RNA 3D Hub

JAR3D Query RF00230-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF00230 T-box leader

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222233333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444555555555555555555555555555555555555555555555555555555555
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456
.....(((........((((..((.....(((.((((((.....((.(....................................((((((................))))))...)))..)..)))))).))......))...))))....)))..........((((((((......(((....................))).....))))).)))(((.............)))........................................................................................................................................................................(((((((.....................................................................................)))))))........(((((.....(...(((...............))).))))))..
>AE017335.3_64645-64865
AUUCGAGCAUU-GA-ACGGA--CAAAGUAGUG-UCUAUU-UCCCUA-UUU--------------------------CAGAGA--GCUGAUGGUU---GGUGUGA--AUCAGU---AUAAAG-AUAUGAC-AUGAAA--UUCA-UCCU-GGAGCA----------UCUUUCAUGAC--GAAUUA-----------------UUACUUGUGAUGAA-AGACGGUAGUUUA----UACCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------ACAAAUAGAGU-GGUGAAGU------------------------------------------------------------------------------------UUCUUCAC---AAC--UAGGGUGGUACCGCGAUC-----AUUU-----AUCGUCCCUACA
>AE017355.1_4358542-4358291
UGAAAGACGAU-GA-UAAGG--AAAAGUAGUA-UAUAC--UAUAAU-CCA--------------------------AAGCGA--GUCAGGGAC----GGUGAGA-GCCUGAU---GAGGCG--GUAUAU-GUGAAG--AACA-CCUU-GGAGUU----------GCUAACCGAAA--UUGAAUCUUGUAU----------UCAAGAGUAGACUU-AGACGGGAAUCCG----GCCUGUUACAAACCGGGAAGUA---------------------------------------------------------------------------------------------------------------------------------------UGUAUUACAUACGA-GUUAAAGU----------------------------------------------------------------------------------UGGUCUUUAUGACAAA--UUGGGUGGUACCGCGAAGU----UUAA--CCUUUCGUCCCUUUA
>AE017355.1_1226056-1226300
AUGAAAUCGUUUAA-GUAAG--AAGAGUACGU-AUAUUG-GAGACG-UUA--------------------------CAGAGA--GCCGGGGAUA---GGUGGGA-GCCCGGU---GCGGUG-CUAUAUA-CGGAA---UGGG-CUUA-CGAGA-----------GGUAUGCUGAA--CAAUUA-----------------UUUUCAGUAGGCA--ACCCGGGUUC-------CGCCGUUACAAGGAUAAGGUAUAUAUUUUG-------------------------------------------------------------------------------------------------------------------------------UACCUGAAUAAAGC-GGGAUGCU-----------------------------------------------------------------------------------UUUGCGUCC---AACA-UGAGGUGGUACCACGGUA-----AAUU----UAUCGUCCUCUAC
>AE017334.2_1340126-1340353
AAGAAAGCGUU-GA-GAGGG--AGGAGUAGUU-GAUUGU-GAAGCC-UCA--------------------------CAGAGA--GUCGGUGGUU---GCUGGAA--ACCGAU----GGUUC--ACGUCG-ACGAAC--AUCG-CCCU-UGAGU-----------GCUAAGCUGAAG-C----------------------GUUUGUCUAGGCUU-AGACGGUAG--------CUCCGUUAUUAGCUAGACUCAU---------------------------------------------------------------------------------------------------------------------------------------UUAUGGGUCACUGA-GGCAAGAG-----------------------------------------------------------------------------------UAUUCUUGC---AAAG-AAGGGUGGUACCGCGAA------AUCU-----UUCGUCCCUUCA
>AE017355.1_1391715-1391963
AUGAAAUCGAU-GA-GCAAG--AAGAGUAUGU-AUAUUU-GAUACG-UU---------------------------CAGAGA--GCUGGGGGAA---GGUGUGA-GCCCGGU---ACGAUA-AAAUAUA-CAGAA---UGGG-CUUG-CGAGA-----------GGUAUGUUGAA--C----------------------AUUGUAGUAGGCA--ACCCGGGUUC-------CGCCGUUAAAAGGAUAGAGUAUCGGAGUUUUUCCU--------------------------------------------------------------------------------------------------------------------------GUACUUGAACAAGU-GGGAUUUA-------------------------------------------------------------------------------------UCAAUCC---AAU--UGAGGUGGUACCACGGUAUUAACAUUACAUAUAUCGUCCUCUAC
>AE017334.2_1382910-1382652
AAAAAUUCAUU-GA-CGAGA--ACGAGUACGU-UAUAGA-ACUGUC-CCC--------------------------CAGAGA--GUUGGCGAUUU--GCUGAAA--GCCAAC---GUUCAG-UGCGUAG-CCGAAA--AUCA-UCUC-CGAGAA----------GUAGAACCGAA--U----------------------GUUGCAGUAAGUUCUUACCGGCUGUC------CCCCGUUACAAGGAACACGUAUCAUGUU---------------------------------------------------------------------------------------------------------------------------------GUACGUUGCAGAGCCGUAUACAUAUAGACUCAUU---------------------------------------------------------------------UCUACAUGUAUA---AAU--UAGGGUGGUAUCGCGGGUAAAU-AUAA-----CUCGUCCCUUUC
>AE017334.2_2727398-2727177
AUAUAUGCGCU-GA-AGAGGA-AACAGUAGUG-CUUAUC-UCACUG-UUA--------------------------AAGAGA--GCUGAUGGUA---GGUGUGA--AUCAGU---ACAAAG--AUAAGC-AUGAAU--UACAGCCUU-GGAGCA----------UCUUUUCCGCC--A----------------------ACUUUUGGAGGGAA-AGACGGUCAAAU-----GAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------AAGAAGAAGAGA-GGUAGACAGG------------------------------------------------------------------------------UAUUUAGUCUAC---AAC--UAGGGUGGUACCGCGAU------AAAU-----AUCGUCCCUACU
>AE017355.1_2768289-2768053
AUGCAUGCGUU-GA-AAGGAAAAGCAGUAGUU-GUUGUU-UCCCUG-UAA--------------------------CAGAGA--GCUGGUGGUC---GGUGUGA--ACCAGU---ACAAAA--ACAAGA-GCGAAU--UACAGUCCU-AGAGCA----------UCUUUUUCGUA--GUAAAGAUAGUAUUUAU------CUUUAUGAAGGGAA-AGACGGUCAGAU-----GAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACAAUGAAGAGA-GGUAGACG--------------------------------------------------------------------------------AAAGAAGUCUAC---AAC--UAGGGUGGUACCGCGAU------AAAU-----AUCGUCCCUACU
>AE017334.2_2761487-2761277
CGAAAAUCGUU-GA-AGGGA--AAUAGUACAU-AUGUCUUCUUGCG-AAA--------------------------GAGAGU--GGAAUUCACCG--GCUGAAA--GAUUCC---UCGUAUAGAAUAUA-UCGAA---CCUA-UCCC-UGAGU------------CUUAAAUGAA---------------------------------AGUUUA-GG-CGUUCGC-------CUGCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UAGGCACCAAGU-GGAUAUCU-----------------------------------------------------------------------------------AUGUAUAUC---AAU--UAAGGUGGUACCGCGGAACA---AUGA-CCGUUUCGUCCUUUUU
>AE017334.2_3964823-3965043
GAAUCGGCGUU-GA-UAGGA--UUUAGUAGUA-UUUCGA-UUUCUGAUUU--------------------------CAGAGA--GCUGGCGGUC---GGUGCGA--ACCAGU---ACAGAA--CGAAUU-AUGAAU--UACC-CCCU-GGAGCU----------UCUUUUGCGAAACG----------------------UAAGAAGUAGUGAA-AGACGGUUAUA------GACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UGUCUAAAGAGU-GGUGAAACG-------------------------------------------------------------------------------AAACUGUUUCAC---AAUU-UAGGGUGGUACCGCGAA-------AUU-----UUCGUCCCUGCA
>AE017334.2_4166233-4166461
AUAUCGGCUUU-GA-AGGAAU-ACCAGUAGCGACUUAUA-UCCCUG-UCU--------------------------CAGAGA--ACUGAUGGUU---GGUGCAA--AUCAGU---ACAUAU--ACAAGC-GUGAAU--UACAAUUCU-GGAGCU----------UCUUUCCCGUA--AUGCUUUUU--------------AUGCAUGAAGAGAA-AGACGGAUCU-------UUCCGUUA------------------------------------------------------------------------------------------------------------------------------------------------------UCUUAAAGUGAGU-GGUAAACAA-------------------------------------------------------------------------------UUACUUGUUUAC---AAA--UAGGGUGGUACCGCGAU------UUUU-----AUCGUCCCUAUC
>AE017334.2_4266551-4266319
AUAAAUGCCUU-GA-AGGGG--AAGAGUAUAA-CAAGAA-ACGUCU-UCA--------------------------GAGAGG--AGAAUCAUUA---GCUGGGA--GAUUCU-CUAGAUAG--UUAUGU-UAGAAG--GUAG-CCCU-GGAGCA----------UCUUUUCUGAAC-GGAAUAG----------------UUCUCAUUAGGAAA-AGACGGAUUU-------GUCCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------UCAAGUUAAGA-GUAUAAGCAAAUUCCUG-----------------------------------------------------------------------GAUUUGUUUGUA---AAU--AAAGGUGGUACCGCGAU------GUCC-----CUCGUCCUUUUU
>AE017334.2_4211066-4210836
AUAUAACCGUU-GA-UAGAG--AAGAGUAAAU-GAGAU--ACACAU-GGA--------------------------AAGAGA--AGAAAUGUCUUAGGCUGAAAACAUUUCU--ACAUGGU--GACUGA-UUGAAU--GACA-CUCU-AGAGGU----------UUCAACUUGAAC-GGCAUAUA---------------CGCUUAGUAGGGAU-GAACGCACAUUU-----AAGCGUUA---------------------------------------------------------------------------------------------------------------------------------------------------------UUAAAAAAGU-GGAAGCAU-----------------------------------------------------------------------------------ACGUGCUUC---AAU--UAGGGUGGCACCACGGGU-----AUAA-UACUCUCGUCCCUACU
>AF188935.1_65116-65336
AUUCGAGCAUU-GA-ACGGA--CAAAGUAGUG-UCUAUU-UCCCUA-UUU--------------------------CAGAGA--GCUGAUGGUU---GGUGUGA--AUCAGU---AUAAAG-AUAUGAC-AUGAAA--UUCA-UCCU-GGAGCA----------UCUUUCAUGAC--GAAUUA-----------------UUACUUGUGAUGAA-AGACGGUAGUUUA----UACCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------ACAAAUAGAGU-GGUGAAGU------------------------------------------------------------------------------------UUCUUCAC---AAC--UAGGGUGGUACCGCGAUC-----AUUU-----AUCGUCCUACAU
>AL591980.1_26617-26392
AUGAAAACAUC-AA-ACAAG--AAUAGUACUU-UUUCAU-CGAUUU-UUA--------------------------AAGAGA--GUUAGCGGUU---GGUGGGA--GCUAAU---AAAUAG-AUGAUUC-AGGAAU--GGGC-CUUG-UGCGU-----------GAUACCUUGAA--------------------------AUCAAGUAGGGGU-GAACGGGUGC-------UCCCGUUAUAGAGCAGCUGCAAAUA------------------------------------------------------------------------------------------------------------------------------------UUGCAGCACGGAGA--UAGGGUU------------------------------------------------------------------------------------UAUCCCUA---AAA--UGAGGUGGCACCGCGA-------UAAC------UCGUCCUCUGA
