----------------G    2

    
    AU---GGC*AAUUUU-----------------------------------------------------------------------------UACAAUC*G-----------------G    2

    
    AU---GGC*AGUUUCUUAAUAAAAUAAAGCUCAAAAAUUAUUCAUUAAGAAUAAAAAGAUAAUUCUAAUUUAAUUUUUGAUUUAAAACAUAUUUUUUUC*G-----------------A    1

    
    AA---AGG*CGAAAACUUUAAGGUAUUACAAAUAAUUGCUGUAACAAAGGUGAUUACUUCUGUAACGAACUUAAAGCAAGUAUAAU-----AAAUAUCC*GGU---------------A    1

    
    AU---GGC*ACUAUGGUUUAAAAGCGGUGGUGCUGGGUCUUUUUCUAAUUUGAUACUUAAUUAAUUAUAUUUGGGCAAUUAAAAU------AUUAAAUC*GU----------------U    1

    
    AUAC-GGC*AGACAACAGAUUUAAAACAAAUAUUUAAAAACAAGUCUACUAAUAGGGGUUGUUUGUUUAAAAACAAGUUUUAA--------UUUAAUUC*G-----------------A    1

    
    AAU--CAA*CGAUAAUUUUGAUGAAAUAAAGAAAAAUGGUUUUAAAAGGUAUUUUAAAAUAGAAAUAU---------------AAAAAUUAUUUAAUUC*A-----------------A    1

    
    AAC--AAG*GCAAAAAAGGGAAAAUCAGUACAUAUGUAAUUUUGGAAGUAUUAAAAGAAAACAAUACAAAGAA------------------AAAUUAUC*G-----------------A    1

    
    A-----GG*CGAAAGUUUAAUAAUUUGCUUAAAAAAGUAUCACAUUUAUAAAUUGACAAAUAACAAUCUAUAAAU----------------UUUACUUC*G-----------------A    1

    
    A-----GG*CGAAAGUUUGAUAAUUUGCUUAAAAAAGUAUCACAUUUAUAAAUUGACAAAUAACAAUCUAUAAAU----------------UUUACUUC*G-----------------A    1

    
    A-----GG*CGAAAGUUUGAUAAUUUGUUUAAAAAAGUAUCACAUUUAUAAAUUGACAAAUAA----------CAAUCUAUAAAU------UUUACUUC*G-----------------A    1

    
    AAU--CGA*CAUAAAUUUGAUUGGAUAAAAACAAUUCUUAUUAUGAUUAAAGAAUGAUUCUAAUAGGA-----------------------UAUUAAAC*GACU--------------U    1

    
    AU---GGC*AAGUUCUUCAAUAAGCAGUUUUUCGAUGUUAGCAUAUGGAAUAAGGAAUGCAAGUAGAAAAAA-------------------ACAUGAUC*G-----------------A    1

    
    AU---GGC*AAGUUCUUCAAUAAGCAGUUUUUCGAUGUUAGCAUAUGGAAUAAGGAAUGCAAGUAGAAAAA--------------------ACAUGAUC*G-----------------A    1

    
    AAU--GAC*AAGGCUGUAAUUCAAGUAAAUGUAAUUUCAAAUAUUGAUUUUAAUAGAAGAUUAAAAUUU----------------------UUACUUUG*U-----------------G    1

    
    A----GAG*GAAUCAAAUGAGUAAAACAAGUAUUAUAGGUAAAUAUUAUGUU---------------------------------------UUUCUAUC*GAUUGUGCCUUGAAAAAGG    1

    
    A----GGC*AGUAGAAGAAUAAUUUUUUAAUUUAGAUAGUAAAUUCAGGUAAGUUUACAUAUCAAAUU-----------------------ACAACUUC*G-----------------G    1

    
    AU---GGC*AAGUUCUUAAAUAAGCAAUUUCGAUAUGAGCAAUGCAAAAGGUGCAAAAUAGGCGAAA------------------------ACAUAAUC*G-----------------A    1

    
    AU---GGC*AAGUUCUUAAAUAAGCAAUUUCGAUAUGAGCAAUGCAAAGGGUGCAAAAUAGGCGAAA------------------------ACAUUAUC*G-----------------A    1

    
    AU---GGC*AAGUUCUUGAAUAAGCAAUUUCGAUAUAAGCAAUGAAAAGGGUGCAAAAUAGGCGAAA------------------------ACAUAAUC*G-----------------A    1

    
    A----GGC*AGUAGAAGAACAAGGUAUAUAAAGAGAACAUCAAAUUAUACAAGUAAGUUUGAGGUUG------------------------AUUAAUUC*G-----------------A    1

    
    AAG--UGA*CGUGAGAUUAAUACAUAAAGAACAAAAAAAUUAAAUCUUAUUAUGAAUUUUCU-----------------------------UAAUACGC*GAC---------------A    1

    
    AAG--UGA*CAACAAGUUCUUGGUAUUAGAACAAAUAGAAAAUAUUUGAUUUAUUAUUGAA------------------------------GAAUUUGC*GGU---------------U    1

    
    AU---GAC*AGUAUUGGAACUUUUCUUUAUAAGUAAUAGCAAAUAUUAUGAAUUAAUGAAGAUU---------------------------UUAGAUGC*G-----------------A    1

    
    AGC--GUG*UUCAGUUUAUUUUUGACGCAGAUCAAAACAAGAUCAAUACACUAAGACUGAUU-----------------------------GGAAAAAC*G-----------------G    1

    
    A----GUC*GAGAAUGAUACAAAUUAUCAAAAUAGAAAAAAUAUACAGGUUUUUGAUAAAACU----------------------------UAACAUUC*G-----------------G    1

    
    A--GCGUG*UUCAGUUCAAACUAGAAUGGAAAGAUCCGCACAAGUAGAAUGCGAAAAACUA------------------------------UUUUUGAC*G-----------------G    1

    
    AAG--UGA*CGUGAGAUUAAUACAUAAAGAACAAAAAAUUAAUUCUUAUUAUGAAUUUU--------------------------------UAAUACGC*GAC---------------A    1

    
    AGC--GUG*UUCAGUUCAAACUAGAAUGGAAAGAUCCGCACAAGUAGAAUGCGAAAAACUA------------------------------UUUUUGAC*G-----------------G    1

    
    AGU--CUA*CGCUUAUGUGAAAAACAAAUAAUUUUUUAAUGUUGGAGUACAUUAAACUUUA------------------------------AAUUAAGC*G-----------------G    1

    
    AU---GGC*AAGUUCUUAAUUUUCAAAAAAUGUUUUAAGAGGAUAAGAAAAAACAUUAUGCA-----------------------------AAACAUUC*G-----------------A    1

    
    A----GAC*AAGACUCAGGAAUUAGAAUAUAAGUUACCAAGUUGAUAAAGGGUAUUUAAAAA-----------------------------UUCUAUGC*G-----------------G    1

    
    A----GGU*AGUCAUAAUAGAAUGUAUAUUUUAAUUAAGUACAUAUGAAAUUACAGUAUAUU-----------------------------AACGAUUC*G-----------------A    1

    
    A----GAC*AAUUAAUUAUUCUAAUCAAAUUAUAGCUAUGGUCUAUAAGUACAAGAAUAUU------------------------------GGUCAUAC*G-----------------A    1

    
    AAG--CGC*GAAGAAUUUCUAAUGUUUGAUUAAGAAUGGUAUUUUGAACCAUUAUUGCU--------------------------------GAAAACUC*G-----------------G    1

    
    AGA--GUG*UUCAGUUCAAACUAGACUGGAAAGAUUCGCAAGAAAUGCGAAUAAUACUA--------------------------------UUUUUGAC*G-----------------G    1

    
    AGC--GUG*CGUACUUCAAACAUUUGAUAAGUGGUCCAUGUGAGAACAACAGGGAAACU--------------------------------UUCUUAGC*G-----------------G    1

    
    AU---GGC*AAGUUUUUGAUAAGCUAUUGCAGUGGACGUGAAAUCCAUUGAUGCAAAACA-------------------------------UAUUCUUC*G-----------------A    1

    
    A----UGC*UAAGACGAACAUGCAAAAAAUAAUAAUUCAAGAGGUGAAUUAAUUUUAUUU-------------------------------UGAUAUUC*G-----------------G    1

    
    A----GUC*AGUGUAGGUAUAAAAAAGAAUGUAUGCUAAUAGAGUAUAUGAUAACAAAA--------------------------------CUUAAUUC*G-----------------G    1

    
    AA---GAC*GAAUAUUACUAAUAUCUUUAAUAUUAUUUAUUGGACAUAAUGAAAGAAG---------------------------------AAAUUUUC*G-----------------U    1

    
    AAU--CGA*CAUUAAAAUAAAACACAUAUAAUAGAAGAAAUUUAUAAAACAAAAA------------------------------------AUCUUUUC*GAC---------------A    1

    
    AGA--GUG*UUCAGUUCAAACUAGACUGGAAAGAUCCGCAAGCAAUGCGAAUAACUA----------------------------------UUUUUGAC*G-----------------G    1

    
    AU---CGC*AUUGACUUGAUAUGAUGAAGAGAUGGGCUGAAUAGUGUCAAUUUGGUCA---------------------------------AAACUUUC*A-----------------U    1

    
    AG---CUA*CAGCAUAUUGACUAAUUUAAUGGCUCGUGAAAGAGCGAAACGAAAAGA----------------------------------AAAUUUGC*G-----------------A    1

    
    AU---GGC*AAGUUCUUAAUUCAAACAAAAUGUUUUAAAGGCGAUAAGAAAAACAUU----------------------------------AAAUUCUC*G-----------------A    1

    
    -----AGG*CAAAUUUUGAUACGUUUGAUAGUAAUAAUCAAAUUUAUUGAAUUCUAAC---------------------------------AAGAAAAC*A-----------------A    1