>AL591980.1_26907-26666
AUGAUAGCAUU-GA-AGAAGA-GUAAGUAGCA-UGAUG---AAAGU-UUU--------------------------UAGAGA--GCUGACGGUU---GGUGAAA--GUCAGU---AGCGGA--CAUGAU-GUGAA---UGGA-CUUC-UGAGCU----------CUG-AUCUGAA--AGGAUU-----------------UUCUUAGUAGGAUA-CAGCGAUUAGGCCU---UAUCGUUACACAAGGCGCCCAUUCGAAAUU-------------------------------------------------------------------------------------------------------------------------------UGGAUGGAUUAAGU-GAACUGUU-----------------------------------------------------------------------------------UUUACAGUU---AAU--CAAGGUGGUACCACGGG-------UCU-----CUCGUCCUUGUC
>AL591980.1_61543-61342
GAAAUAGCGAU-GA-AUUGG--AGUAGUAAUC-UGCAUAUUUUGAU-GUG--------------------------AAGAGA--GCUGACGGUU---GGUGCAA--GUCAGU---CACAAA--AUCUGG-AUGAA---CUUA-CCAU-GGAGCU----------UGGGUG-----------------------------------------UAU-CCCCGUUUU--------CCGCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------AGGAAUUGAUAAGUUGAGUGGUC-------------------------------------------------------------------------------------AAACACU---AAU--GUGGGUGGUACCGCGGGAGA---AGCA--UCUCUCGUCCCAUGG
>AL596169.1_7643-7416
UUAAAACUAGC-GA-CAGAG--AAAAGUAAGA-AAAUC--CAUGCU-AUA--------------------------CAGAGAAUUUAUCCCAUUUG-GCUGAAA--GGAUAAAGAUAGUCA--UAUUUU-CCGAAA-AGACA-CUCU-CGAGGU----------UUCUUGUUGAA---------------------------AACAGUAAACAA-GAACGUAUUC-------AGGCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACUGACUUAAGU-GAGGACUU--------------------------------------------------------------------------------AUUAAUAGUUCU---AAU--UAGGGUGGUACCACGGGUGUAA-AUAA--ACUCUCGUCCCUUGU
>AL596169.1_42600-42374
CUAAAUGCGAU-GA-AGAGG--AAGAGUAGGU-CAUUU---AUUUU-UCU--------------------------AAGAGA--GAAAGCGGUC---GGUGUAA--GCUUUC---AAAAAU---AAUGU-CUGAAG--GUAG-CCUU-GGAGCA----------GUUUUCCUGAA-------------------------AUAAUAGUAGGGAAUAACCGGUAGAUCUCGUCUAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACACAAUGAAGU-GCCUACAUU-------------------------------------------------------------------------------UCUUAUUGUAGG---UAA--AAAGGUGGUACCGCGAAU-----AAUACUCUUUUCGUCCUUUUA
>AL596169.1_50920-50690
AACAAAGUGAU-GA-AAAGG--ACAACCAAUU-UAACG---GAAAA-UUA--------------------------UAGAGA--GGAAGGGCUA---GCUGGGA-ACCUUCU---AUUGGA--ACUUAA-AUUUGG--ACCA-CCUU-GGAACU----------UCUAUUAGGAAC-GUUUU------------------UUACUAGUAAUAAU-AGACGGAUCG-------CUCCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------CAGGCGACAAGAGU-GAAGUAGUUAA-----------------------------------------------------------------------------UUUUAGCUAUUUCUGAAUC-UUGGGUGGAACCACGAGC-----AUAA----ACUCGUCCCUUGA
>AL596169.1_99989-99781
AAAAUGACUAU-GA-ACGGA--CGAAGUAGUU-GCUUAU-UCUUAU-UCC--------------------------UAGAGA--GCUAGUGGUU---GGUGGAA--ACUAGU---AGAGAU--AAGUAG-ACGAAU--UACA-UCCC-GGAGUCAC--------GCUGCACAGGA------------------------------UAAUGGUGC-GGCCGGUGUUG------AGCCGUUA----------------------------------------------------------------------------------------------------------------------------------------------------------UUUUUUGAA-GUAGGAUU------------------------------------------------------------------------------------UUUUCCUA---AAAG-UAGGGUGGUACCACGUUA-----AUUA----AUACGUCCCUUCG
>AL596169.1_133792-133568
ACGAAAACAUG-AA-ACAAG--AAUAGUACUU-UUCAU--CGAUUU-UCA--------------------------AAGAGA--GUUAGCGUUU---GGUGCGA--GCUAAU---AAAUAG--AUGAAAUAGGAAU--GGGC-CUUG-UGCGU-----------GAUACCUUGAA--------------------------CUGAAGUAGGGGU-GAACGGGAGC-------UCCCGUUAUAGAGCAGCUGCAAAA-------------------------------------------------------------------------------------------------------------------------------------AAGCAGCACUGAGA-UAGGGGGA-------------------------------------------------------------------------------------UUCCCCU---AAAA-UGAGGUGGCACCGCGA-------UAAC------UCGUCCUCUGA
>AL596169.1_134084-133841
AUGAUAGCUUU-GA-UGAAGA-GUAAGUAGCA-UGAUG---AAAGU-UUU--------------------------UAGAGA--GCUGACGGUU---GGUGAAA--GUCAGU---AGCGGA--CAUGAU-GUGAA---UGGA-CUUC-UGAGCU----------CUG-GUUUGAA--AAGGAAUU---------------UCCUUAGUAGGAUG-CAGCGAUUAGGCCU---UAUCGUUACACAAGGCGCCCAUUCGGAAUU-------------------------------------------------------------------------------------------------------------------------------UGGAUGGAUUAAGU-GAACUGUU-----------------------------------------------------------------------------------UUUGCAGUU---AAU--CAAGGUGGUACCACGGG-------UCU-----CUCGUCCUUGUC
>AE017180.1_2085740-2085459
AAACAGGCCGU-GA-AGAGG--AGUAGUAGUC-CGACCC-CUUAUC-UUUGUCGGUAGCAGCGAAAAUGCCGACGCCAGAGA--GCCGGUGCUU---GGUGCAA--ACCGGU---AUAAGG--AA--GG-ACGAA---CUCG-CCUC-GGAGCC----------GCCCCCGCGAA--AUCGGUCGUUGUCGAUUGACGAUCCGCAGGUAGUUGG-GGCCGUAUC--------CCGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAAAAUGA-GGUUCUUGUGUCGCCGUUUAUCGGC---------------------------------------------------------------GCAUGCGAGGACGA-AAA--AAGGGUGGUACCGCGAGC-----GCAA--GCCUUCGCCCCUUUA
>BX571857.1_386293-385924
GUAAACACAAU-AA-AGAGG---AAAGUAAAA-CACACC-CUGCUU-AUA--------------------------CAGAGA--GUCUUUAGUA---GCUGAGA--GAAGAU---UUUGAA-AGCGUGU-UUGAAA--AUGG-CCUU-GGAGUG----------UUGAUGCCAAU------------------------------AUGAGGUGU-CUACGGGUUC-------GCCCGUUAUAGCGAUACAGUAUUAACAUUGAUGUUAAAUGGCGUACUGGAUUCUUUACGCACGAUUUUUUGUUAAUAAGUAUGGGAUAGCACAUUACUAUAUCCUUACUUACUGACUUUAAUUGUGAUAAUUGUUCAGUAAGCAUAUUUACUUUUAAUGCGUACUGAAUAA-GGUUAUUUCAG-----------------------------------------------------------------------------CGAUGGAAUAAC---AAAU-AAAGGUGGUACCGCGAAAC----AUAA--GCUUUCGUCCUUUUU
>BX571857.1_1715591-1715290
UUUAAUAUAGG-AU-UUGGG--AAGAGUAAGU-UCAAA---UUAUU-UUA--------------------------AAGAGA--GCAUAUGAUUU--GGUGUGA--GUAUGU---AAAUGA--UUUUUA-CUGAAG--GUAG-CCCACAGAGUA----------UCUUAGCUGAAC-GUGA-------------------UUAAUAGUAGGCUA-AGACGUGUUU-------GAGCGUUAA----------------------------------------------------------------------------------------------------------------------------------------------------UCAUAAUCUAGAGU-GCUUGAAGAGAUGAAGCAUUUCAAAUUUCACGAUGAUAGUAUUGGUAUGAUUAUUCCAAUUAUGUUAAAAGAGUGAAUUUGAUAUUAAACAUCCUUCUUG---AAU--AUAGGUGGUACCACGGA-------AUA-----UCCGUCCUAUUU
>BX571857.1_12485-12696
CAUUGUUCG-------UAGG--ACAAGUAAUA-UAUAGU-GUUCGA-UAU--------------------------CAGAGA--GCUUGUGGUU---AGUGUGA--ACAAGA---AUCAAC--AUAUAU-AUGAA---UCUA-CCUA-----------------CUUAAUUUAAA----------------------------------AGAAC-AAUCGGUGAU-------AACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UUUUAGUGAAGU-GCAAUUUAGGUUUAGUGUAUCUUUA---------------------------------------------------------------UAACUUAAAUUGUU-AAA--UAGGGUGGCAACGCGUA-------GAC-----CACGUCCCUUGU
>BX571857.1_1674695-1674518
AUUCGUAU--------AAAG--AUGAGUAGUU-AAUGA--UUUGUU-UAU--------------------------CAGAGA--UGUACUGGUU---GGUGAAA--AGUACA---ACAAA----CAUUA-GUGAAC--GCUA-CUUU----AUG----------C-----------------------------------ACAACUGUA----------------------------UAG-------------------------------------------------------------------------------------------------------------------------------------------------------UCGAUUUAAAGU-GAUAAAUGUGUUG---------------------------------------------------------------------------AAUUGCAUUUAU---AAC--UAGGGUGGUACCGCGAU------AACG-----UUCGUCCCUUUU
>BX571856.1_12478-12693
UAAGACAUUGU-UC-GUAGG--ACAAGUAAUA-UAUAGU-GUUCGA-UAU--------------------------CAGAGA--GCUUGUGGUU---AGUGUGA--ACAAGA---AUCAAC--AUAUAU-AUGAA---UCUA-CCUA-CUUAUU----------U------------A----------------------AAAGAACAA--------UCGGUGAU-------AACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UUUUAGUGAAGU-GCAAUUUAGGUUUAGUGUAUCUUUA---------------------------------------------------------------UAACUUAAAUUGUU-AAA--UAGGGUGGCAACGCGUA-------GAC-----CACGUCCCUUGU
>AM180355.1_917359-917569
ACAAAUCCAAU-GA-UAGAG---AAAGUAGCA-UAUA----UGGAU-UUA--------------------------CAGCGA--GUUAGGGGUU---GGUGUAA-GCCUAGC---AAUGAA--GUCUAU-GUGAAG--AGAG-CUCU-GGAGGA----------GAUUAUCAGAA-------------------------ACUUUAGUAUGAUA-AUUGGUUUAC-------CCGCCUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAUUGAGA-GGAUAAGU---------------------------------------------------------------------------------ACUUACUUAUC---AAA--AAGAGUGGUAACGCGGAU-----AUAA-----UUCGUCUCUUAG
>AM180355.1_17621-17826
UAAAAAGCUGU-GA-AGGAA--AAUAGUAAAA-AACAG---AUUGU-AUU--------------------------CAGAGA--AUGAGUGGAU---GGUGAAA--ACUCAU---UACAAU---GGUUU-UUGAA---UCUA-CUCU-AGAGCU----------UCUAGUU-------------------------------------AAAGCU-AGACGUUUAC-------CUACGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------UAGGUCUGAGA-GGAUUAUACAU-----------------------------------------------------------------------------UUUAGUAUAGUC---AAU--UAGGGUGGCAACGCGGAUAA---AAGA---UUUUCGUCCCUUUU
>AM180355.1_2066647-2066854
UUAAAUCCUGU-GA-GAAAG---AGAGUAACU-UCUAU---GUGUU-UUA--------------------------UAGAGA--GCUGAGGAU----GGUGGAA-GCUUGGC---AAAUAA--GUAUUA-GUGAAA--AGAA-CUUU-GGAGGA----------UACUAAUUGAA---------------------------UUUAGUAUGUUA-GUAGGUAAUC-------UCGCCUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGAGAAAGAGU-GGAUAAGU----------------------------------------------------------------------------------UUAUCUUAUC---AAU--UAGAGUGGUAACGCGGAU-----AUAU-----UUCGUCUCUUGG
>AM180355.1_1762876-1763128
AUAAAUGCUAU-GA-AGAGA--AGAAGUAGGG-CUAGAU-UUUAUU-UAA--------------------------CAGAGA--GUUCCAGUUU---GGUGAAA--UGGAAU---AAAUUG-AUUUAGU-UUGAA---UACA-UCUC-AGAGCA----------CUAUCUCUGAA--AGAUAA-----------------CAACCAUUAAGAGA-UAUCGGAUUAGU-----ACACGUUAUAGUACACGAGUAUAUGUA----------------------------------------------------------------------------------------------------------------------------------AUUGUACUCUAAGA-GAUUAAUAUCG-----------------------------------------------------------------------------UGAGAUAUUGAUG--AAC--UAAGGUGGUAACACGUAA-----GCAA-UGCUUUCGUCCUUUUA
>AM180355.1_1488475-1488713
ACAAAUACAGU-GA-UAAGG--AAUAGUAAAA-UAUUU--GAUGUC-UUA--------------------------CAGAGA--GAGGGAAAU----GCUGGAA--GCCCUU---AGAAUA--UGAUAU-UUGAA---GCAG-CCUU-UUAGUA----------GCAAUCUUGAA--CAAUUUAUCUUUUAUAAAGAAG-AUUUAAGUAGAGAU-UGACGGUAG--------UUACGUUAUAGCUA-----------------------------------------------------------------------------------------------------------------------------------------------AGGUUUUCCGAAGA-UAUCAUAC----------------------------------------------------------------------------------UUUGUAUGAU---AAU--UAGGGUGGUACCGCGAU------UGUC-----CUCGCCCCUAUA
>AM180355.1_73005-73213
AAAUUAGCUAU-GAUAAAGA--AAUAGUAAAA-UGAUG--AAAUCU-UCA--------------------------CAGAGA--GAAAACGGU----GGUGAGA--GUUUUC---AAGAGG--AAGUCU-UUGAA---CCUG-UCUU-UUAGCU----------UAAAGGUAUAA---------------------------------AAAUCU-UUACGGUAGG-------AACCGUUA------------------------------------------------------------------------------------------------------------------------------------------------------UAUUCCCAAAAGA-GAGCUAUU-----------------------------------------------------------------------------------CAUAUAGCU---AAC--UAGAGUGGUACCGCGGAA-----AUUAAACCUUUCGUCUCUAUA
>AM180355.1_1152611-1152857
AAAAAAGUGAU-GA-AUAGA--AGUAGUAAGA-ACAAU---GAAAC-UUU--------------------------CAGAGA--GCUAAAGGAU---GGUGUGA--UUUAGU---AGUUGA---UAGUU-CUGAA---CUUG-UCUA-GGAGCU----------GUUUUCUAAGA-------------------------UUUAAAUCUUAGAAUAAUCGGAGUAAUU----CCACGUUAUAGGAAAUAUAGUCAUUAUAAUUAUUGUAUU----------------------------------------------------------------------------------------------------------------------GGCUAUUACUAAGG-GAGCUUUU-----------------------------------------------------------------------------------UAGAAAGCU---AAA--UAGAGUGGUACCGCGAGC-----AAAA----CCUCGUCUCUAAU
>AM180355.1_1830935-1831175
AAAAAGGCGAU-GA-AUAGG--AAGAGUAAAU-CUAAUU-CGAUUA-CCA--------------------------GAGAGA--AGAGUCCGUUG--GCUGGAA--GACUUU---UUAAAUUAGAGGGA-UUGAAA--ACUA-CCUA-GGAGCU----------ACU-UUCUGAA--GUCAUCUGCAUUAGUAG------AUUUUAGUAAGAAU-AGUCGUUAG--------CUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUGUAAAGU-GAGUUUUCAUGA----------------------------------------------------------------------------CAUAUGAAAACU---AAA--UUAGGUGGAACCGCGGGA-----AUAA-UACUCUCGUCCUUAUG
>AM180355.1_849427-849661
GUAAAUGCAAU-GA-AAGAG--GAAAGUAUUU-UGAUUA-AACUUA-GUA--------------------------AAGAGAU-AAACACCUAG---GCUGGGA--GUGUUU--UCUAAGA--GGUCAU-GAGAAG--UUCC-CUCU-GGAGUA----------ACAGAGCUGAAA-U----------------------UUUACAGUAGGCUU-UGACGUCAAAA------ACGCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------AGUUUGUUAGAGGU-GGUUUGAUGAUUUUU-------------------------------------------------------------------------AAAUUGUUAAAC---UAC--UAGGGUGGUACCGCGAAACU---AUAG--CCUUUCGUCCCUAGA
>AM180355.1_1831241-1831476
AUAAAAGCGAU-GA-AUAGG--AAGAGUAAAU-UUAAU---UCGAC-UAU--------------------------CAGAGA--GGAAAGUUCACAGGCUGAAAGACUUUCU--AAGUUUG---AGAAA-UUGAAA--ACUA-CCUA-GGAGC-----------UGUGGUCUGAA--GUUACUUUAAAAA----------GUUUUAGUAAGACU-AACCGUUAA--------CUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUGUAAAGU-GGAUUUUAUCAAUA--------------------------------------------------------------------------AAUGAUAAAAUC---AAA--UUGGGUGGAACCGCGAGU-----AUGG----ACUCGUCCCUUUA
>AM180355.1_2451314-2451545
UGAAAGGCAUU-GA-UUAGG--AAGAGUAAAU-CUGAA---UCGAU-UAC--------------------------CAGAGAA-GGAAACUACUA--GCUGAAA-UGUUUCC-CUAAUUAG---AAGGA-UUGAAA--ACUA-CCUA-GGAGCU----------UCUAU-CCGAA--GUUAUCUUAAUG-----------AUUUUAGUAGGAAU-AGACGUUUUUAUUAC--UUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUAUCAAGU-GGAUUUUU-------------------------------------------------------------------------------------UAAAAUC---AAU--UUGGGUGGAACCGCGGGA-----AACA-GAUUCUCGUCCCUUUU
>AM180355.1_683160-683398
AUCAUAGUGUU-GA-AGAGG--AAGAGUAGAG-UAGAA---ACCAU-UCU--------------------------CAGAGA--AUUUGGGUCUAUGGCUGAGAGCCCAUGU---AAUAGG---UCUAU-UUGAAA--ACUA-CCUU-GGAGC-----------UGAGCUUAUUA--GCAGUAUUUGUAUUUAUACU---AUACGUGAAAGUGC-UC-GGGUGAC-------GACC-UUA-----------------------------------------------------------------------------------------------------------------------------------------------------UAGUCAUCAAGAGG-GUUGUAUAU-------------------------------------------------------------------------------ACUUGUAUACGCC--AAC--UUGGGUGGAACCGCGAA------UUAA----UAUCGUCCCAAAC
>CP000232.1_18501-18733
GCCAAAGCGAU-GA-AGGGG-----AGUGCCG-GCGGCCCACUCCG-GUAGGC-----------------------GAGAGA--GCUGGUGGUU---GGUGGGA--ACCAGC---CCGGAG--GCUGUC-GGGA----GGCA-CCCC-UGAGU-----------ACCCGGCGAGA--AAUCCUGUU--------------AAGGAAUUAAGCCG-GGGCGGUCAU-------GUCCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------CGCAUGUCGAGG-GGGUCAGGUUUGGCAU------------------------------------------------------------------------AAUAACCUGGCC---AAG--CAGGGUGGCACCGCGGGU-----AAAA---CUCUCGUCCCUUUU
>CP000918.1_1745988-1745765
UCAACAAA--------UCAG--AAAAGUAACU-AUUU----UUGAU-CUU--------------------------CAGGGA--GCCUGUGGUG---AUUGUGA--AUAGGU---GGUUGG---AAGUA-GUGAAA-GUGGG-CUGA----UUUUGAAAA----UGAAUUUGAAA-----------------------------CAAUGAAAAU-UC-GGUGCGC-------ACACCUUACAGUGCAGCUUGUUGUU------------------------------------------------------------------------------------------------------------------------------------AAACAAGGCAGAGAUGUAAAGGG--------------------------------------------------------------------------------AUAGUCCCUUUAU--AAU--UGAGGUGGCACCGCGUU-------ACC-----AACGCCCUCACA
>AE005176.1_68627-68394
AAAUUUAA-AA-CA-ACAAG---AAAGUAACU-UUGAUUUUGAAAU-CUU--------------------------UAGGAA--GUUGGUGGU----UGUGCAA--ACCAAC---GUUUUC--AGCAAA-GUGAA---UGGG-CUUG-UGAUUAACUAAUAAAUUUGAUUUAAAA----------------------------AAAUAAAGAAU-CA-CGGCCGC-------UUCCGUUACAGAGCAACUUGUUUU-------------------------------------------------------------------------------------------------------------------------------------UUGACAAGUUCUAA-GAAAAUCA-----------------------------------------------------------------------------------UUUGAUUUU---AAAUUUACGGUGGCACCGCGCU-------CAA-----AGCGCCCGUAGG
>AE005176.1_1228400-1228613
ACGAGAGA--------UGAA--AAGAGUAGUC-UUAGG---UAUCA-GUU--------------------------GAGAGA--GCCUU--GUU---GCUGAGA--AAAGGU---CUGAUA---UUGGG-AUGAAC--CACA-CUCA----UCGCUAUCUU---ACUCACAUUAU---------------------------------UAUGUG-AG-CGUUAG--------CUGCGUUAAUGCUAAGUUG------------------------------------------------------------------------------------------------------------------------------------------UUAUAACUUACCGA-GGUCACUUUUG-----------------------------------------------------------------------------UGAAAAAGUGAU---AAAU-UAAGGUGGAACCACGAU-------UAA-----ACCGUCCUUUAA
>CP001033.1_1194722-1194505
UUAACCAU--------UCAG--AAAAGUAAUC-AUAC----AAACU-UUU--------------------------UAGAGA--GUCUGUGGUA---GCUGAAA--ACAGAU---AAGUGG---CAAUG-AUGAAAAUUGGG-CUGA----AUG----------CUA-UUUAGAA--U----------------------UUGAAAUUAUAAAAAUUCGGUAAGC-------ACACCUUACAGUGCAUCUCGUUA--------------------------------------------------------------------------------------------------------------------------------------UUGCGAGACUGAGC-GAUAGGGA----------------------------------------------------------------------------------AAUUCCCUAU---AAU--UGAGGUGGUACCGCGC-------AUCG------ACGUCCUCACA
>AP008230.1_2186652-2186888
CGAACAACGAU-GA-AAGAG-----AGCAUCU-GUUAGC-CCAGAC-CUU--------------------------CAGGGA--ACUAAAGUCGGAGACUGAAAGCUUUAGU---GGUUGCUGGUAACA-GAGA----UUCA-CUCU-GGAGUU----------GCAUUCCUGAA-------------------------CUCAAAGUAGGGAA-UGCCGGCCGC-------UUCCGUUAAGAGCCUUGAUUCAUUCC-----------------------------------------------------------------------------------------------------------------------------------AGGAUCAUGUGAGU-GGCUGUUG----------------------------------------------------------------------------------UACAUACAGC---AAA--AAGGGUGGUACCGCGUGA-----CUUA----ACUCGUCCCUUAU
>AE005176.1_2251117-2250951
AACAAGUU--------GACG--AGGAGUAAUA-AAGC----AAGAC-UUA--------------------------UAGAGA--GAACACGGUU---GGUGAAA--GUGUUC---AGUCAA---ACUUU-AUGAAG--GUUG-CGUC----AUU----------U--------------------------------------CAAGAA-----------------------AA---UUAU----------------------------------------------------------------------------------------------------------------------------------------------------GGCAUAAAAUGAGU-GUCGUCAA-------------------------------------------------------------------------------------UUGACGA---AAA--UCAGGUGGUACCGUGC-------GGAA------GCACCCUGGAG