    
    -----AGG*CGAAAUUUAAUUAAAAUUGAAAAGUAUCAAUUAACAUAUUAAAUUUACA---------------------------------AAUUAUUC*G-----------------A    1

    
    A-----GG*CGUUCUUUUACAAAAUAUUAAUUGCUAAAUAUUUACUGAAAAAUAC---------------------------------UUAACAAGAAC*G-----------------A    1

    
    AAU--CGA*CAUUAAAAUAAAACACAUAUAAUAGAAGAAUUUAUAAACAAAAA--------------------------------------AUCUUUUC*GAC---------------A    1

    
    AG---CUA*CAGCAUAUUGACUAAUAAAUGGCUCGUGAAAGAGCGAAACGAAAAGA-----------------------------------AAAUUUGC*G-----------------A    1

    
    AG---CUA*CAGCAUAUUGACUAAUUAAUCGCUCGUGAAAGAGCGAAACGAAAAGA-----------------------------------AAAUUUGC*G-----------------A    1

    
    AG---CUA*CAGCAUAUUGACUAAUUAAUGGCUCGUGAAAGAGCGAAACGAAAAGA-----------------------------------AAAUUUGC*G-----------------A    1

    
    AG---CUA*CAGCAUAUUGACUAAUUAAUGGCUCGUGAAAGAGUGAAAUGAAAAGA-----------------------------------AAAUUUGC*G-----------------A    1

    
    AU---GAC*GGGUGAGAAAUUUAUCUAUUUAACAAUUUUAAUAGUUUUGGUAAGUA-----------------------------------AAUUUAUC*A-----------------A    1

    
    AU---GAC*GGGUGAGAAAUUUAUCUAUUUAACAAUUUUAAUAGUUUUGGUAAGUA-----------------------------------AAUUUAUC*G-----------------A    1

    
    A----GAC*UAGAAUCAAUUCUUGAAUAUAUCUAAAGGGUAGAUAUGAUUAAAUAA-----------------------------------ACUAAUUC*A-----------------A    1

    
    AUUGCUGC*AGCAAUAGUGAGUAGAAGAACAAAGAUGCAUGAUCUUUGCUAU---------------------------------------AUGAAUUC*---G--------------U    1

    
    A----AGC*AAUGACUGUAGUAAUUUUACAAGUCAAAUGAUGAAGAUUUGAAGAA------------------------------------AAUAAUUC*G-----------------C    1

    
    A----UGC*AGCAAUUUAUUUACAGAUGACAAAUAAUAAAAAUGGGACUCUUAU-------------------------------------GUAAAUGC*GU----------------U    1

    
    AA--CGGC*GUAUUGAUUAAUGGCUUUUUAACUUUUUAGUGACACUUGUUAUA--------------------------------------AAAAGUUC*U-----------------G    1

    
    AU---GGC*AUGAUAAAAAUAAAGCGAAUAGGUGUAAGACAUAAGAUACAACUA-------------------------------------UGAUAUUC*G-----------------A    1

    
    A----CGC*CAAGACUUGAAGAAUCAAAUUUAGAUUGAUAUUCUAAAAAUAAAU-------------------------------------UAAUUUUC*A-----------------U    1

    
    A----GAG*GCGUAAUAUUUCUAAAAUAGUUGACAUUAAUUAUUGGGCAAAUGU-------------------------------------UAUUAAUC*G-----------------G    1

    
    A----GGC*UUUCUUUAAGGAAAAGCUAUUCAAAAAUCUGAUGAAAAUGUUUUA-------------------------------------UCUUUUGG*U-----------------G    1

    
    A----UAC*AGGGACAUAUGGUAAAAAGAAUAUUUUUGAAGAUUAUUAUUUUAC-------------------------------------UUCUUGUC*G-----------------G    1

    
    AAU--CGC*AGUGACAAAAUGAUAUUAGAAGAAAAUGUUUUAUUGAAGAACA---------------------------------------UCUUAUUC*A-----------------U    1

    
    AGA--CAG*CAAGUUCAAUGGAACAAUUCUAGAAAAGAAUUAUUGAUUGA-----------------------------------------UUAAUUGC*GGU---------------U    1

    
    AU---GAC*AGUAUUGAAAACAAAUCUUUUCUUUGUAAUGUAUUAAAAAAAUU--------------------------------------UCAAAUGC*G-----------------A    1

    
    UA---GGC*GUUGAAGAGAAAAUAACUUUUGUUUGCGGACAAAAAAAAUGAUA--------------------------------------GGUUAUUC*G-----------------A    1

    
    AAG--CGC*AAAUAACAAGAUGAUGGAAGAUGAAAAUGGUCAGUAGUCUU-----------------------------------------UGAAUUUC*GU----------------A    1

    
    AAU--CGC*AAUGACACACAUUUUUUGAUGAUAUUUAGAAAAAUAUAAUGA----------------------------------------AAAAAUUC*A-----------------U    1

    
    AAU--CUG*CAACGAUUUUAACAGAUGAGUAUUUUAAUAUUUGGAAAUAUG----------------------------------------UAAUCUUC*A-----------------G    1

    
    A----UGG*AGAAAGUCUCAUCUUCCAGCUUGCGACAUCUGAUCAACCAUCG---------------------------------------CUUAUUGC*G-----------------A    1

    
    AU---GAC*AGGAUGAAGAUUAUUCUAUUACAUAAUUGGUGUAAGAAAAUA----------------------------------------AAAAGUGC*A-----------------U    1

    
    A-----CG*CGAGAGCAUUUUAGAAAAAUGAACUUGUUUGAAGAGUUUGGU---------------------------------------UUCAUAUGC*G-----------------G    1

    
    A----GGC*AAUAAAAGAUUAUUUAUGAUAUUGAACAAUUAUCAAUGAAUA----------------------------------------AAACAAUC*G-----------------A    1

    
    A----UGC*CGAGCCAAAUGUUGAUAGCAAGCGAUAUAAGAACGCUAAAAA----------------------------------------ACAUUUGA*U-----------------G    1

    
    AU---GAC*GUUACGAAUUGAAGAUUUAGAUACAUGUUUUUUUGUAAUCC-----------------------------------------UAAAUUUC*G-----------------A    1

    
    AUC--GAG*AUAAUUACAGGAUAUUUAAAAGAUAUUAGCAAUUAUCUUA------------------------------------------CAAACAUC*G-----------------A    1

    
    AUC--UAC*AAGAUAAAAUUAAGAGCAAAAAAGAGAGCAAAAAACUCAA------------------------------------------AUAAUAAC*G-----------------G    1

    
    AU---GGC*AGCAAACAAAAAGUUUCCUCAAUAGAGUAUUGAGUUUUU-------------------------------------------AAAACAUC*G-----------------A    1

    
    G----GGG*CUAAAUUUGAUUUUUCGAGAGUUGUCGAAUUACAAGUUUG------------------------------------------AAAAAUUC*A-----------------A    1

    
    AAA--GAC*AGUUUUUGAUAACUUAGAUAUAAAGUUGUAUAUUAUU---------------------------------------------CUAAAUGC*G-----------------G    1

    
    AAU--CGA*CAUUGAAACUAUAUUUUACUAAUAGAUUAAAAAAAUA---------------------------------------------AUAAGUUC*G-----------------A    1

    
    A----CAC*GAGAGCAGGUUGACCAAGAAGAUCAUAAUAUUUCUUAA--------------------------------------------UUCAACUC*G-----------------U    1

    
    AAA-CCCU*GGAAAUUUUAAAAAGAUGUCAUUUAAACACUUAU------------------------------------------------UUAAAAUC*G----------------UC    1

    
    AAA-CCCU*GGAAAUUUUUUUGAUAUGUCAUUUACAUUUUAUA------------------------------------------------AAAAAAUC*G----------------UC    1

    
    AAAAUGUG*CAGACACUACAUUAGAAUGUAUUAAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAC-CCU*GGAAAUUUUUUUGAUAUGUCAUUUACAUUUUAUA------------------------------------------------AAAAAAUC*----------------GUC    1

    
    AU---GGC*AUUUAUUAUAAAAUAAAAUCUUUCGAAUGAUUAUCGA---------------------------------------------AAAACUUC*G-----------------A    1

    
    -AAACCCU*GGAAAUUUUUUUAAUAUGUCAUUUACAUUUUAU-------------------------------------------------AAAAAAUC*G----------------UC    1

    
    A-----GG*CGAUUUUACAAAUCAAGAAUAAUUGGUAAUUCUAAUGC--------------------------------------------UGAAUGAC*G-----------------A    1

    
    A-----GG*CGUUCUUUUACAAGAAUAUUUUUGGUAAAUAUUUUAAU--------------------------------------------GAAAAUGC*G-----------------A    1

    
    A----GGC*GAAGAAAUAAAUUUUAUAAGAGGAUUUAUAGAAAAUU---------------------------------------------AAUGAUAA*U-----------------G    1

    
    AA---GUG*UGCAGAUAAAACAUUUGGAUAUGUUUAUGCUUAAAA----------------------------------------------UAUAUUUC*G-----------------A    1

    
    AAAA-GUG*CAGACGAUACAUUAUUGUAUGUUAAUGCUUAAAA------------------------------------------------CAUAUUUC*G-----------------U    1

    
    AAAC-CCU*GGAAAUUUUUUUAAUAUGUCAUUUACAUUUUAU-------------------------------------------------AAAAAAUC*----------------GUC    1

    
    AAAC-GUG*CAGACGAUACAUUAGAAUGUAUUAAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGACGAUACAUUAGAAUGUAUUAAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGACGAUACAUUAUUGUAUGUUAAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGACGAUGCAUUAGGAUGUAUUAAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGAUAAAACAUUUAGAUAUGUUUAUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGAUAAAACAUUUGGAUAUGUUUUUGCUUAAAA------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAGU-GUG*CAGACGAUACAUUAUAGUAUGUUAGUGCUUAAAA------------------------------------------------CAUAUUUC*G-----------------U    1