Rfam family RF00230 maps to these 12 chains: 4LCK|1|C, 4LCK|1|F, 4TZP|1|C, 4TZP|1|F, 4TZV|1|C, 4TZW|1|C, 4TZZ|1|C, 4TZZ|1|F, 4TZZ|1|I, 4TZZ|1|L, 6PMO|1|A, 6POM|1|A 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: 8-17, 147-152
  • Loop 2IL Column numbers: 20-23, 140-144
  • Loop 3IL Column numbers: 24-30, 132-139
  • Loop 4IL Column numbers: 31-32, 129-131
  • Loop 5IL Column numbers: 32-34, 128-129
  • Loop 6IL Column numbers: 38-39, 121-124
  • Loop 7IL Column numbers: 39-45, 118-121
  • Loop 8IL Column numbers: 46-48, 116-117
  • Loop 9IL Column numbers: 48-85, 112-116
  • Loop 10HL Column numbers: 90-107
  • Loop 11IL Column numbers: 167-168, 214-216
  • Loop 12IL Column numbers: 172-179, 204-210
  • Loop 13HL Column numbers: 181-202
  • Loop 14HL Column numbers: 221-235
  • Loop 15HL Column numbers: 412-498
  • Loop 16IL Column numbers: 517-523, 549-550
  • Loop 17IL Column numbers: 523-527, 547-549
  • Loop 18HL Column numbers: 529-545

Loop 1 Internal loop

Column numbers: 8-17, 147-152 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CAUU-GA-AC*U-GGAG    2

    
    CGAU-GA-AU*A-GGAG    2

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

    
    CGUUUAA-GU*A-CGAG    1

    
    CUAU-GAUAA*U-UUAG    1

    
    UAGG-AU-UU*ACAGAG    1

    
    CAAU-AA-AG*U-GGAG    1

    
    CAAU-GA-AA*U-GGAG    1

    
    CAAU-GA-UA*U-GGAG    1

    
    CAGU-GA-UA*U-UUAG    1

    
    CAUC-AA-AC*G-UGCG    1

    
    CAUG-AA-AC*G-UGCG    1

    
    CAUU-GA-AG*C-UGAG    1

    
    CAUU-GA-CG*C-CGAG    1

    
    CAUU-GA-UU*A-GGAG    1

    
    CCGU-GA-AG*C-GGAG    1

    
    CCUU-GA-AG*U-GGAG    1

    
    CGAU-GA-AA*U-GGAG    1

    
    CGAU-GA-AG*C-UGAG    1

    
    CGAU-GA-AG*U-GGAG    1

    
    CGAU-GA-AU*U-GGAG    1

    
    CGAU-GA-GC*G-CGAG    1

    
    CGAU-GA-UA*U-GGAG    1

    
    CGCU-GA-AG*U-GGAG    1

    
    CGUU-GA-AA*U-AGAG    1

    
    CGUU-GA-AG*C-UGAG    1

    
    CGUU-GA-GA*U-UGAG    1

    
    CGUU-GA-UA*U-AGAG    1

    
    CGUU-GA-UA*U-GGAG    1

    
    CUAU-GA-AC*C-GGAG    1

    
    CUAU-GA-AG*C-AGAG    1

    
    CUGU-GA-AG*U-AGAG    1

    
    CUGU-GA-GA*U-GGAG    1

    
    CUUU-GA-AG*U-GGAG    1

    
    CUUU-GA-UG*C-UGAG    1

    
    UAGC-GA-CA*U-CGAG    1

    
    UGAU-GA-AA*U-GGAA    1

    
    UGAU-GA-AU*A-GGAG    1

    
    UGUU-GA-AG*U-GGAG    1

    
    UUGU-UC-GU*A-CUUA    1

    
    A-AA-CA-AC*G-UGAU    1

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

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

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

    
    Omitted sequenced and counts

    
    CG-------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_69229.3

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

78.72 9.48 3 2

Kink-turn

2

Motif group IL_70923.9

Basepair signature:
cWW-tSS-tSH-L-tHS-tHS-cWW

72.34 -0.86 3 1

Kink-turn

3

Motif group IL_01488.3

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

72.34 -9.29 4 2

Kink-turn

4

Motif group IL_94910.1

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

46.81 -40.11 5 3

Kink-turn

5

Motif group IL_74051.1

Basepair signature:
cWW-tSS-tSH-L-tHS-cWW-L

25.53 -47.15 5 3

Kink-turn

6

Motif group IL_77870.1

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

23.40 -37.79 6 4

7

Motif group IL_78472.1

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

17.02 -44.51 7 5

8

Motif group IL_77045.1

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

12.77 -58.09 7 5

Kink-turn

9

Motif group IL_64900.1

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

12.77 -82.97 6 5

Kink-turn

10

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

10.64 -748.20 8 7

Loop 2 Internal loop

Column numbers: 20-23, 140-144 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    G--A*CUA-C    7

    
    G--A*GGG-C    4

    
    G--A*ACA-C    3

    
    G--A*UAG-C    3

    
    GA-G*GGA-C    2

    
    A--C*UCA-U    2

    
    G--A*GGC-C    2

    
    G--A*UCG-C    2

    
    AAAA*ACAGU    1

    
    AU-A*ACAAU    1

    
    GA-A*ACAGC    1

    
    A--A*ACA-C    1

    
    A--A*ACA-U    1

    
    A--A*CUA-C    1

    
    A--A*CUA-U    1

    
    A--A*CUG-U    1

    
    A--A*UCA-U    1

    
    A--A*UUG-U    1

    
    A--C*ACA-U    1

    
    A--U*ACC-C    1

    
    G--A*CAG-C    1

    
    G--A*CCA-C    1

    
    G--A*UUA-C    1

    
    G--A*UUG-C    1

    
    G--G*UCC-C    1

    
    Omitted sequenced and counts

    
    G---*GAA-C    1

    
    G---*GAG-C    1

    
    G---*GCA-C    1

    
    G---*GGG-C    1

    
    G---*UCA-C    1

    
    G---*UGG-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_82107.4

Basepair signature:
cWW-cWW

88.10 37.31 3 0

Multiple bulged bases

2

Motif group IL_15052.4

Basepair signature:
cWW-L-cWW-L

78.57 17.77 2 1

Minor groove platform

3

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

76.19 -4.16 3 1

4

Motif group IL_42626.2

Basepair signature:
cWW-cWW

71.43 1.44 4 1

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

69.05 8.40 2 1

Major groove intercalation

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

66.67 -2.49 4 1

Intercalated cWS

7

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

64.29 7.48 4 1

8

Motif group IL_95583.2

Basepair signature:
cWW-L-cWW

64.29 -2.44 3 1

Minor groove platform, major groove intercalation

9

Motif group IL_76709.2

Basepair signature:
cWW-L-cWW-L

64.29 -6.93 3 1

10

Motif group IL_73355.1

Basepair signature:
cWW-L-cWW-L

64.29 -8.85 4 1

Loop 3 Internal loop

Column numbers: 24-30, 132-139 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AGAGUAA*UGAAA--A    4

    
    AAAGUAG*UGAAA--U    2

    
    AAAGUAG*UGAAG--A    2

    
    AUAGUAC*GGAAU--G    2

    
    CAAGUAA*UGAA---U    2

    
    GUAGUAA*UGAA---C    2

    
    UAAGUAG*UGAA---U    2

    
    AAAGUAA*UGAAAAUU    1

    
    AAAGUAA*CGAAA-AG    1

    
    AAAGUAA*UGAAA-GU    1

    
    AAAGUAA*UGAAA--A    1

    
    AAAGUAU*AGAAG--U    1

    
    ACAGUAG*UGAAU--U    1

    
    AGAGUAA*UGAAG--G    1

    
    AGAGUAA*UGAAU--G    1

    
    AGAGUAG*UGAAA--A    1

    
    AGAGUAG*UGAAC--C    1

    
    AGAGUAG*UGAAG--G    1

    
    AGAGUAU*AGAAG--G    1

    
    CAACCAA*UUUGG--A    1

    
    CCAGUAG*UGAAU--U    1

    
    CGAGUAC*CGAAA--A    1

    
    GAAGUAG*CGAAU--U    1

    
    GCAGUAG*CGAAU--U    1

    
    GGAGUAA*UGAAG--G    1

    
    GGAGUAG*CGAAC--A    1

    
    UGAGUAG*UGAAC--G    1

    
    UUAGUAG*UGAAU--U    1

    
    AAAGUAA*UGAA---U    1

    
    AGAGUAC*GGAA---U    1

    
    AGAGUAU*AGAA---U    1

    
    AUAGUAA*UGAA---C    1

    
    AUAGUAA*UGAA---G    1

    
    AUAGUAA*UGAA---U    1

    
    AUAGUAC*CGAA---C    1

    
    GAAGUAG*UGAA---U    1

    
    GUAGUAG*CGAA---C    1

    
    --AGCAU*AGA----U    1

    
    --AGUGC*GGA----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_61286.1

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

75.00 5.00 6 2

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

2

Motif group IL_26307.2

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

60.42 20.00 3 1

7x6 Sarcin-Ricin; G-bulge

3

Motif group IL_24254.1

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

56.25 6.65 5 2

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

4

Motif group IL_88269.4

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

45.83 -5.40 5 2

6x5 Sarcin-Ricin; G-bulge

5

Motif group IL_16458.4

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

37.50 -11.07 5 3

Sarcin-Ricin target in LSU H95; G-bulge

6

Motif group IL_29198.2

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

35.42 -27.43 5 3

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

7

Motif group IL_41756.4

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

27.08 -19.14 5 3

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

8

Motif group IL_04346.10

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

27.08 -37.75 4 3

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_62654.1

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

25.00 -39.70 6 3

tSH-tHH-tHS

10

Motif group IL_33886.1

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

25.00 -40.74 7 4

Kink-turn with embedded cWW pair

Loop 4 Internal loop

Column numbers: 31-32, 129-131 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AA*U-U    5

    
    AU*A-U    5

    
    CU*A-G    4

    
    UA*U-A    4

    
    UC*G-A    4

    
    CA*U-G    3

    
    GU*A-C    3

    
    UG*C-A    3

    
    CG*C-G    2

    
    GA*U-C    2

    
    UU*A-G    2

    
    UU*G-A    2

    
    UU*AUA    1

    
    AG*U-U    1

    
    GG*U-U    1

    
    GU*G-C    1

    
    GU*U-C    1

    
    UA*U-G    1

    
    UU*A-A    1

    
    UU*C-A    1

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

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 18.02 2 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

95.83 25.59 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

91.67 20.04 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

89.58 18.01 3 1

Intercalated cWS

5

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

85.42 4.51 1 1

Single bulged G

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

79.17 16.90 3.5 1

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

79.17 10.63 3 1

Major groove intercalation

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

79.17 4.98 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

77.08 10.29 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

77.08 6.85 2 1

Single stack bend

Loop 5 Internal loop

Column numbers: 32-34, 128-129 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    A-U*AU    7

    
    U-A*UA    5

    
    A-A*UU    4

    
    U-U*AA    4

    
    A-C*GU    2

    
    C-U*GG    2

    
    G-U*AC    2

    
    U-C*GA    2

    
    U-G*GA    2

    
    U-U*UA    2

    
    GAC*GC    1

    
    A-U*CU    1

    
    A-U*UU    1

    
    C-A*UG    1

    
    C-C*GG    1

    
    G-C*GC    1

    
    G-C*GU    1

    
    G-G*UC    1

    
    G-U*AU    1

    
    U-C*GU    1

    
    U-G*AG    1

    
    U-G*CA    1

    
    U-G*CG    1

    
    U-U*AG    1

    
    U-U*AU    1

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

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

89.58 14.49 2 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

81.25 19.93 3 2

Multiple bulged bases

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

79.17 15.01 3 1

Multiple bulged bases

4

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

72.92 -1.00 1 1

Single bulged G

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

70.83 12.05 3.5 1

Intercalated cWS

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

70.83 11.25 4 1

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

68.75 6.12 3 1

Major groove intercalation

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

68.75 1.15 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

64.58 5.30 2 1

Single stack bend

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

64.58 0.76 5 1

Loop 6 Internal loop

Column numbers: 38-39, 121-124 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GU*C--A    3