    
    AAU--GUG*CAGAUGAACGAUACUGAUAUUGUUAUGCUUAAAAC-----------------------------------------------AAAUAUUC*A-----------------U    1

    
    AAU--GUG*CAGAUGAACGAUACUGAUAUUGUUAUGCUUAAAAC-----------------------------------------------AAAUAUUC*G-----------------U    1

    
    AU---GGC*AUUACGAUCGAUAAAGAAAUCAAUGCAUGGUUGAUG----------------------------------------------UUUUCUUC*G-----------------A    1

    
    UC---CCG*AGCUCUUUUUAACCAACGUAAAAUUGGGAAAAAUGA----------------------------------------------GGCAAUUC*G-----------------A    1

    
    A-----GA*CAAGAAAUUGGAUUAAAUAGAAAUAUUGAAAUUUG-----------------------------------------------AUUUCUGC*GGU---------------U    1

    
    AA---GUG*UGCAGAUAAAACAUUGGAUAUGUUUAUGCUUAAAA-----------------------------------------------UAUAUUUC*G-----------------U    1

    
    AA---GUG*UGCAGAUAAAACAUUUGGAUAUGUUAUGCUUAAAA-----------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAAC-CCU*GGAAAUUUUAAAAAGAUGUCAUUUACACUUAU--------------------------------------------------UUAAAAUC*----------------GUC    1

    
    AAAU-GUG*CAGAUAAAACAUUGGAAAUGUUUAUGCUUAAAA-------------------------------------------------UCUAUUUC*G-----------------U    1

    
    AAAU-GUG*CAGAUAAAACAUUUGGAUAUGUUAUGCUUAAAA-------------------------------------------------UAUAUUUC*G-----------------U    1

    
    AAUU-GUG*CAGAUAAAACAUUGGAUAUGUUUAUGCUUAAAA-------------------------------------------------UAUAUUUC*G-----------------U    1

    
    GA---GAC*AGGUUCUGAGUCAGGAAAAAAUAAGAUCACAGA-------------------------------------------------ACAAAUGC*AG----------------U    1

    
    GA---GAC*AGGUUCUGAGUCAGGAAAAAAUAAGAUCACAGA-------------------------------------------------ACAAGUGC*AG----------------U    1

    
    AAAU-GUG*CAGAAAAUUUGCAAGAUAUAUUGUGCUAAAA---------------------------------------------------UAUUAUUC*G-----------------U    1

    
    AAC--CCU*GGAAAUUUUAAAAAGAUGUCAUUUACACUUAU--------------------------------------------------UUAAAAUC*G-----------------U    1

    
    AGU--CCG*UACACAAUAUUUUAUUAUAAGACGAAUAAUAU--------------------------------------------------AUAAUAUC*G-----------------U    1

    
    GA---GAC*AGGUUCUGAAUCAGGAGAAAUAAGAUCACAGA--------------------------------------------------ACAAAUGC*AG----------------U    1

    
    GA---GAC*AGGUUCUGAGUCAGGAAACAGAAGAUCACAGA--------------------------------------------------AUAAGUGC*AG----------------U    1

    
    UA---GGC*GUGAAAUGAUGAAACAGUAUGUUUAAAAUUGUU-------------------------------------------------UAAAAUUC*G-----------------A    1

    
    A----GAC*AAUGACAUUUAGAAGAAAAGAUGCAAAAAUCUU-------------------------------------------------UACUAAUG*G-----------------A    1

    
    AAU--CCG*UGCAAAGAAUUUAUUUAAUUGGAUUAUAAUA---------------------------------------------------AUAAUUUC*G-----------------C    1

    
    AAUC-GUG*CAUAAAAUUACAAGAGAUAUUGUGCUAAAA----------------------------------------------------UAUUAUUC*A-----------------U    1

    
    AU---GGC*AGAAACAAAUAAUCAAGGCUCUGCAUGAACCA--------------------------------------------------AAACAUUC*G-----------------A    1

    
    AC---GGC*ACGAUUUCAUUCUAACAAUUGUUGAGCACAA---------------------------------------------------CAACAUUC*G-----------------A    1

    
    GA---GAC*AGGUUCUAUAAUGACAAGAAGAUCGUCAGG----------------------------------------------------AAAACUGC*AG----------------U    1

    
    A----GAC*AAUGACUAAGAAGAAAAGAUGCAAAAAUCUU---------------------------------------------------UACUAAUG*G-----------------A    1

    
    AGU--CCG*UACAAAUUUCUUAUUAUAAGUCGAAUAAU-----------------------------------------------------AAUAAAUC*G-----------------U    1

    
    AGU--CCG*UACAAAUUUCUUAUUAUAGAGUGAAUAAU-----------------------------------------------------AAUAAAUC*G-----------------U    1

    
    A----AGC*AAGGACUCUUGUAAAAAAGAAAUUACUAAG----------------------------------------------------GAAAUUUC*G-----------------G    1

    
    AA--UGCG*CAGAUAAAA-UCAGACCAAUAUGCUAAAU-----------------------------------------------------UGAUUAUC*G-----------------U    1

    
    A---GUGC*AUUUCAGAAGGUUUCACAGUCAAUGAAA------------------------------------------------------AUAUGUUC*G-----------------G    1

    
    AAG--UUG*GAAUAUAUUAGAAGAUAUUAUAAGAU--------------------------------------------------------UGAUAUGC*G-----------------G    1

    
    AAG--CCG*UGCAAAUUUCUUAAUUGGAUUAUAA---------------------------------------------------------UUAUAUUC*G-----------------C    1

    
    AU---GGC*AAAACAAAAUUUUUUUGCAAAUCAAA--------------------------------------------------------AAAACUUC*G-----------------A    1

    
    AU---GGC*AAAACAAAAUUUUUUUGCAAAUCAA---------------------------------------------------------AAAACUUC*G-----------------A    1

    
    AAUC-GAC*AAUCUUAUAUUAACAGAAAUA------------------------------------------------------------UGGACAUUA*G-----------------U    1

    
    A----UAC*CUGGUUGCGCAUACCAUAAAAAUG----------------------------------------------------------CAUUUAUC*G-----------------A    1

    
    AAG--GAC*UAGAAUAUUAGAAAAUAAUAA-------------------------------------------------------------AGCUUUUC*A-----------------A    1

    
    A----GAG*UAGAUAUAUGGCAAGAAUUAUA------------------------------------------------------------CAUUUAUC*G-----------------G    1

    
    AU---GGC*AAAUGUUUGGUUGGCAAAA---------------------------------------------------------------AACAAAUC*G-----------------A    1

    
    AU---GGC*AUCCUUAACGGGACAGAA----------------------------------------------------------------UGAUGAUC*G-----------------G    1

    
    A----GGC*GAGAAGAAUUAAAGAAUU----------------------------------------------------------------AAUAGUAA*U-----------------G    1

    
    AAG--UUG*GAAUAUAUUAGAAGAU------------------------------------------------------------------UAAUAUGC*G-----------------G    1

    
    AU---GAC*GGGUUUUUGAAAAAUCA-----------------------------------------------------------------AAACUAUC*G-----------------G    1

    
    AAC--UUG*GAUAUAUUAGAAGAU-------------------------------------------------------------------UAAUAUGC*G-----------------G    1

    
    AAUC-CGC*ACAAAAUUAAAAA--------------------------------------------------------------------CAAUUUUGC*G-----------------G    1

    
    A----GGC*GAGAAAAAUU------------------------------------------------------------------------AAUGAUAA*U-----------------G    1

    
    A----GGC*GAGAAAGAUU------------------------------------------------------------------------AAUGAUAA*U-----------------G    1

    
    AAU--CGU*GAAACAA---------------------------------------------------------------------------AAUUUUGC*G-----------------U    1

    
    AAU--CGU*GAAACA----------------------------------------------------------------------------AAAUUUGC*G-----------------U    1

    
    Omitted sequenced and counts

    
    AUC--GGC*AAGAUUAAAUGAUACUAUUAGGUACAAUAUAUA--------------------------------------------------GAACGCA*------------------U    3

    
    A----GGC*UAGUCCAGACAAGAAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC-----------------------------------UUUUAUAC*------------------G    2

    
    AUC--UAC*GUUUGAAGAUAAUUCUUUCCGAAUGGCAUUUAUUCAAAAA------------------------------------------GAAAAAUC*------------------G    2

    
    AAUC-GAC*AAUCUUACAUUAACUGG----------------------------------------------------------------AACAUUGCA*------------------U    2

    
    AA---UAA*AGUCUACGCUUUAUUAACAAGUGCAAUUAUUUUGUUUAAGGUGAA-------ACAAACAAAUUACAGUUCCUAAAAAAG--GGAAAAUGU*------------------G    1

    
    AACU-UAC*GCUAUGAUUAACAAAUUAACUUUUGUUCUAGUGCGAUAGAAAAAAGAGCAAUUACUGCAUACG------------AGAGUAUGAAAAUGU*------------------G    1

    
    AAU--UUA*CGCUUCUAUUAACAAUUAUGAUUGCGUUUAGUGCGAAAAAAG------------------CAAUUUACUGUACACAAAAGGUGUAAAUGU*------------------G    1

    
    AUU-CUGC*AAUCCCUUGGUUGGGAAGUGUUGUCCAUAUAGUUCAAGAUGGAGACAUGAAUACAAGAUUA-----------------------UAUUAC*------------------U    1

    
    AU---GAC*ACAGCUCAAAUAUGAUACGUUGUGCAUGAGUUAUGAGUAAUAGUAACUGAUGAACCUUA-----------------------AAAAAUUC*------------------U    1