    
    AU*G-AU    2

    
    UU*G-AU    2

    
    CU*UAGA    1

    
    GC*CUGG    1

    
    UU*UUAG    1

    
    CC*A-AG    1

    
    GA*G-UG    1

    
    UG*G-CU    1

    
    UU*A-AA    1

    
    AA*G--U    1

    
    AU*U--A    1

    
    CC*G--A    1

    
    CC*G--G    1

    
    GA*A--C    1

    
    UA*A--A    1

    
    UA*A--G    1

    
    UA*U--A    1

    
    UC*G--A    1

    
    UU*A--A    1

    
    UU*C--A    1

    
    Omitted sequenced and counts

    
    G-*A--C    2

    
    A-*G---    2

    
    --*G---    2

    
    A-*A--U    1

    
    C-*A--U    1

    
    C-*G--G    1

    
    G-*A--A    1

    
    G-*G--A    1

    
    U-*A--G    1

    
    U-*A--U    1

    
    U-*G--A    1

    
    U-*U--G    1

    
    --*A--G    1

    
    G-*A---    1

    
    G-*U---    1

    
    U-*A---    1

    
    U-*G---    1

    
    U-*U---    1

    
    --*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_07039.3

Basepair signature:
cWW-L-cWW

72.00 13.93 3 1

Major groove platform

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

48.00 3.00 4 1

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

48.00 2.74 3 1

Intercalated cWS

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

48.00 2.10 3 1

Major groove intercalation

5

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

48.00 -4.36 2 1

Single stack bend

6

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

48.00 -4.36 2 1

Single stack bend

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

44.00 -4.08 4 1

8

Motif group IL_42771.1

Basepair signature:
cWW-cWW

40.00 1.05 3 1

Multiple bulged bases

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

40.00 -15.25 3 1

Stack and bulge

10

Motif group IL_84476.1

Basepair signature:
cWW-cWW

36.00 -17.37 3 2

Multiple bulged bases

Loop 7 Internal loop

Column numbers: 39-45, 118-121 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U-GUUCG*CAAC    2

    
    U-UCCCU*AAAG    2

    
    ---AAAG*CGGA    2

    
    AUUUUGA*CAAA    1

    
    CCACUCC*GGAG    1

    
    UUCUUGC*GUAU    1

    
    UUUGAAA*UUUC    1

    
    A-AACUU*AAGA    1

    
    A-ACGUC*AUAG    1

    
    A-ACUGU*UCAG    1

    
    A-UCCCU*AUAU    1

    
    A-UUUCU*AGAA    1

    
    C-CCAGA*UUGC    1

    
    C-CUGCU*UGAA    1

    
    C-CUUAU*AAGG    1

    
    C-UCACU*AAAG    1

    
    G-GAGAC*GGUG    1

    
    U-CGAUU*AAAU    1

    
    U-CGAUU*AUAG    1

    
    U-GAAGC*GUUC    1

    
    U-GAUAC*GAUA    1

    
    U-UCCCU*AAAA    1

    
    U-UCUUA*AGAU    1

    
    U-UUUAU*AUUG    1

    
    --AAAUC*GAGG    1

    
    --ACACA*UGGU    1

    
    --CAUGC*GUCA    1

    
    --CGAUU*AUAG    1

    
    --GAUGU*AAUA    1

    
    --UAUAA*GGCG    1

    
    ---AAAC*GUGG    1

    
    ---AAGA*UCAA    1

    
    ---ACCA*UAGG    1

    
    ---AUUG*CAAU    1

    
    ---AUUU*AAAU    1

    
    ---GAAA*UGGA    1

    
    ---GAAA*UUGA    1

    
    ---GUGU*AUAA    1

    
    ---UAUC*GAUA    1

    
    ---UCGA*UUAG    1

    
    ---UCGA*UUUG    1

    
    ---UGGA*UGAA    1

    
    ---UUAU*AUGA    1

    
    ---UUGA*UUGG    1

    
    --UUUGU*AAA-    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_11344.2

Basepair signature:
cWW-cSS-L-cWW

18.75 -49.20 6 4

180 degree turn

2

Motif group IL_05192.4

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

16.67 -39.73 6 3.5

3

Motif group IL_69145.3

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

8.33 -39.40 6 3

Pseudoknot

4

Motif group IL_90346.1

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

8.33 -43.20 6.5 4

5

Motif group IL_70096.1

Basepair signature:
cWW-L-cWW-cWW

8.33 -54.60 7 4

Kink-turn related

6

Motif group IL_75294.1

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

8.33 -59.95 6 4

7

Motif group IL_99498.1

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

8.33 -61.05 7 5

8

Motif group IL_31558.1

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

8.33 -96.57 7 4

9

Motif group IL_34737.1

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

6.25 -52.78 6 4

10

Motif group IL_33141.1

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

6.25 -55.32 8 4.5

Loop 8 Internal loop

Column numbers: 46-48, 116-117 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U-U*AA   11

    
    A-U*AU    5

    
    C-U*AG    4

    
    G-U*AC    4

    
    U-U*AG    4

    
    A-G*CU    2

    
    U-A*UA    2

    
    U-G*CA    2

    
    GAU*AC    1

    
    A-C*UU    1

    
    C-C*GG    1

    
    C-C*GU    1

    
    C-U*AU    1

    
    G-A*UC    1

    
    G-G*CC    1

    
    G-U*GC    1

    
    U-A*UU    1

    
    U-C*GA    1

    
    U-C*GG    1

    
    U-C*GU    1

    
    U-U*AC    1

    
    Omitted sequenced and counts

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

Motif group IL_84476.1

Basepair signature:
cWW-cWW

97.87 25.11 3 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

97.87 20.18 2 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

87.23 19.42 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

85.11 16.90 4 1

Intercalated cWS

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

85.11 12.35 3 1

Major groove intercalation

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

85.11 6.42 4 1

7

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

85.11 3.27 1 1

Single bulged G

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

76.60 16.19 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

74.47 10.93 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

74.47 6.30 2 1

Single stack bend

Loop 9 Internal loop

Column numbers: 48-85, 112-116 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UUU--------------------------CAGAGA--G*U---A    4

    
    UUA--------------------------AAGAGA--G*U---A    3

    
    UUU--------------------------UAGAGA--G*U---A    3

    
    UAA--------------------------CAGAGA--G*U---A    2

    
    UAU--------------------------CAGAGA--G*A---A    2

    
    UCU--------------------------CAGAGA--A*U---A    2

    
    UUA--------------------------UAGAGA--G*C---A    2

    
    UUUGUCGGUAGCAGCGAAAAUGCCGACGCCAGAGA--G*U---A    1

    
    AUA--------------------------CAGAGAAUU*AAGAU    1

    
    GUAGGC-----------------------GAGAGA--G*C---C    1

    
    UAC--------------------------CAGAGAA-G*C-CUA    1

    
    GUA--------------------------AAGAGAU-A*U--UC    1

    
    UCA--------------------------GAGAGG--A*U-CUA    1

    
    GGA--------------------------AAGAGA--A*U--AC    1

    
    UAU--------------------------CAGAGA--G*U--AA    1

    
    AAA--------------------------GAGAGU--G*C---U    1

    
    AUA--------------------------CAGAGA--G*U---U    1

    
    AUU--------------------------CAGAGA--A*U---U    1

    
    CCA--------------------------AAGCGA--G*U---G    1

    
    CCA--------------------------GAGAGA--A*U---U    1

    
    CCC--------------------------CAGAGA--G*C---G    1

    
    CUU--------------------------CAGGGA--A*U---G    1

    
    CUU--------------------------CAGGGA--G*U---G    1

    
    CUU--------------------------UAGGAA--G*C---G    1

    
    GUG--------------------------AAGAGA--G*U---C    1

    
    GUU--------------------------GAGAGA--G*U---C    1

    
    UAU--------------------------CAGAGA--U*A---A    1

    
    UCA--------------------------AAGAGA--G*U---A    1

    
    UCA--------------------------CAGAGA--G*C---A    1

    
    UCC--------------------------UAGAGA--G*U---A    1

    
    UCU--------------------------AAGAGA--G*C---A    1

    
    UUA--------------------------CAGAGA--G*U---A    1

    
    UUA--------------------------CAGAGA--G*U---G    1

    
    UUA--------------------------CAGCGA--G*C---A    1

    
    UUA--------------------------UAGAGA--G*U---A    1

    
    UU---------------------------CAGAGA--G*U---A    1

    
    Omitted sequenced and counts

    
    UCA--------------------------CAGAGA--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_64048.1

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

63.83 -121.30 6 4

2

Motif group IL_15218.1

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

2.13 -168.61 6 4

3

Motif group IL_58960.1

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

2.13 -187.27 5 3

Loop 10 Hairpin loop

Column numbers: 90-107 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CGGUU---GGUGAAA--G    3

    
    UGGUU---AGUGUGA--A    2

    
    UGGUU---GGUGUGA--A    2

    
    AGUCGGAGACUGAAAGCU    1

    
    GGUCUAUGGCUGAGAGCC    1

    
    GUUCACAGGCUGAAAGAC    1

    
    UGUCUUAGGCUGAAAACA    1

    
    CCAUUUG-GCUGAAA--G    1

    
    CUACUA--GCUGAAA-UG    1

    
    CCGUUG--GCUGGAA--G    1

    
    CGAUUU--GCUGAAA--G    1

    
    GGAUA---GGUGGGA-GC    1

    
    GGCUA---GCUGGGA-AC    1

    
    GGGAA---GGUGUGA-GC    1

    
    GGGUU---GGUGUAA-GC    1

    
    UCACCG--GCUGAAA--G    1

    
    UGAUUU--GGUGUGA--G    1

    
    AGGAU---GGUGUGA--U    1

    
    AGUUU---GGUGAAA--U    1

    
    CAUUA---GCUGGGA--G    1

    
    CCUAG---GCUGGGA--G    1

    
    CGGUC---GGUGCGA--A    1

    
    CGGUC---GGUGUAA--G    1

    
    CGGUU---GGUGCAA--G    1

    
    CGGUU---GGUGGGA--G    1

    
    CGUUU---GGUGCGA--G    1

    
    GGAC----GGUGAGA-GC    1

    
    GGAU----GGUGGAA-GC    1

    
    UAGUA---GCUGAGA--G    1

    
    UGCUU---GGUGCAA--A    1

    
    UGGAU---GGUGAAA--A    1

    
    UGGUA---GCUGAAA--A    1

    
    UGGUA---GGUGUGA--A    1

    
    UGGUC---GGUGUGA--A    1

    
    UGGUG---AUUGUGA--A    1

    
    UGGUU---GCUGGAA--A    1

    
    UGGUU---GGUGAAA--A    1

    
    UGGUU---GGUGCAA--A    1

    
    UGGUU---GGUGGAA--A    1

    
    UGGUU---GGUGGGA--A    1

    
    AAAU----GCUGGAA--G    1

    
    CGGU----GGUGAGA--G    1

    
    UGGU----UGUGCAA--A    1

    
    --GUU---GCUGAGA--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_86109.1

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

18.75 -39.20 6 4

2

Motif group HL_68572.1

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

6.25 -44.36 6.5 5

3

Motif group HL_68767.1

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

4.17 -49.16 7 5

tRNA D-loop

4

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

4.17 -59.53 6 4

5

Motif group HL_16991.1

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

4.17 -65.13 7 6

G-quadruplex fragment

6

Motif group HL_29958.1

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

2.08 -73.98 7 5.5

7

Motif group HL_41543.1

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

2.08 -84.86 7 6

8

Motif group HL_12870.1

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

2.08 -1320.63 7 6

Loop 11 Internal loop

Column numbers: 167-168, 214-216 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UU*A-A    9

    
    UA*U-A    5

    
    AA*U-U    3

    
    UU*AUA    2

    
    AU*A-U    2

    
    CC*G-G    2

    
    CU*A-G    2

    
    GA*U-C    2

    
    UA*U-G    2

    
    AG*CUU    1

    
    AG*C-U    1

    
    AG*U-U    1

    
    CA*U-G    1

    
    GG*U-C    1

    
    UA*C-A    1

    
    UC*G-A    1

    
    UG*C-G    1

    
    UG*U-A    1

    
    UU*A-G    1

    
    Omitted sequenced and counts

    
    --*---    3

    
    UA*--A    2

    
    A-*AAU    1

    
    G-*A-C    1

    
    G-*G-C    1

    
    U-*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

Basepair signature:
cWW-cWW

100.00 25.87 3 2

Multiple bulged bases

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 24.97 2 1

Multiple bulged bases

3

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 23.34 2 1

Major groove platform

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

97.44 24.59 3 1

Intercalated cWS

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

89.74 15.56 3 1

Major groove intercalation

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

89.74 11.05 4 1

7

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

89.74 6.46 1 1

Single bulged G

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

82.05 22.79 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

79.49 15.36 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

79.49 13.27 2 1

Single stack bend

Loop 12 Internal loop

Column numbers: 172-179, 204-210 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    UGAA--GU*UUAGUAA    2

    
    UGAC--GA*CUUGUGA    2

    
    CGAAACG-*GAAGUAG    1

    
    GGAAC-GU*CUAGUAA    1

    
    UGAAC-GG*UCAUUAG    1

    
    UGAAC-GG*UUAGUAG    1

    
    UGAAC-GU*AUAGUAG    1

    
    AUUA--GC*CGUGAAA    1

    
    CGAA--AU*CAGGUAG    1

    
    CGAA--GU*UUAGUAG    1

    
    CGUA--AU*CAUGAAG    1

    
    CGUA--GU*UAUGAAG    1

    
    GAAA--UU*AGAGUAG    1

    
    GAGA--AA*GAAUUAA    1

    
    UGAA--AA*UUAGUAG    1

    
    UGAA--AG*CCAUUAA    1

    
    UGAA--AG*UUAGUAG    1

    
    UGAA--CA*UAAGUAG    1

    
    UGAA--CA*UCAGUAG    1

    
    UGAAA-U-*ACAGUAG    1

    
    UGAAG-C-*UGUCUAG    1

    
    AGAA--U-*AAAUUAU    1

    
    CGAA--U-*GCAGUAA    1

    
    CGCC--A-*UUUGGAG    1

    
    UGAA--C-*GUAGUAG    1

    
    AAAA----*AAAUAAA    1

    
    AAGA----*AAAUCUU    1

    
    AGAA----*UUAGUAU    1

    
    UGAA----*AAAGUAG    1

    
    UGAA----*ACAGUAA    1

    
    UGAA----*AUAGUAG    1

    
    UGAA----*CAAGUAG    1

    
    UGAA----*GAAGUAG    1

    
    UGAA----*UUAGUAU    1

    
    GAAA----*-CAAUGA    1

    
    AGGA----*--UAAUG    1

    
    CAAU----*--AUGAG    1

    
    AUAA----*-----AA    1

    
    UGAA----*-----AG    1

    
    UUAU----*-----UA    1

    
    Omitted sequenced and counts

    
    ------A-*GAACAA-    1

    
    --------*ACUGUA-    1

    
    --------*CAAGAA-    1

    
    UAAA----*------A    1

    
    --------*-----AA    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_26307.2

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

38.10 -48.89 4 2

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_16458.4

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

26.19 -48.52 5.5 3

Sarcin-Ricin target in LSU H95; G-bulge

3

Motif group IL_24254.1

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

26.19 -60.86 6 2

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

4

Motif group IL_61286.1

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

21.43 -42.22 6 3

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

5

Motif group IL_41756.4

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

16.67 -80.92 6 4

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

6

Motif group IL_65594.1

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

16.67 -98.25 5.5 4

8x7 Sarcin-Ricin; G-bulge

7

Motif group IL_88269.4

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

11.90 -55.86 5 3

6x5 Sarcin-Ricin; G-bulge

8

Motif group IL_29198.2

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

11.90 -86.40 6 4

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

9

Motif group IL_04346.10

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

11.90 -102.94 5 3

8x7 Sarcin-Ricin; G-bulge

10

Motif group IL_47346.2

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

9.52 -93.47 7 4

tSH-tSH-tHH-tHS

Loop 13 Hairpin loop

Column numbers: 181-202 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    UUA-----------------UU    3

    
    --------------------AC    3

    
    --------------------UU    3

    
    --------------------AU    2

    
    --------------------GU    2

    
    GGUCGUUGUCGAUUGACGAUCC    1

    
    UUUAUCUUUUAUAAAGAAG-AU    1

    
    GUAUUUGUAUUUAUACU---AU    1

    
    AAGAUAGUAUUUAU------CU    1

    
    AUCUGCAUUAGUAG------AU    1

    
    AAUCUUGUAU----------UC    1

    
    ACUUUAAAAA----------GU    1

    
    AUCUUAAUG-----------AU    1

    
    CCUGUU--------------AA    1

    
    CUUUUU--------------AU    1

    
    AUAUA---------------CG    1

    
    GAAUU---------------UC    1

    
    AUAG----------------UU    1

    
    AUU-----------------UU    1

    
    UAA-----------------CA    1

    
    UU------------------UU    1

    
    A-------------------UU    1

    
    --------------------AA    1

    
    --------------------CU    1

    
    --------------------UA    1

    
    Omitted sequenced and counts

    
    ----------------------   13

    
    ---------------------A    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 HL_56131.2

Basepair signature:
cWW-F-F

21.21 -1091.26 3 2

2

Motif group HL_32346.4

Basepair signature:
cWW-F

21.21 -6813.47 3 2

3

Motif group HL_56334.1

Basepair signature:
cWW-F

21.21 -6825.05 3 2

Mini UNCG

4

Motif group HL_75660.5

Basepair signature:
cWW-F

21.21 -6841.38 3 2

5

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

18.18 -5301.95 4 2

6

Motif group HL_48778.2

Basepair signature:
cWW-F

18.18 -6498.28 2 1

Mini UNCG

7

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

15.15 -3352.51 4 2

8

Motif group HL_69752.2

Basepair signature:
cWW-F

15.15 -6860.85 4 2

9

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

12.12 -5263.40 4 3

10

Motif group HL_70782.2

Basepair signature:
cWW-F

12.12 -6513.15 4 2

Loop 14 Hairpin loop

Column numbers: 221-235 - This loop does not map to nucleotides in a 3D structure with xyz coordinates. 
    Scored sequences and counts