    
    AUU-CUGC*AACCCUCUUUAGGGUAUGUGUUAGCCAUAUUUUAGGAUGGAAACAUGAAUACAAGAUAU-------------------------AUUUAC*------------------U    1

    
    AUAC-UGC*AGCCCCUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUUGAAUCAAG---ACAU------------------------AUUUAC*------------------U    1

    
    AUA-CUGC*AGCCCUUUUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUAUUACAAGAU----------------------------AUUUAC*------------------U    1

    
    AUA-CUGC*AGCCCUUUUGGGGUUUGUUGUCCAUAUAGUUUAAGAUGGAAACAUAUUACAAGAU-----------------------------AUUUAC*------------------U    1

    
    AUUU-UGU*ACGAUGACAAAAAUACAGCGAGUUUAUAAUUAGGUAAUUAUAAAUAUAUGAAA-----------------------------CAUAUUGU*------------------U    1

    
    AAU--CUG*CAAGAUUACAUGGAUAAUUAGGAUUAACAAGAAAAAAGGGUUUUUUAAAUU-------------------------------AAUGCUUC*------------------G    1

    
    GU---GAC*ACACAAGCACAAAAGGUUAUAACGUUCGACUCGUUACUCGAAAAAGU-----------------------------------UAAUUUGC*------------------U    1

    
    A----GGC*UAGCUCAAACUAGAAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC-----------------------------------UUUUAUAC*------------------G    1

    
    AAU--CUA*CAUAUACUGAGAGAAAAUGAUAGUAUACAAGGUCAAUGUAUAACAA------------------------------------UUUUUGCC*-------------------    1

    
    A----GGC*UAGUCCAGACAAGAAAAUUUGACGAACCUUAGAAUAGGUAAUUAAC------------------------------------UUUUAUAC*------------------G    1

    
    AUC--UAC*AUGUAAAACAAGAAAUUUUCUUAUGUUCCUUUUUGAACUAAA----------------------------------------AAGUUUUC*------------------G    1

    
    AUC--UGC*UAUAGAUAAAGAAAAUAAUGGAGCAGAACUCCCUAUAGUUUA----------------------------------------AAUUUUUC*------------------G    1

    
    AUC--UGC*UAUAGAUAAAGAAAAUAAUGGAGCAGAACUCCUUUUAAUUUA----------------------------------------AAUUUUUC*G------------------    1

    
    AA--CCCG*ACAUUAUGAAUAAUUCUAUUAUAAUGGGUAUAAAAAUUAUU-----------------------------------------AUUACUUC*------------------G    1

    
    AAC--CCG*ACAUUAUAAAUAAUUCUAUUAUAAUUGGUAUAAAGACUAUU-----------------------------------------AUUACUUC*------------------G    1

    
    AAC--CCG*ACAUUAUGAAUAAUUCUAUUAUAAUGGGUAUAAAAAUUAUU-----------------------------------------AUUACUUC*------------------G    1

    
    AUC--UAC*GUUUGAAGAUAAUUCUUUCCGAAUGGCAUUUAUUCAAAAAG-----------------------------------------AAAAAAUC*G------------------    1

    
    AAC--CCG*ACUUUAUUACAAUAAUAUGAUCUAAUUUUAUUAUG-----------------------------------------------ACUAUUUC*------------------G    1

    
    AC---GCC*GUGAUUUCACUUUGUUAAAUAGGCAAUAACUUAGA-----------------------------------------------UCUCACGC*------------------C    1

    
    AU---GAC*GGGUGAGAAAUUUAUCUAUUUAAUAAUUCUAAUGA-----------------------------------------------UUUUGAUA*------------------A    1

    
    AG---CUC*UCGGUGAAGAACCGGUCUGUAUCAACCGCUAGAU------------------------------------------------ACUCAAGC*------------------U    1

    
    AU---CUA*CGUUGGAUAUAACGUUUACGUAUGGGUAAAAAAAUCUA------------------------------------------------UUAU*------------------G    1

    
    AU---GUC*GUAGUAUUGGUACUCUCUAAAAAUUAACUAGUAA------------------------------------------------CGAUCUGC*------------------C    1

    
    A----GGC*AAACAAACAGAUAAUUAUAUGAAAGCAUAUCAU-------------------------------------------------AACAAAUC*-------------------    1

    
    AU---GCC*GAAAUAUUAGCUUAUAUGAGAUAAG---------------------------------------------------------AUUUUUGC*------------------C    1

    
    A---CACC*GGAUAGUAGUUUCUAGUAAAUGAU----------------------------------------------------------GAUCCUGC*------------------C    1

    
    AC---GCC*GAAAAAAAGAAAUCCUUAACCCGU----------------------------------------------------------UUUUUCGC*------------------C    1

    
    AU---GUC*AACGUUCAGUUUAUGGAGUAUAAA----------------------------------------------------------AAGAUCGC*------------------C    1

    
    AUC--CCU*UGUGAAGAUAAAACACAUUGG-------------------------------------------------------------UUAAAAUC*G------------------    1

    
    AUC--CGC*GACAUAUAAGAUCACUCCUUU-------------------------------------------------------------UAUGUAGC*------------------C    1

    
    A----GAG*GCAGUUUACAAUAACU-------------------------------------------------------------------AUUGGUG*------------------U    1

    
    A----GAG*GCAGUUUACGAUAACU-------------------------------------------------------------------AUUGGUG*------------------U    1

No Matches Found View All Results for this Loop

Loop 37 Hairpin loop

Column numbers: 855-856 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CA  102

    
    GC   51

    
    AC   32

    
    CG   29

    
    GU   18

    
    GG   15

    
    CU   11

    
    UG   11

    
    CC    8

    
    GA    7

    
    UA    4

    
    AA    1

    
    UU    1

No Matches Found View All Results for this Loop

Loop 38 Hairpin loop

Column numbers: 945-951 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUGAAUG  136

    
    CUGAAAG   38

    
    CUGAAGA   24

    
    CUGAAUA   12

    
    CUGAAG-    9

    
    CUGAACG    7

    
    CCGAAAG    6

    
    CUCUUG-    5

    
    CUGAAA-    5

    
    AUGAAUU    4

    
    CGGAAC-    4

    
    CUGAAU-    4

    
    CCGAAA-    3

    
    ACA----    3

    
    CGCAUUG    2

    
    CUGAAAA    2

    
    GUGAAUG    2

    
    GUGAAUU    2

    
    UUGAAUG    2

    
    UCUAUU-    2

    
    ACAUG--    2

    
    GUG----    2

    
    ACACAUG    1

    
    AUGAAAU    1

    
    CCGGAAG    1

    
    CCGUAAG    1

    
    CUGAAUU    1

    
    AAGUAA-    1

    
    C-GAAUG    1

    
    CUAAAG-    1

    
    CUGACG-    1

    
    CUGUAU-    1

    
    UCUAUC-    1

    
    UGGAAC-    1

    
    UGUGGU-    1

    
    CUAAC--    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_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	85.86	15.92	3	1
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	77.24	13.84	3	1
3	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	76.21	7.96	2	2
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	68.97	-189.07	1	1
5	Motif group HL_28075.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	64.48	-15.61	2	2
6	Motif group HL_01609.3 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F	62.41	-12.35	1	1	T-loop with 2 bulged bases not stacked
7	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	60.00	-3.40	2	1	Pseudoknot geometry with 3' bulge
8	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	55.86	-180.72	2	2
9	Motif group HL_77436.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	53.79	-14.75	2	2	T-loop related
10	Motif group HL_59735.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	53.10	-1630.50	2	2

Loop 39 Internal loop

Column numbers: 987-989, 1019-1021 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-G*C-A   55

    
    C-A*U-G   36

    
    G-A*U-G   33

    
    G-A*U-C   29

    
    C-G*C-G   26

    
    G-G*C-C   21

    
    U-U*A-G   15

    
    U-G*C-G   14

    
    G-U*AAC    7

    
    U-A*U-A    7

    
    A-A*U-U    6

    
    A-G*C-U    4

    
    C-U*A-G    4

    
    A-U*AGU    3

    
    G-A*UGC    3

    
    A-C*G-U    3

    
    G-A*U-U    2

    
    G-G*C-G    2

    
    G-U*A-G    2

    
    U-U*A-A    2

    
    AAG*CUU    1

    
    AGA*UCU    1

    
    GUG*CAG    1

    
    AAA*U-U    1

    
    C-A*UAG    1

    
    G-A*UAC    1

    
    G-G*CAC    1

    
    UUU*A-A    1

    
    A-U*A-U    1

    
    C-A*C-G    1

    
    C-U*G-G    1

    
    C-U*G-U    1

    
    G-A*C-C    1

    
    G-G*C-U    1

    
    G-G*U-U    1

    
    U-U*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_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	85.17	19.16	3	1	Multiple bulged bases
2	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	85.17	15.61	2	1	Major groove platform
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	83.45	14.57	3.5	1	Intercalated cWS
4	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	79.66	20.39	3	2	Multiple bulged bases
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	77.59	13.84	3	1
6	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	73.45	0.38	1	1	Single bulged G
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	73.10	8.44	2	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	73.10	3.12	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.41	8.10	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.41	4.87	2	1	Single stack bend

Loop 40 Hairpin loop

Column numbers: 991-1017 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-------UA-A--CCAGU-------C   32

    
    G-------UA----UCAAU-------C   29

    
    G-------UA-A--UCAAU-------C   20

    
    G-------UG----AAAUU-------C   12

    
    G-------UA-A--CCAAU-------C    8

    
    G-------UA-A--CCAUU-------C    7

    
    G-------UA-A----AGU-------C    7

    
    G-------UA-A--UCAGU-------C    6

    
    A-------UA-A--CCAAU-------U    5

    
    G-------UA-A--ACAAU-------C    5

    
    G-------UA-A--GCAAU-------C    5

    
    G-------UA-A--UCAUU-------C    5

    
    C-------UG----CUAGU-------G    5

    
    GU------UA-AAUUCGCU------CC    4

    
    G-------UA-AAGGUAAU-------C    4

    
    G-------UA-A--ACAGU-------C    4

    
    G-------UA-A--GCAUU-------C    4

    
    G-------UA-A--UCAAC-------C    4

    
    G-------UA----UUAUU-------C    4

    
    G-------UU----UCAAG-------C    4

    
    G-------UA-A----AAU-------C    4

    
    G-------UA-A----AUU-------C    4

    
    G-------UAGC--AAAAU-------C    3

    
    G-------UA-G--CCAAU-------C    3

    
    G-------UA-G--CCAUU-------C    3

    
    G-------UA-G--UCAAU-------C    3

    
    G-------CA----UCAAU-------C    3

    
    G-------UA----UCAUU-------C    3

    
    G-------UACAAAAUAAU-------C    2

    
    AG------GA-A--AAGAU------CU    2

    
    A-------UA-A--CCACU-------U    2

    
    G-------CA-A--UCAAU-------C    2

    
    G-------GA-A--CCUAU-------C    2

    
    G-------UA-G--AAAGU-------C    2

    
    G-------UA-G--ACAAU-------C    2

    
    G-------UA-G--UCAUU-------C    2

    
    C-------UG----CCAAU-------G    2

    
    C-------UG----CUGGU-------G    2

    
    G-------CA----UUAAU-------C    2

    
    G-------UG----AAGUU-------C    2

    
    G-------UG----AUAUU-------C    2

    
    G----------A--UAAAU-------C    2

    
    G-------UAAA-----UC-------C    2

    
    AAUACAAAUACA--AUCUA-UUUGAUU    1

    
    G-------UAAAAAUUAAUU------C    1

    
    GA------UAAU-CUAAAC------UC    1

    
    G-------UAUGAAAAAUC-------C    1

    
    G-----UAUAAA--AGAAU-------C    1

    
    GA------UAAU--CGAGU------UC    1

    
    GA------UAAU--UAAAU------UC    1

    
    GA------UUAU--GCAAG------UC    1

    
    GG------UAAU--UUAGU------CC    1

    
    AG------GA-A--AAGGU------CU    1

    
    G-------UA-AAAAGAAU-------C    1

    
    G-------UA-AUCUGAGU-------C    1

    
    G-------UAAU-UCCAAU-------C    1

    
    G-------UAGA-AAGAGC-------C    1

    
    GC------CA-G--UAGAG------CU    1

    
    GG------UA-G--ACAUU------CC    1

    
    CG------UG-A--CCAAU------C-    1

    
    G-------UACA--UGAAU-------C    1

    
    G-------UAGA--CGAAU-------C    1

    
    A-------AA-A--CCAAU-------U    1

    
    A-------UA-A--UCAAU-------U    1

    
    G-------AA-A--CUAAU-------C    1

    
    G-------CA-A--CCAAU-------C    1

    
    G-------CA-C--UAAAU-------C    1

    
    G-------UA-A--ACAAC-------C    1

    
    G-------UA-A--CCAUC-------C    1

    
    G-------UA-A--GCAGU-------C    1

    
    G-------UA-A--UCAGC-------C    1

    
    G-------UA-A--UGAAU-------C    1

    
    G-------UA-C--UCAAU-------C    1

    
    G-------UA-C--UCAUU-------C    1

    
    G-------UA-G--UAAAU-------C    1

    
    G-------UA-G--UUAGC-------C    1

    
    G-------UC-G--CCAAG-------C    1

    
    G-------UC-G--CCGAG-------C    1

    
    G-------UC-G--CCGUG-------U    1

    
    G-------UC-G--UCGAG-------C    1

    
    G-------UG-A--AGAAU-------C    1

    
    G-------UU-G--CCAUG-------C    1

    
    G-------UU-U--ACAAU-------C    1

    
    A-------GA-G--A-GAU-------U    1

    
    C-------GA----AAGAU-------G    1

    
    C-------GA----AGGAU-------G    1

    
    C-------GA----GAGAU-------G    1

    
    G-------UA----CCAAU-------C    1

    
    G-------UA----GCAAU-------C    1

    
    G-------UA----UCAAC-------C    1

    
    G-------UA----UUAGU-------C    1

    
    G-------UA----UUGAU-------C    1

    
    G-------UC----ACAAU-------C    1

    
    G-------UC----ACAGU-------C    1

    
    G-------UG----ACAUU-------C    1

    
    G-------UU----CUAAU-------C    1

    
    G-------UU----UCGUU-------C    1

    
    U-------UA----GCAGU-------A    1

    
    U-------UG----UUGAU-------A    1

    
    C-------CA-----UCGC-------G    1

    
    G-------UA-A----AUC-------C    1

    
    G-------UG-A----AAU-------C    1

    
    --------GACA---------------    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_04171.7 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F-F-F	69.66	-12.73	6	4
2	Motif group HL_38808.1 View motif instance in 3D Basepair signature: cWW-cWW	67.59	-59.64	5	3
3	Motif group HL_61996.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F	40.00	-41.13	3	3
4	Motif group HL_27670.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F	40.00	-90.87	2	2	T-loop with unstacked turn
5	Motif group HL_98864.1 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F-F-F	33.79	-32.57	4	4	T-loop with unstacked turn
6	Motif group HL_25847.2 View motif instance in 3D Basepair signature: cWW-F-cSH-tHW-F-F-F	30.69	-60.21	4	4
7	Motif group HL_81545.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F	18.97	-31.51	4	4
8	Motif group HL_20167.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	14.48	-58.10	4	3
9	Motif group HL_01609.3 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F	11.03	-96.77	3	2	T-loop with 2 bulged bases not stacked
10	Motif group HL_08510.1 View motif instance in 3D Basepair signature: cWW-F-F-cSH-F-F	10.00	-214.61	7	5

Loop 41 3-way junction loop

Column numbers: 1027-1060, 1134-1139, 1247-1250 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GCUUCGU--------------------------G*CU--AG*CU-C   22

    
    UCAUUUAA--------------------------*----UC*AG-G   19

    
    CUUAA----------------------------C*G----A*U--G   11

    
    GUUUAU---------------------------G*C---UG*U--C    6

    
    GCAUUG---------------------------G*C----G*C--C    6

    
    GGCAAA----------------------------*----AG*U--C    6

    
    GAAAAUG--------------------------G*C---UG*C--C    5

    
    GCGUAG---------------------------C*GG--UU*A--C    5

    
    GCAUACG--------------------------G*C----A*U--C    4

    
    GCUUGG---------------------------A*U---UG*U--C    4

    
    ACUUCGGUA------------------------G*C---CA*UA-U    3

    
    ACUUGAAAU-------------------------*----GC*GA-U    3

    
    UCAACGG--------------------------G*U---CG*C--G    3

    
    GUUUUAGG-------------------------U*A---UG*CA-C    2

    
    GAUUUAAA--------------------------*----UU*AAAC    2

    
    CAAUUG---------------------------C*G---AU*AA-G    2

    
    CCAUUAAA--------------------------*----CC*AG-G    2

    
    CCAUUAAA--------------------------*----UC*AG-G    2

    
    CCAUUGAA--------------------------*----CC*AG-G    2

    
    CCAUUUAA--------------------------*----UC*AG-G    2

    
    GCAUUGG--------------------------G*C---UG*U--C    2

    
    ACAAGG---------------------------U*A---UU*A--U    2

    
    GAAAUG---------------------------G*C---UG*C--C    2

    
    GAAUUG---------------------------G*C---UG*C--C    2

    
    GACCAG---------------------------C*G---UG*C--C    2

    
    UGUUCG---------------------------G*C---CC*G--A    2

    
    GAUACAA---------------------------*----AC*G--C    2

    
    GCAAG----------------------------G*U---GG*U--C    2

    
    GGUUU----------------------------G*U---GG*C--C    2

    
    GUUUU----------------------------G*C---GG*C--C    2

    
    GAUU-----------------------------G*U---GG*C--C    2

    
    GCUUG----------------------------G*U----U*A--C    2

    
    GCUU-----------------------------G*U----G*C--C    2

    
    GUUUGUGA--UGUGUGGUAUAAUUCCAUAUA--A*UGUCUA*U--C    1

    
    GCAUUGUGCGAAUGUAUGCUGUU--CUUAAGUGG*C---UU*A--C    1

    
    GCAUUGUGCGAAUGUGUGCUGUU--CUGAUAUGG*C---UU*A--C    1

    
    CAA-------AGAUAUGAAGA----AUAUCUAAG*U---GA*UC-G    1

    
    GUUUU-----UAGUGUUGUU-----GCACUAUUG*C---GG*U--C    1

    
    GAUUAA----AGGU--GAAGA------ACCUGUG*U---GG*C--C    1

    
    GUAUUAGUGUUUCGUCGC---------------U*A---UA*U--C    1

    
    GCAAGUGUACA----------------------G*U---UA*U--C    1

    
    UGUUCGUU-------------------------G*CCUUCA*U--A    1

    
    GCUUCGU--------------------------G*CC--AG*CU-C    1

    
    GGGAUAU--------------------------G*UC--UU*AC-C    1

    
    GCGUAGCA--------------------------*GG--UU*A--C    1

    
    GUAAGUGU-------------------------A*UU---A*U--C    1

    
    UCUAGG---------------------------G*CU--AG*UU-G    1

    
    ACUAUGC--------------------------G*C---GG*C--U    1

    
    ACUAUGU--------------------------U*A---UA*U--U    1

    
    AUCAUAG--------------------------G*C----G*CG-U    1

    
    CAAUUA---------------------------U*A---AC*GA-G    1

    
    CCAUUAAA--------------------------*----AC*AG-G    1

    
    CCAUUAAA--------------------------*----UU*AG-G    1

    
    GACGAUG--------------------------G*C---UG*C--C    1

    
    GAUUUUG--------------------------G*C---UC*G--C    1

    
    GCAAGUCG-------------------------G*U----G*C--C    1

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

    
    GCAUCGU--------------------------G*C---UA*U--C    1

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

    
    GCAUUGGCA-------------------------*----UA*U--C    1

    
    GCUAAGG--------------------------G*U---UG*U--C    1

    
    GCUAUGU--------------------------A*U---UA*U--C    1

    
    GCUUCG---------------------------U*U---AG*CU-C    1

    
    GCUUUGU--------------------------G*C---UU*A--C    1

    
    GUUUAU---------------------------G*C---AG*CC-C    1

    
    GUUUGAC--------------------------G*C---UG*C--C    1

    
    GUUUUAU--------------------------G*C---UG*C--C    1

    
    UAAAAAACA-------------------------*----UA*U--G    1

    
    UCAUUCAA--------------------------*----UC*AG-G    1

    
    UCAUUUAA--------------------------*----CC*AG-A    1

    
    UCGUUAAA--------------------------*----UC*AG-G    1

    
    UCUAUGG--------------------------G*U---CG*C--G    1

    
    ACACG----------------------------G*U---GG*UC-U    1

    
    ACUAGG---------------------------C*G---UU*A--U    1

    
    ACUUGU---------------------------G*C---UA*U--U    1

    
    CCUAGG---------------------------U*A---UA*U--G    1

    
    CCUCGG---------------------------U*A---UU*A--G    1

    
    CUUAAC---------------------------U*A---GA*U--G    1

    
    GACAGU---------------------------G*U---GG*C--C    1

    
    GACCAG---------------------------U*G---UG*C--C    1

    
    GACUAG---------------------------U*A---UG*C--C    1

    
    GAGCUG---------------------------G*C---UG*C--C    1

    
    GAUGUG---------------------------G*C---UG*C--C    1

    
    GAUUUG---------------------------A*U---CU*A--C    1

    
    GCAAGG---------------------------G*C---UG*U--C    1

    
    GCAUUGAC--------------------------*----AA*U--C    1

    
    GCUAG----------------------------G*C---AG*UU-C    1

    
    GCUUGG---------------------------G*C---UG*U--C    1

    
    GCUUGG---------------------------G*U---UG*U--C    1

    
    GCUUGU---------------------------G*C---AA*U--C    1

    
    GCUUUGAC--------------------------*----CG*U--C    1

    
    GGUUCG---------------------------G*C---CC*G--C    1

    
    GGUUUG---------------------------G*C---UA*U--C    1

    
    GUAAA----------------------------G*C---GG*CC-C    1

    
    GUAUAU---------------------------U*A---UA*U--C    1

    
    GUUCUG---------------------------G*C---UG*C--C    1

    
    GUUUAU---------------------------G*C---AG*C--C    1

    
    UCUCG----------------------------G*C---GG*UC-A    1

    
    UCUUGA---------------------------U*A---UU*A--A    1

    
    UCUUGA---------------------------U*A---UU*A--G    1

    
    UGGACG---------------------------G*C---CC*G--A    1

    
    UUUUGG---------------------------A*U---UG*C--G    1

    
    ACAGAG---------------------------A*U----U*A--U    1

    
    ACGUAG---------------------------G*C----G*C--C    1

    
    ACUAUG---------------------------U*U----A*U--U    1

    
    ACUCGAC---------------------------*----AC*A--U    1

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

    
    CGUUUC---------------------------G*C----C*G--A    1

    
    GAAUG----------------------------G*C---UG*C--C    1

    
    GAUUCU---------------------------G*C----C*G--C    1

    
    GCAUAG---------------------------G*C----G*C--C    1

    
    GCGGAG---------------------------A*U----U*A--U    1

    
    GCGGUG---------------------------U*A----A*U--C    1

    
    GCUAGUC---------------------------*----AG*U--C    1

    
    GCUCUG---------------------------A*U----A*U--C    1

    
    GCUUGAA---------------------------*----AG*U--C    1

    
    GCUUGAC---------------------------*----CG*U--C    1

    
    GCUUUG---------------------------A*U----A*U--C    1

    
    GGUA-----------------------------G*C---AG*UU-C    1

    
    GGUUG----------------------------U*A---CU*A--C    1

    
    GUGUCA---------------------------G*C----G*C--C    1

    
    GUUUA----------------------------G*C----G*CC-C    1

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

    
    UCUUGAA---------------------------*----UU*A--A    1

    
    UGCUAC---------------------------G*C----C*G--A    1

    
    UGUAUC---------------------------G*C----C*G--A    1

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

    
    ACUAU----------------------------G*U----A*U--U    1

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

    
    GAAUU----------------------------G*C----G*C--C    1

    
    GAUGU----------------------------G*C----G*C--C    1

    
    GCAAG----------------------------G*C----G*C--C    1

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

    
    GCUU-----------------------------G*U----G*UC-C    1

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

    
    GGUCC----------------------------G*U----U*G--C    1

    
    GUUUA----------------------------G*C----G*C--C    1

    
    GUUUA----------------------------G*U----G*C--C    1

    
    UCACG----------------------------G*C----G*C--A    1

    
    UCUAG----------------------------U*A----U*A--A    1

    
    GAUU-----------------------------G*U----G*C--C    1

    
    Omitted sequenced and counts

    
    UCUUGAAA--------------------------*-----U*A--A    7

    
    GCUUAGACA-------------------------*-----G*U--C    4

    
    GCUUUGACA-------------------------*-----G*U--C    4

    
    GCUUGACA--------------------------*-----G*U--C    4

    
    GGUUCAAA--------------------------*-----A*U--C    4

    
    CAUCCAAAAAG-----------------------*-----G*CG-G    2

    
    GACUAGAAAU------------------------*-----G*U--C    2

    
    GCUUUGACC-------------------------*-----G*U--C    2

    
    GCUUUGAUA-------------------------*-----G*U--C    2

    
    GCUUGACA--------------------------*-----G*C--C    2

    
    ACAUCCGAGAAG----------------------*-----G*CGGU    1

    
    GCUUGAAAUUAUUU--------------------*-----G*C--C    1

    
    CCUUUGAAAAC-----------------------*-----A*UU-G    1

    
    CCUUUGUAAAG-----------------------*-----G*CG-G    1

    
    ACAUUAAAAG------------------------*------*GG-U    1

    
    CCAUCAAAAC------------------------*------*CG-G    1

    
    UCUUUGGAAA------------------------*-----U*A--G    1

    
    GCUUUAAAAA------------------------*------*G--C    1

    
    GCUUUGACA-------------------------*-----A*U--C    1

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

    
    CAGAAAAAG-------------------------*------*G--G    1

    
    GCUUGUCA--------------------------*-----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
1	Motif group J3_28621.5 View motif instance in 3D Basepair signature: 13	9.39	-301.39	7	5
2	Motif group J3_70599.1 View motif instance in 3D Basepair signature: 11	8.57	-230.96	7	4
3	Motif group J3_11375.2 View motif instance in 3D Basepair signature: 10	5.31	-293.35	8	4
4	Motif group J3_12003.2 View motif instance in 3D Basepair signature: 9	4.08	-447.65	7	4
5	Motif group J3_01052.1 View motif instance in 3D Basepair signature: 13	3.27	-197.12	8	6
6	Motif group J3_47324.1 View motif instance in 3D Basepair signature: 10	1.63	-301.67	9	7
7	Motif group J3_26675.1 View motif instance in 3D Basepair signature: 9	1.22	-235.93	9	5
8	Motif group J3_51910.1 View motif instance in 3D Basepair signature: 12	1.22	-279.02	10	6
9	Motif group J3_62630.1 View motif instance in 3D Basepair signature: 12	0.82	-206.09	10	6
10	Motif group J3_33494.1 View motif instance in 3D Basepair signature: 12	0.82	-251.05	8	5

Loop 42 Hairpin loop

Column numbers: 1064-1130 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    -----------------------------GAAA----------------------------------   49

    
    C----------------------------AUUU---------------------------------G   11

    
    C----------------------------UUCG---------------------------------G    8

    
    -----------------------------UUUUA---------------------------------    8

    
    -----------------------------GCAA----------------------------------    8

    
    -----------------------------CUUUG---------------------------------    5

    
    -----------------------------GUAGA---------------------------------    4

    
    -----------------------------GUAA----------------------------------    4

    
    CGCAGCAUGG-------------------CUUAU-----------------------CC-UGUUGCG    3

    
    UACGAUAUGG-------------------CUCAA-----------------------CU-UAUUGUA    3

    
    UCCAAGCAC--------------------UUGU-------------------------GUGCGAGGA    3

    
    CGGC-------------------------GUUUGA----------------------------GUCG    3

    
    -----------------------------UUUAA---------------------------------    3

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

    
    AAUACAG----------------------UUCG---------------------------CUGUGUA    2

    
    G----------------------------UGUAUU-------------------------------C    2

    
    -----------------------------UGAAAG--------------------------------    2

    
    -----------------------------UUAAU---------------------------------    2

    
    -----------------------------UUUAU---------------------------------    2

    
    -----------------------------UUCG----------------------------------    2

    
    -----------------------------UUUA----------------------------------    2

    
    AAUUAAGG--ACGAACAUCACAAUCCAUCCGUAG---GGUGCGAGAGU-AUGUU-GUAGAAUUAAUU    1

    
    UUUAACGGUUAGGGGCGACUUAUAG----UUUAA--------CUACAAGUGGCAACAGACGGUUUAA    1

    
    AUAAUUAGUUUUCA---------------GUAA--------------------UGAAAAUCAAUUAU    1

    
    UUUGUGG-GGC------------------CGUUG----------------------GCACAAUCAAA    1

    
    -CUCCAAGCAU------------------UUGU-----------------------GUGCAAGGAGC    1

    
    UCCAAGCAC--------------------UUGU-------------------------GUGCGAAGA    1

    
    UCCAAGCGC--------------------CUUU-------------------------GCGCAAGGA    1

    
    UCCAAGCGC--------------------UUUU-------------------------GCGCAAGGA    1

    
    UUGAUAAA---------------------CAAUG-------------------------UUUAUCAG    1

    
    UAGC-------------------------GUUUGA----------------------------GCUA    1

    
    UGGA-------------------------GAGGUC----------------------------UCCA    1

    
    AUAU-------------------------CGGAC-----------------------------AU-U    1

    
    UUG--------------------------CAAAUA-----------------------------CAA    1

    
    ACC--------------------------GAAA-------------------------------GGU    1

    
    GAU--------------------------GAGA-------------------------------ACC    1

    
    GGU--------------------------GAGA-------------------------------ACC    1

    
    UGC--------------------------UUCG-------------------------------GCG    1

    
    UGC--------------------------UUCG-------------------------------GUA    1

    
    UUG--------------------------UUUU-------------------------------CAA    1

    
    GU---------------------------AGAGU-------------------------------GC    1

    
    GU---------------------------GGAAA-------------------------------AC    1

    
    -----------------------------CUUAGUGU------------------------------    1

    
    AG---------------------------CGCA--------------------------------AU    1

    
    AG---------------------------GAAA--------------------------------CU    1

    
    AG---------------------------UGUA--------------------------------CU    1

    
    CC---------------------------GAAA--------------------------------GG    1

    
    CC---------------------------UCCG--------------------------------GG    1

    
    G----------------------------GGUAUA-------------------------------C    1

    
    GG---------------------------UGUUU--------------------------------C    1

    
    UC---------------------------UUCG--------------------------------GA    1

    
    UU---------------------------UUGU--------------------------------AA    1

    
    C----------------------------CUAUG--------------------------------G    1

    
    G----------------------------UGUUU--------------------------------C    1

    
    U----------------------------AAUAU--------------------------------A    1

    
    -----------------------------UUUAUU--------------------------------    1

    
    A----------------------------GCAA---------------------------------U    1

    
    C----------------------------AUAA---------------------------------G    1

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

    
    C----------------------------UGGC---------------------------------G    1

    
    G----------------------------CUUG---------------------------------C    1

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

    
    U----------------------------UUAU---------------------------------A    1

    
    -----------------------------CAAAG---------------------------------    1

    
    -----------------------------CAUUG---------------------------------    1

    
    -----------------------------CUUGG---------------------------------    1

    
    -----------------------------GUAAA---------------------------------    1

    
    -----------------------------GUUCG---------------------------------    1

    
    -----------------------------GUUUC---------------------------------    1

    
    -----------------------------UAAAC---------------------------------    1

    
    -----------------------------UGUUU---------------------------------    1

    
    -----------------------------UUUGA---------------------------------    1

    
    -----------------------------AUAA----------------------------------    1

    
    -----------------------------AUUU----------------------------------    1

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

    
    -----------------------------GGAA----------------------------------    1

    
    -----------------------------GUGA----------------------------------    1

    
    -----------------------------GUUA----------------------------------    1

    
    -----------------------------GUUU----------------------------------    1

    
    -----------------------------UUAU----------------------------------    1

    
    -----------------------------UUUG----------------------------------    1

    
    -----------------------------UUUU----------------------------------    1

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

    
    -----------------------------UUU-----------------------------------    1

    
    Omitted sequenced and counts

    
    -------------------------------------------------------------------   98

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	61.46	-1196.67	2	1
2	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	56.25	-1561.24	2	2	Mini UNCG
3	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	47.40	-1452.67	2	2
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	47.40	-1670.11	2	1.5
5	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	46.35	-1191.84	3	2
6	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	43.75	-1472.05	3	2	tRNA D-loop
7	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	41.67	-1137.61	2	1.5	GNRA
8	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	35.94	-1099.57	3	2
9	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	35.94	-1681.31	3	2
10	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	34.90	-3490.51	3	2

Loop 43 Internal loop

Column numbers: 1146-1149, 1233-1240 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-AA*UCAGA--C  153

    
    G-AU*ACAGC--C   25

    
    G-AA*UCAGC--C   24

    
    A-CA*UCAGG--U   10

    
    A-AA*UCAGC--U    6

    
    A-UA*UCAGG--U    6

    
    G-AA*UCGGA--C    5

    
    GAAU*ACAUA--C    4

    
    A-CU*ACGGG--U    4

    
    A-UA*UCAGA--U    4

    
    C-AA*UCCGU--G    4

    
    A-AA*UCAGG--U    3

    
    G-GU*AUGUG--C    3

    
    G-AG*-CAUUCUC    2

    
    A-AA*UCACU--U    2

    
    A-AA*UCAGA--U    2

    
    C-GU*AGGGC--G    2

    
    G-AG*UGCGA--C    2

    
    AAAA*UCACA--G    1

    
    AAAA*UCAUC--G    1

    
    AAAU*ACAGC--G    1

    
    G-AA*-GAGGCUC    1

    
    GAAA*UCACG--C    1

    
    GAAA*UCAGA--C    1

    
    GAAU*ACAGA--C    1

    
    A-AA*UCAGU--U    1

    
    A-AU*ACAGC--U    1

    
    A-CC*-UCACA-U    1

    
    A-GU*AGGGC--U    1

    
    A-UG*UUCGC--U    1

    
    G-AG*-UAGAG-C    1

    
    G-AG*CAGGA--C    1

    
    G-AU*ACAGA--C    1

    
    G-CG*CCGGC--C    1

    
    G-UA*UCAAA--C    1

    
    G-UA*UCAAG--C    1

    
    G-UU*UCGGA--C    1

    
    U-AA*UCAGA--G    1

    
    Omitted sequenced and counts

    
    ----*-GAGU---    5

    
    G---*-------C    3

    
    G---*CAUUC--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
1	Motif group IL_10389.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-cWW	88.97	27.08	3	1
2	Motif group IL_07173.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	88.97	3.73	5	3
3	Motif group IL_91592.1 View motif instance in 3D Basepair signature: cWW-L-tHH-L-cWW-L-L	82.21	-3.88	7	3
4	Motif group IL_49061.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	59.07	9.93	5	1
5	Motif group IL_33323.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L-L	58.72	7.20	5	2
6	Motif group IL_14177.2 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	58.01	-3.83	5	2
7	Motif group IL_98347.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	56.58	9.15	6	2
8	Motif group IL_97273.1 View motif instance in 3D Basepair signature: cWW-tSH-cWW-L-cWW-L	19.93	-24.98	6	3
9	Motif group IL_51191.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L-L	8.19	-14.47	7	4
10	Motif group IL_43622.1 View motif instance in 3D Basepair signature: cWW-cWW-L-cWW-L	7.83	-20.69	4	4

Loop 44 Internal loop

Column numbers: 1151-1153, 1179-1231 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U-U*G---------------------------------------------------G   50

    
    U-A*U---------------------------------------------------G   38

    
    C-A*U---------------------------------------------------G   37

    
    U-U*A---------------------------------------------------G   25

    
    C-U*A---------------------------------------------------G   20

    
    U-C*G---------------------------------------------------G   15

    
    C-C*A---------------------------------------------------G   13

    
    C-U*G---------------------------------------------------G    9

    
    GUU*A--------------------------------------------------GC    8

    
    C-C*C---------------------------------------------------G    7

    
    C-G*U---------------------------------------------------G    5

    
    G-U*A---------------------------------------------------C    5

    
    C-U*A---------------------------------------------------U    4

    
    G-U*U---------------------------------------------------C    4

    
    U-A*U---------------------------------------------------A    4

    
    A-U*G---------------------------------------------------U    3

    
    C-C*G---------------------------------------------------G    3

    
    U-G*U---------------------------------------------------G    3

    
    C-C*U---------------------------------------------------G    2

    
    U-C*A---------------------------------------------------G    2

    
    U-C*U---------------------------------------------------U    2

    
    U-U*AGAGUAUGCGUGA--------------------------GCUGCUCCUAAU-A    1

    
    GAG*C---------------------------------------------------A    1

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

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

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

    
    C-G*C---------------------------------------------------G    1

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

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

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

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

    
    Omitted sequenced and counts

    
    ---*---------UGUAGUAGGAAGUCGAGAGCCUAUGA------------------    3

    
    --C*G----------------------------------------------------    3

    
    ---*-------AAAGAAGCAUAAAUAGCUAAUCUGUGGGCGGU--------------    2

    
    GAG*C----------------------------------------------------    2

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

    
    --A*-----------------------------------------------------    2

    
    ---*-------AAAGAAGCAGAAAUAGCUAAUCUGUGGGCGGU--------------    1

    
    ---*---------UGUAGUAGGGAGUCGAGAACCUAUGA------------------    1

    
    ---*---------UUUAGUAGGAAGUCGAGAGCCUAUGA------------------    1

    
    ---*---------GUCAACCGGAGUUGCAAACCGGGG--------------------    1

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

    
    A-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 View motif instance in 3D Basepair signature: cWW-L-cWW	85.87	-13.74	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	75.09	-34.15	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	66.17	-34.35	3	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.34	-39.83	3	1	Intercalated cWS
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	56.13	-39.39	2	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	56.13	-43.86	3	1
7	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	55.76	-44.57	2	1	Single bulged G
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	37.92	-42.65	4	1
9	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	29.37	-51.52	3	1	Stack and bulge
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	26.77	-48.66	3	1	Single stack bend

Loop 45 Internal loop

Column numbers: 1155-1158, 1174-1177 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    U--A*U--A   58

    
    G--G*C--C   29

    
    A--A*U--U   23

    
    -A-G*C--G   17

    
    -A-A*G--G   14

    
    -C-A*G--A    7

    
    A--G*C--U    7

    
    U--G*U--A    7

    
    UA-G*C-GA    6

    
    -A-A*G--A    6

    
    A--G*U--U    6

    
    U--G*C--A    6

    
    U--U*U--U    6

    
    GG-A*U-CC    4

    
    U--C*G--G    4

    
    AU-G*U-AU    3

    
    AU-G*U-GU    3

    
    UG-G*C-CA    3

    
    -A-A*U--G    3

    
    G--A*C--C    3

    
    G--A*U--C    3

    
    G--U*G--C    3

    
    U--A*G--A    3

    
    AC-G*C-GU    2

    
    AU-A*U-AU    2

    
    AU-G*U-UU    2

    
    CC-A*U-GG    2

    
    UA-A*U-UA    2

    
    -A-A*A--G    2

    
    C--A*U--G    2

    
    U--A*U--G    2

    
    U--A*U--U    2

    
    U--G*U--G    2

    
    -GAG*CG-A    1

    
    AA-G*U-UU    1

    
    AC-G*U-GU    1

    
    AG-A*U-CU    1

    
    AG-G*C-CU    1

    
    AG-U*C-CU    1

    
    AU-A*U-GU    1

    
    AU-G*C-AU    1

    
    CG-G*C-CG    1

    
    UA-C*G-UA    1

    
    UA-G*C-UA    1

    
    UA-U*A-UG    1

    
    UC-G*C-GA    1

    
    UG-C*G-CA    1

    
    UG-C*G-UA    1

    
    UG-C*G-UG    1

    
    A-UU*C--U    1

    
    AG-U*C--U    1

    
    C--G*C-AA    1

    
    CU-G*C-U-    1

    
    GG-C*--CC    1

    
    U--U*A-UU    1

    
    -A-A*A--A    1

    
    -A-U*A--G    1

    
    -U-A*G--A    1

    
    A--A*C--U    1

    
    A--G*A--U    1

    
    C--G*U--G    1

    
    C--U*U--C    1

    
    G--U*A--C    1

    
    U--A*A--A    1

    
    U--C*G--A    1

    
    U--G*C--U    1

    
    U--G*U--U    1

    
    U--U*A--A    1

    
    U--U*G--A    1

    
    Omitted sequenced and counts

    
    ----*----    9

    
    U---*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_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	81.79	15.14	2	1	Multiple bulged bases
2	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	79.64	-0.54	3	1	Stack and bulge
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	70.36	-2.42	4	2	Multiple bulged bases
4	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	66.79	-5.06	2	1	Single stack bend
5	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	66.43	-4.63	2	1	Single stack bend
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	66.07	-2.40	3	1	Major groove intercalation
7	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	64.64	3.31	2	1	Major groove platform
8	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	56.79	-0.55	3	1	Intercalated cWS
9	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	54.29	-23.68	1	1	Single bulged G
10	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	53.93	-18.86	4	1

Loop 46 Internal loop

Column numbers: 1161-1162, 1166-1171 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GU*U----C  155

    
    CG*G----G   31

    
    GU*U----A   22

    
    GU*A----C    7

    
    UU*U----A    6

    
    GU*A----A    4

    
    UG*G----G    4

    
    AC*ACA--U    3

    
    GC*U----C    3

    
    GG*G----C    3

    
    AG*G----U    2

    
    CU*U----A    2

    
    GU*G----C    2

    
    GU*U----G    2

    
    GU*A----G    1

    
    GU*C----C    1

    
    UA*G----G    1

    
    UU*A----A    1

    
    Omitted sequenced and counts

    
    -U*U----A   14

    
    --*------    9

    
    -U*UA----    7

    
    -A*UACAA-    4

    
    -G*------    3

    
    GU*U-----    2

    
    U-*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 View motif instance in 3D Basepair signature: cWW-L-cWW	70.40	1.54	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	69.20	-3.50	3	2	Multiple bulged bases
3	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	5.20	-14.21	2	1
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	4.40	-14.38	4	1	Intercalated cWS
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	4.40	-17.10	2	1
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	4.40	-18.11	2	1	Major groove intercalation
7	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	4.00	-14.37	4	1	Multiple bulged bases
8	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	4.00	-23.25	2	1	Single bulged G
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	3.20	-23.88	3	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	3.20	-25.94	5	1

Loop 47 Hairpin loop

Column numbers: 1162-1166 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UCG*CU  122

    
    UAG*CU   57

    
    GA-*CG   40

    
    UUG*CU   27

    
    UCG*CA   12

    
    AAC*GU    4

    
    CCG*CU    3

    
    CCG*UA    3

    
    U-G*CU    3

    
    ACG*CG    1

    
    UAG*AU    1

    
    UAG*CG    1

    
    UCG*CC    1

    
    UCG*CG    1

    
    -CG*CA    1

    
    UG-*CA    1

    
    Omitted sequenced and counts

    
    ---*--    9

    
    GGC*A-    2

    
    GGC*G-    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	53.28	2	0	Major groove platform
2	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	98.92	48.12	2	0	Single stack bend
3	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	98.92	38.96	2	0	Single stack bend
4	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	98.92	21.67	4	1
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	98.92	21.34	2	1	Major groove intercalation
6	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	98.92	-0.43	2	0	Major groove platform
7	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	98.56	24.68	3	1	Multiple bulged bases
8	Motif group IL_51454.3 View motif instance in 3D Basepair signature: cWW-cSH-cWW	98.56	14.99	2	0	Minor groove platform
9	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	98.56	14.38	2	1	Stack and bulge
10	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	97.12	-7.82	3	1

Loop 48 Hairpin loop

Column numbers: 1164-1165 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GC  229

    
    CG    5

    
    GU    3

    
    CA    2

    
    GA    1

    
    Omitted sequenced and counts

    
    -C   41

    
    --    9

No Matches Found View All Results for this Loop

Loop 49 Hairpin loop

Column numbers: 1308-1328 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CGAAG---------------G  114

    
    UGAAUAAAA-----------G   31

    
    UGAAG---------------A   31

    
    CGAAA---------------G   30

    
    GGAAG---------------C   18

    
    GGAAA---------------C    9

    
    AGAAG---------------U    7

    
    UGAACAAAA-----------G    5

    
    CUAAAA--------------A    5

    
    UGAAG---------------G    5

    
    GGAAGUC-------------U    3

    
    GGAGGA--------------C    3

    
    AGAAA---------------U    3

    
    UCCCACGUAAGCCA------A    2

    
    GUUAAUAG------------C    2

    
    GUAAC---------------G    2

    
    UGAAA---------------G    2

    
    -UUGUAUAAGCCGUACACUA-    1

    
    ---CCACGUAAGCCAAUACG-    1

    
    CGAACAAAA-----------A    1

    
    UGAACAAAA-----------A    1

    
    UGAAGAAAA-----------G    1

    
    GAUAAAA-------------A    1

    
    AGAAAC--------------A    1

    
    GGAAGC--------------C    1

    
    UGAGAA--------------A    1

    
    UGAGGA--------------A    1

    
    ---AGAAAA------------    1

    
    AAAAC---------------A    1

    
    AGAAA---------------A    1

    
    GGAAG---------------U    1

    
    UGAAA---------------A    1

    
    Omitted sequenced and counts

    
    ---------------------    3

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	80.84	-26.00	1	1
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	80.84	-58.98	2	1
3	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	79.44	-68.37	1	1
4	Motif group HL_87954.2 View motif instance in 3D Basepair signature: cWW-tSW-F	79.44	-92.77	2	1
5	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	79.09	-73.09	2	2
6	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	79.09	-150.82	2	1	Pseudoknot geometry
7	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	78.75	-0.66	0	0	GNRA
8	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	78.75	-51.25	2	2
9	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	78.05	-145.35	3	1
10	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	78.05	-152.46	1	1

Nucleotide numbers Coloring options:

JAR3D Query RF03087-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF03087 ROOL RNA

Input Summary

Jump to results for:

Loop 1 Internal loop

Loop 2 Internal loop

Loop 3 Hairpin loop

Loop 4 Internal loop

Loop 5 Internal loop

Loop 6 Internal loop

Loop 7 Internal loop

Loop 8 Internal loop

Loop 9 4-way junction loop

Loop 10 Internal loop

Loop 11 Internal loop

Loop 12 Internal loop

Loop 13 Internal loop

Loop 14 Internal loop

Loop 15 Internal loop

Loop 16 Hairpin loop

Loop 17 Internal loop

Loop 18 Internal loop

Loop 19 Internal loop

Loop 20 Internal loop

Loop 21 Internal loop

Loop 22 Hairpin loop

Loop 23 Hairpin loop

Loop 24 Internal loop

Loop 25 3-way junction loop

Loop 26 Internal loop

Loop 27 Hairpin loop

Loop 28 Hairpin loop

Loop 29 Internal loop

Loop 30 Internal loop

Loop 31 Hairpin loop

Loop 32 Hairpin loop

Loop 33 Internal loop

Loop 34 Hairpin loop

Loop 35 Internal loop

Loop 36 Internal loop

Loop 37 Hairpin loop

Loop 38 Hairpin loop

Loop 39 Internal loop

Loop 40 Hairpin loop

Loop 41 3-way junction loop

Loop 42 Hairpin loop

Loop 43 Internal loop

Loop 44 Internal loop

Loop 45 Internal loop

Loop 46 Internal loop

Loop 47 Hairpin loop

Loop 48 Hairpin loop

Loop 49 Hairpin loop

JAR3D Query RF03087-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.