    
    AUUAGGCCU---UAU    2

    
    GUAGUUUA----UAC    2

    
    GCCGC-------UUC    2

    
    GGUUC-------CGC    2

    
    GUGAU-------AAC    2

    
    UUAG--------CUG    2

    
    GUAGAUCUCGUCUAU    1

    
    UUUUUAUUAC--UUG    1

    
    GAGUAAUU----CCA    1

    
    GGAAUCCG----GCC    1

    
    CACAUUU-----AAG    1

    
    GAUUAGU-----ACA    1

    
    GUCAAAU-----GAU    1

    
    GUCAGAU-----GAU    1

    
    GCUGUC------CCC    1

    
    GUGUUG------AGC    1

    
    GUUAUA------GAC    1

    
    UCAAAA------ACG    1

    
    GAUCG-------CUC    1

    
    GAUCU-------UUC    1

    
    GAUUU-------GUC    1

    
    GGAGC-------UCC    1

    
    GGUGC-------UCC    1

    
    GGUUC-------GCC    1

    
    GUAGG-------AAC    1

    
    GUCAU-------GUC    1

    
    GUGAC-------GAC    1

    
    UAAGC-------ACA    1

    
    UAAUC-------UCG    1

    
    UAUUC-------AGG    1

    
    UGCGC-------ACA    1

    
    UGUUU-------GAG    1

    
    UUCGC-------CUG    1

    
    UUUAC-------CCG    1

    
    UUUAC-------CUA    1

    
    GUAG--------CUC    1

    
    GUAG--------UUA    1

    
    UAUC--------CCG    1

    
    UUAA--------CUG    1

    
    UUUU--------CCG    1

    
    ------------AA-    1

    
    Omitted sequenced and counts

    
    ---------------    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_22622.1

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

14.89 -445.18 5 4

2

Motif group HL_13529.1

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

10.64 -106.02 5 4

3

Motif group HL_64690.6

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

10.64 -240.39 4 4

4

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

10.64 -258.59 5 4

tRNA anticodon loop with synthetase

5

Motif group HL_77082.1

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

10.64 -282.87 4 3

Pseudoknot geometry

6

Motif group HL_78197.1

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

10.64 -303.69 4 3

7

Motif group HL_50006.2

Basepair signature:
cWW-F-F

10.64 -324.12 4 4

8

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

10.64 -447.71 5 4

9

Motif group HL_04259.3

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

8.51 -146.48 5 4

GNRA with extra cWW

10

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

8.51 -258.65 4 4

T-loop with unstacked turn

Loop 15 Hairpin loop

Column numbers: 412-498 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U-----------------------------------------------------------------------------------UUU    3

    
    U------------------------------------------------------------------------------------UU    3

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

    
    AGGUUUAGUGUAUCUUUA---------------------------------------------------------------UAACUU    2

    
    GAGAUGAAGCAUUUCAAAUUUCACGAUGAUAGUAUUGGUAUGAUUAUUCCAAUUAUGUUAAAAGAGUGAAUUUGAUAUUAAACAUCC    1

    
    GUGUCGCCGUUUAUCGGC---------------------------------------------------------------GCAUGC    1

    
    UAUAGACUCAUU---------------------------------------------------------------------UCUACA    1

    
    CAAAUUCCUG-----------------------------------------------------------------------GAUUUG    1

    
    GUUUGGCAU------------------------------------------------------------------------AAUAAC    1

    
    UGAUUUUU-------------------------------------------------------------------------AAAUUG    1

    
    AUCAAUA--------------------------------------------------------------------------AAUGAU    1

    
    GUGUUG---------------------------------------------------------------------------AAUUGC    1

    
    CAUGA----------------------------------------------------------------------------CAUAUG    1

    
    ACAU-----------------------------------------------------------------------------UUUAGU    1

    
    AUCG-----------------------------------------------------------------------------UGAGAU    1

    
    UCAG-----------------------------------------------------------------------------CGAUGG    1

    
    UUAA-----------------------------------------------------------------------------UUUUAG    1

    
    UUUG-----------------------------------------------------------------------------UGAAAA    1

    
    AGG------------------------------------------------------------------------------UAUUUA    1

    
    AA-------------------------------------------------------------------------------UUACUU    1

    
    AU-------------------------------------------------------------------------------ACUUGU    1

    
    CG-------------------------------------------------------------------------------AAACUG    1

    
    UU-------------------------------------------------------------------------------UCUUAU    1

    
    G--------------------------------------------------------------------------------AAAGAA    1

    
    G--------------------------------------------------------------------------------AUAGUC    1

    
    U--------------------------------------------------------------------------------AUUAAU    1

    
    U---------------------------------------------------------------------------------ACUUA    1

    
    A----------------------------------------------------------------------------------AAUU    1

    
    C----------------------------------------------------------------------------------UUUG    1

    
    G----------------------------------------------------------------------------------UACA    1

    
    U----------------------------------------------------------------------------------UGGU    1

    
    U----------------------------------------------------------------------------------UUAU    1

    
    A-----------------------------------------------------------------------------------UUU    1

    
    G-----------------------------------------------------------------------------------UAU    1

    
    U-----------------------------------------------------------------------------------ACG    1

    
    U-----------------------------------------------------------------------------------AUG    1

    
    U-----------------------------------------------------------------------------------CAU    1

    
    U-----------------------------------------------------------------------------------UAG    1

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

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

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

Motif group HL_56131.2

Basepair signature:
cWW-F-F

31.25 -1260.30 3.5 2

2

Motif group HL_78677.1

Basepair signature:
cWW-F-F

31.25 -4769.33 4.5 3

3

Motif group HL_32346.4

Basepair signature:
cWW-F

29.17 -3686.72 3 2

4

Motif group HL_56334.1

Basepair signature:
cWW-F

29.17 -3691.33 3 3

Mini UNCG

5

Motif group HL_48778.2

Basepair signature:
cWW-F

25.00 -3472.24 3 2

Mini UNCG

6

Motif group HL_70782.2

Basepair signature:
cWW-F

22.92 -3459.90 4 3

7

Motif group HL_13189.1

Basepair signature:
cWW-F-F

20.83 -1944.97 4.5 3

8

Motif group HL_48417.5

Basepair signature:
cWW-F-F

16.67 -1065.17 4 2

9

Motif group HL_46501.1

Basepair signature:
cWW-cWS

16.67 -2168.62 4 3

10

Motif group HL_94980.1

Basepair signature:
cWW-F-F

16.67 -4772.78 4 2.5

Loop 16 Internal loop

Column numbers: 517-523, 549-550 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    GUGGUAC*UC   26

    
    GUGGAAC*UC    6

    
    GUGGCAC*UC    4

    
    GUGGCAA*UC    3

    
    GUGGUAA*UC    3

    
    GUGGUAC*CC    3

    
    GUGGCAC*CC    2

    
    GUGGUAU*UC    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

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

31.25 -9.75 3 3

2

Motif group IL_51191.1

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

6.25 -17.05 7 3

Loop 17 Internal loop

Column numbers: 523-527, 547-549 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CCGCG*CGU   26

    
    CCACG*CGU   10

    
    ACGCG*CGU    5

    
    CCGCG*CGC    4

    
    ACACG*CGU    1

    
    CCGUG*CAC    1

    
    UCGCG*CGU    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_28788.1

Basepair signature:
cWW-L-R-cWW

77.08 15.89 5 1

2

Motif group IL_10389.1

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

35.42 -2.68 5 3

3

Motif group IL_57881.1

Basepair signature:
cWW-L-cWW

33.33 5.51 5 2

Multiple bulged bases

4

Motif group IL_63596.11

Basepair signature:
cWW-cWS-cSH-tWH-cWW-L

33.33 -1.03 4 1

C-loop

5

Motif group IL_06549.2

Basepair signature:
cWW-cWW

22.92 -19.09 6 2

6

Motif group IL_89984.3

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

22.92 -23.37 7 3

7

Motif group IL_66997.2

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

22.92 -25.56 6 2

8

Motif group IL_36516.3

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

14.58 -17.46 4 2

9

Motif group IL_11415.1

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

12.50 -6.33 5 2

10

Motif group IL_49061.1

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

12.50 -29.88 3 2

Loop 18 Hairpin loop

Column numbers: 529-545 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UC-----AUUU-----A    2

    
    U------AAAU-----A    2

    
    A-------GAC-----C    2

    
    G-------UCU-----C    2

    
    -------UAAC------    2

    
    UAUUAACAUUACAUAUA    1

    
    GUGUAA-AUAA--ACUC    1

    
    AACA---AUGA-CCGUU    1

    
    AA-----AUUAAACCUU    1

    
    AACU---AUAG--CCUU    1

    
    AU-----AAUACUCUUU    1

    
    GAGA---AGCA--UCUC    1

    
    AA-----GCAA-UGCUU    1

    
    AAC----AUAA--GCUU    1

    
    AGU----UUAA--CCUU    1

    
    AUAA---AAGA---UUU    1

    
    GA-----AACA-GAUUC    1

    
    GA-----AUAA-UACUC    1

    
    GU-----AUAA-UACUC    1

    
    GUAAAU-AUAA-----C    1

    
    GC-----GCAA--GCCU    1

    
    GU-----AAAA---CUC    1

    
    GA-----CUUA----AC    1

    
    GC-----AAAA----CC    1

    
    GC-----AUAA----AC    1

    
    GU-----AUGG----AC    1

    
    UA-----AAUU----UA    1

    
    UA-----AUUA----AU    1

    
    A------UUAA----UA    1

    
    AU-----AUAA-----U    1

    
    AU-----AUAU-----U    1

    
    A------AUCU-----U    1

    
    U------AACG-----U    1

    
    U------GUCC-----C    1

    
    U------UGUC-----C    1

    
    U------UUUU-----A    1

    
    A-------AUA-----U    1

    
    A-------AUU-----U    1

    
    U-------ACC-----A    1

    
    U-------CAA-----A    1

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

    
    -------AUCG------    1

    
    -------GGAA------    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

Basepair signature:
cWW-F

33.33 -1633.98 4 3

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

31.25 -337.15 4 2

3

Motif group HL_48417.5

Basepair signature:
cWW-F-F

29.17 -96.01 3 2

4

Motif group HL_48778.2

Basepair signature:
cWW-F

27.08 -1668.58 3 2

Mini UNCG

5

Motif group HL_56334.1

Basepair signature:
cWW-F

25.00 -3356.80 3.5 2.5

Mini UNCG

6

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

22.92 -153.80 4 3

7

Motif group HL_56131.2

Basepair signature:
cWW-F-F

22.92 -331.92 4 3

8

Motif group HL_75660.5

Basepair signature:
cWW-F

22.92 -1648.46 3 2

9

Motif group HL_69752.2

Basepair signature:
cWW-F

22.92 -1656.38 5 3

10

Motif group HL_32346.4

Basepair signature:
cWW-F

22.92 -3375.09 3.5 2.5

Coloring options: