JAR3D on RF00168

RF00168 Lysine riboswitch aptamer

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222222222222222222222222222222222222222222222222222222222
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777
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.((((((((((.....((((((.(((..(.........(((((((...(((..............))).........))))).)).....)..))).).)))))...(((((((((((((.......)....)))))))).))))(((((((.((((.......))))))))))).(((((((((.(((.....)))....................................................))))))))).....)))))))))).
>U00006.1_98763-98567
CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
>J03294.1_2297-2476
GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--UGCCUUUGGAGA-------AAGAUGGAUUCUGUG---AAAAAGG-CU-GAAAGG-GGA-GCGUCGCCGAAGCAAAUAAAACCCCAUCG------GUAUUAUU-UGCUGGCCGUG-CAUU--GAAUAAAUGUAAGGCUGUCAAGAAA--UCA------------------------------------------------------------UUUUCUUGG-AGGGCUAUCUCGUUG
>AF269536.1_680-500
AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUGAAGUUGG-UUGAA-CAAUAAAAACAUCACAACCACGAAU--GCU--------------------------------------------------------------UUCUUCA-AUAUUUAUUUGAAUU
>AF270308.1_2156-2331
AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUUGGGACAA-CUUUC-GAAUAGAAGUUGUACUGUCACU-----UUA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
>M93419.1_332-511
AGUGAAGAUAGAGGU-GCGAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------GAAUGAGCUUCAAUG---AAAAGCU-UU-GAAAGG-GAACG-UUCGCCGAAGUGAAGAAAAA---CUCAUU----UUUUUCUU-UGCUGGUCCUG-CAUU--UAAGAGAUGCCGGAUUGUCAAGGCGG-UGC-------------------------------------------------------------CGCCUUGG-AGAGCUAUCUCACUG
>AF306669.1_1019-1194
AUAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AAGUUUAGAUUAC------UGUCUGCUAACAG------CUAAAU-UU-GAAAGG-GUG-C-GAUGCCGAAGC-AAUUAUAAU--AGCA-G----UUAUAAUU-UGUUGGACUUUUUGGU--UAAGAGCUGAGAGUUUGUCAUUAUU--UAA------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
>X00008.1_296-492
CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUAAG-GGGGCUGAAU-CCC-CUGGGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
>X15196.1_270-75
GCAGCCAGAAGAGGC-GCGUUG-CCA-A-----GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
>AL591976.1_186683-186486
UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCGACG---ACAAAGA-AU-GAACAG-GUU-G-AUCGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGGGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
>AL596166.1_112469-112272
UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCAAUG---ACAAAAA-AC-GAACAG-GUU-A-AUCGCCGAAGUGACUAUUUUUU-CUUU-GUAUCGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
>AAMR01000029.1_5147-5324
AUCGCACGUAGAGGC-GCAAUU-AUA-AAAA--GUA--GUUUUCGUU----------GGGGUGAUGCCAAUG---AGCGGGA-AU-GAAAGG-UCU-A-AUUGCCGAAGUAAAUUGUAU---AUCU------AAGCAAUU-UGCUGGGGUUG-UGCU--CAAUAGGUACAACACUGCCAUAGUC--UUAAUUUU-------------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
>CP000002.3_2878377-2878198
GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--GGCUUGAUGAGGA------AGAUGGAUUCCGAUG---AAGAAAG-CC-GAAAGG-GGA-GCGUCGCCGAAGCGGGGAAAAAUC-CACU-C----GUUUUUCC-UGCUGGCUUUA-CAUU--GAAUAAAUGUGAGGCUGUCAAGAAA--UCA-------------------------------------------------------------UUUCUUGG-AGAGCUAUCUCGUUG
>BX950851.1_4451556-4451748
CAAGCCAGAAGAGGC-GCGUCG-CCC-AG----GUA--AGAUAUCGGAGG-------AACCGUAAUCCGCUG---AUGAUAU-CC-GAGGGG-GAG-C-GACGCCGAGAUGCGGUGAAAUU-CGGC------UUUCACCC-UAUCGACUACA-GAGGCUGAAU-CCUCUG-GGUUGUCACCGGA--UUCGUCCUGAUGGACGUCCA-------------------------------------------GCAAGGUGG-AGCGCUUCUGGGUGU
>EF419299.1_175-1
AAAAGAGUUAGAGGUUGCGUCU-UUA-AUUA--GUA--ACACUUCAGAAGUUAUU--AAGGAACGUGUGUUG---A--AAGU-GU-GGAAGG-UAA-A-GAUGCCGAAAUGAAUGAUACC--CUUA-A----UUAUCAUU-UGUUGGGACAG-UUAUC-GAAUAGAAACUGUACUGUCACA-----AUU----------------------------------------------------------------UGUGA-UGUGCUACC-GACGG
>CP000046.1_1759610-1759435
AAUUGAGUUAGAGGUUGCAUGU-UUA-AUUA--GUA--ACUUGUCAGAAGUAUUU--AUGGUACAUAAGUUG---A--ACAA-GU-GAAAGG-UAA-A-GAUGCCGAAAUAGAUAUAAACC-AUAA------AUUAUAUC-UAUUGGGACAG-UUUUC-GAAUAGGAACUGUACUGUCACA-----GAA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
>BA000037.2_1373591-1373770
UAUCGACGUAGAGGC-GCAAUG-GUA-AAGA--GUA--ACUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GAAAGG-UAU-CCAUUGCCGAAGUGAAUUGCAU---AUCA------AAGCAGUU-UGCUGGGGUUG-CAUCC-GAAA-GGAACAACACUGCCAUAGUA--UUUAAUGUA------------------------------------------------------UAACUAUGG-AGCGCUACUGUAGGU
>CP000647.1_4829910-4829675
AUUGCCAGAAGAGGU-GCGUUG-CCC-AG----GUAA-CCGUAUUGGA---------GGAACCAGUCCGGGG---AAGAUAC-GU-GAGGGG-GAG-C-AACGCCGAGGUGAAAGAGCGUCUGGUC-A----CGCUCC-U-CGCCGGCCACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AACGUUCGCAGUCGGGCGUUUCAUACCCGAACACCUCAGCGCCCAAAGCGGUGAGUCGGGUCUACAAGGUGG-AGCACUUCUGGGUGA
>BA000004.3_1819757-1819575
AGUGAGGAUAGAGGU-GCAAAA-ACC-AAGA--GUA--CACAAUUGGAGGA------GAAUGAGAUCCGUUG---AGAAUUG-UG-GAAAGG-GGA-A-UUUGCCGAAGC---UGGAAGAAUCUCA-U----GUUCUGAA-GGCUGGUUCUG-UAUU--AAAUAAAUACAGAACUGUCAUAUAGCGGAUGUU---------------------------------------------------------GCUAUAUGG-AGGGCUAUCUCACGC
>ABCF01000065.1_4547-4725
AGUGGUGAUAGAGGU-GCGGAC-UUUCAUCA--GUA--GAUGCUUCGAGGA------GUAUGGGCUCUUAUG---AAGGGUA-UC-GAAAGG-GAA-A-UUCGCCGAAGUGGAAGCAGGCU-CAUA------UCUGUUUG-CGCUGGUUCUG-UGUU--UAAGAGAUGCAGGAUUGUCAAGAUUA-ACA--------------------------------------------------------------GUCUUGG-AGAGCUAUCUCACGU
>AE017143.1_992934-993104
ACAAAUUGUAGAGGU-GCAAAU-CCG-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAGCGAUG---AAGGGGA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAGUU-GGUUGGGGUCG-UUGCC-GAAA-GGGACGACACUGUCGUAAUU--CAA-------------------------------------------------------------UAUUACGG-AGUGCUACUAUUAGG
>CP000002.3_3366091-3365915
UAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--GCAUGUGUGAGG-------CUGAUGGGGCCGAUG---AUCAUAU-GC-AAAAGG-CAU-C-AGCGCCGAAGCAUAAGGAAGCC-AUUC------AUUCUUUA-UGCUGGGUCUG-CAUU--GAAUAAGUGCAGGACUGCCGCGGGU--AUU--------------------------------------------------------------CCCGCGG-AGGGCUAUCCGGAGA
>CP000029.1_981298-981477
AGAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AACUUUAGAUAAU------UUGUCUGCUAACAAU---UAUAGAG-UU-AAAAGG-GUG-A-GAUGCCGAAAUGAUUCAUAAU--AGCA-G----UUAUGAAU-CGUUGGACUUAAUGGU--UAAGAGCUAUAAGUUUGUCAUUAUU--AUU------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
>AAWP01000069.1_5541-5721
UAUUGCCGUAGAGGU-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGA-GGAUUGCCGAAGUAGGUGGCCU---AUCG------AAGCCACU-UGCUGGGGUUG-UCUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
>AAKK02000085.1_12844-12662
UGUUGCCGUAGAGGC-GCGGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUAACUC---AUCA------AAGUUACU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUAUUCACAUU---------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
>CP000416.1_1669940-1669758
UCGAAUAGAAGAGGC-GCGACC-AAC-AAGA--GUC--GCUUUCCGGAGA-------UGGGUCACAUUGCUG---AUGGAAG-GU-UAAAGG-GGC-G-GUCGCCGAAAUUUACGCAUUUU-GACC-G----GAUGCGUG-GGUUGGGUCCU-GGUU--GAACAAGUCAGGGACUGUCGCAGUCA-AAUAAU---------------------------------------------------------CGGCUGCGG-GGCGCUUUCAACGAU
>AM263198.1_783761-783564
UGGUGAGGUAGAGGUUGCAAGA-UUC-ACAA--GUA--AUUUUUUAGAAGCGAA---ACAAAGACGCUGAUG---ACAAAGA-AU-GAACAG-GAU-G-AUUGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
>AP006716.1_1558409-1558233
AGAAAUUGAUGAGGC-GCAUCA-AUC-AUCA--GUA--UAUAUUAGAU---------AAACUGUCUGCAACA---GCUAAUA-UA-GAAAGG-GUG-C-GAUGCCGAAAUGAAUCAUAAU--CGCA-G----CUAUGAUU-UGUUGGACUUUGUGGU--UAAGAGCUGAAAGUUUGUCAUUAUU--AUU------------------------------------------------------------UAAUAAUGG-AGUGCAUCACUUGUA
>ABDQ01000005.1_49327-49153
AACUAAGAUAGAGGU-GCGAGA-UUU-AAGA--GUA--GUAUUAUG-----------GAGUUAAGUGCUAAG---AAGUAAU-AA-GAAAGG-AAA-U-UUCGCCGAAGCUUAUAGAUAAUACUUU-A----AUGCUAUU-UGCUGGGAUUA-CAUA--AAAUAUAUGUAAGACUGUCACAAAU--AAA-------------------------------------------------------------GUUUGUGG-AGAGCUAUUAUUUUA
>AE016827.1_1325416-1325239
UACACAUGUAGAGGU-GCGAAU-AUU-AUAA--GUA--UUUUUCCA-----------GAGUGGAUAACAAUG---AAGGAAA-UU-GAAAGG-AAU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAACU-GGUUGGUAACG-UCACC-GAAA-GGAACGUUACUGCCAUAGUC--AUUUUUGAU------------------------------------------------------UAACUAUGG-AGCGCUACUCGUGGG
>CP000569.1_516240-516411
ACAAAUCGUAGAGGU-GCAAAU-CCG-AUAA--GUA--CUUUUUCU-----------GAGUGGAGAACGAGG---AGGAAAA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUACC-GAAA-GGGACGACACUGUCGUAAUC--CUU------------------------------------------------------------GUAUUACGG-AGUGCUACUGCUAGG
>BA000031.2_1190723-1190903
UGUUGCCGUAGAGGC-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUCGUAU---AUCA------AAACGCCU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
>CP000425.1_2337129-2337310
CACAUCGAUAGAGGUCGCAACU-GAU-AUGA--AUC----UACGCCGAGU-------UGGAGCACAACAAAG---ACGCGUA-UUAGAGGGGGAGA-A-GUUGCCGAAAGAAUUUUGAC---GCUC-A----G-CAAAGU-UCUUGGGCUAG-UGAG--GAAAACUCACUAGACUGUCGCAAAUGGUUAAGA---------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
>AASA01000017.1_10332-10501
ACAAAUUGUAGAGGU-GCGAAU-UCA-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAACGAUG---AAGGGGA-AG-GAAAGG-UGA-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUGUC-GAAA-GAAACGACACUGUCGUAGUA--AAU--------------------------------------------------------------GCUACGG-AGUGCUACUGUUAGG
>AP008934.1_1400599-1400421
AGGUUUUGAUGAGGC-GCAUCA-AUC-AUUA--GUA--AAGAUUAGAAGA-------AUCUGACUGCUAGCA---GCUAAUU-UU-GAAAGG-GUG-A-GAUGCCGAAACGGUUAUAAU---AGCA-G----CUUAUAACAUGUUGGACUUUAUGGU--UAAGAGCUAAGAGUCUGUCAUUAUU--UUA------------------------------------------------------------AGAUAAUGG-AGUGCAUCACUUGUA
>AAOX01000015.1_22460-22639
AGUGAAGGUAGAGGU-GCAAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------AGAUGAGUUUCCGUG---AAAAGCU-UU-GAAAGG-GAAUG-UUUGCCGAAGAAAAGGAAGUCU-CAUU------UCUUUCUU-UUCUGGUCCUG-UAUU--GAAUAAAUACUGGAUUGUCAAGACA--GCG------------------------------------------------------------CCGUCUUGG-AGAGCUAUCUCACUG
>AL009126.3_3421348-3421169
CAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--ACACAUGCUA---------GGCUGACAGGGGCUGUUAAACAUGU-GU-AAAAGG-CAU-C-AGCGCCGAAGUGUGGAGAAAGCCGAUC------CUUCUCUA-UGCUGGGACUG-UAUCU-GAAUAAGUGCAGGACUGCCGCGUGC--UUU--------------------------------------------------------------UUCGCGG-AGGGCUAUCCGGAGA
>AE008691.1_719320-719498
CGCAUAAAUAGAGGA-GCUGCC-AAGCAU----GUA--UUUGGCGAGGUGUUAAGGAGAAGAACCUCCAAUA---CUCGCUG-AA-GAA-GG-UUU-G-GCUGCCGAAAGGGUGAGCUUG--UUCU-U----GAGCUCAU-CCUUGGUGGUA-AAC-A-CAAA--GUUUACCACUGUCAUGGGA--CCU--------------------------------------------------------------CCCAUGA-AGCGCUAUUUAUGCA
>AE004439.1_1026545-1026371
UACUUGUGUAGAGGA-GCGAUC-ACU-AUAA--GUA--UUUUUUCU-----------GAGUGGAUAACGAAG---AGGAAAA-AG-GAAAGG-AGU-G-ACCGCCGAAAUCAAUUGAAA---GUCA------UUUUGAUU-GGUUGGUGGCG-UAUUC-GAAA-GGAACGUCAUUGUCAUAGUC--UUUUUU---------------------------------------------------------AAACUAUGG-AGCGCUACUGGUUGG
>CP000436.1_843556-843727
UACAUAUGUAGAGGU-GCGGCU-GUU-AUAA--GUA--AUUUUUU------------GAGUGGAUAACGAUG---A-AAAAA-AU-GAAAGG-AAU-A-GUUGCCGAAAUCAAUUAAAA---GUCA------UUUUAAUU-GGUUGGGGGCG-UAUUC-GAAA-GAAACGUCACUGUCAUAGUA--UUU-AU---------------------------------------------------------CCACUAUGG-AGCGCUACUGGUUAG
>CP001186.1_1355449-1355630
CUCAAAGGUAGAGGCCGCGAUA-GGA-AAGA--GUA--AGCUAUGGGAGAU------UUAAUGGAAUCUGUG---AUCAUAGGUU-GAAAGG-GAC-U-AUUGCCGAAAUAUAAGAAUAAC-CAUC-U----UAUUCAUA-UAUUGGGACUA-CAUU--GAAUAAAUGUAGUACUGUCAUAAGA--UUU------------------------------------------------------------AUUUUAUGG-AGAGCUAUUUGGAGA
>AE005176.1_2276232-2276414
CACAUCGAUAGAGGUCGCAACU-GAU-AUGAAUCUACGCCGAGUUGG----------AGCACAACAAAGACG---CGUAUUU-AG-AGGAGG-AGA-G-GUUGCCGAAAGAAUUUUGUU---GCUC------AGCAAGGU-UCUUGGGCUAG-UGAG--AAAAACUCACUAGACUGUCGCAAAUG-GUUAAUA--------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
>CP000923.1_1076332-1076143
AGGUGAGGUAGAGGC-GCGGGUUAUC-AAGA--GUA--GUAUACCAGAGGU------AUUUAAGGGCCGAUG---AAGGUAU-AU-GAAAGG-GAU-G-CUCGCCGAAGC-GCGUAAAUUCCUUAA-A----GUUUACGC-AGCUGGGCCUA-UGCC--GAAUAGGUAUAGGACUGUCACUGGA--GGUUUCCCGAGC---------------------------------------------------CUUCAGUGA-AGAGCUAUCUCGCUA
>AE008691.1_1930427-1930616
AGGUGAGGUAGAGGC-GCGGGU-CAUCAAGA--GUA--ACAUGCCAGAGG-------UGUUAAGGGCCGAUG---AAGGUGU-GU-GAAAGG-GGU-G-CCCGCCGAAGC-GCGUAAACUUCCUUAAG----GUUUACGC-AGCUGGGCCUA-UGCC--GAACAGGUAUAGGACUGUCACUGAAG-GCUCCCCAGGC----------------------------------------------------CUUCAGUGG-AGAGCUAUCUCGCUA
>CP000826.1_4955718-4955911
CAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--GAGUGUCAGAGG-------AGCCGUUGUCCAAUG---ACGGCGC-UU-GAGGGG-GAG-C-GACGCCGAGGUAAGGUGAUGUG-CGGC------AUUCAUCG-UAUCGACUACA-GGGGCUGAAU-CCCCUG-AGUUGUCACCAGGG-AUUGUCCGUAGGGGCAAUCA-------------------------------------------GCAAGGUGG-GGCGCUUCUGGGUGU
>AL935263.2_928916-929097
AUCGAAAGAAGAGGAUGCGGUU-AAC-AAUA--GUA--GCCGGCUGGAAGU------GGGUCACCACUUAUG---AAGGUCA-GU-GAACGG-GGC-A-ACCGCCGAAAUCGAUGGAUCAGUGACC------GAUUCAUC-CGUUGGGCCUU-GGUU--GAAUAAAUCAUGGACUGUCGCAGCUA-GAA------------------------------------------------------------UAGUUGCGG-GGCGCUAUCGACGAU
>AALE02000022.1_49827-50019
UAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--AAGUGUCAGAGG-------AGCCGUGAUCCGCUG---AAGACAU-UC-GAGGGG-GAG-C-GACGCCGAGACACGGUGAUUUC-GGCC-------AUCAGCG-UGUCGACUGCA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGU--GCCGUUCCUUUAGGGCGGUCA------------------------------------------ACAAGGUGG-AGCGCUUCUGGGUGU
>FQ670178.1_927246-927070
UACAAAAGUAGAGGC-GCAAUU-AUU-AUAA--GUA--UUUUUUCA-----------GAGUGGAUAACGAAG---AAGAAAA-AA-GAAAGG-AAU-A-GUUGCCGAAAUCAAAUAAAA---GUCG------UUUUGUUU-GGUUGGUGGCG-UGCUC-GAAA-GGGGCGACACUGUCAUAGUU--UUUCUGAU-------------------------------------------------------UAACUAUGG-AGUGCUACGGUUGUU

Rfam family RF00168 maps to these 16 chains: 3D0U|1|A, 3D0X|1|A, 3DIG|1|X, 3DIL|1|A, 3DIM|1|A, 3DIO|1|X, 3DIQ|1|A, 3DIR|1|A, 3DIS|1|A, 3DIX|1|A, 3DIY|1|A, 3DIZ|1|A, 3DJ0|1|A, 3DJ2|1|A, 4ERJ|1|A, 4ERL|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: 21-22, 98-100
Loop 2IL Column numbers: 22-24, 96-98
Loop 3IL Column numbers: 26-29, 91-94
Loop 4IL Column numbers: 29-39, 85-91
Loop 5IL Column numbers: 40-41, 82-84
Loop 6IL Column numbers: 45-49, 68-78
Loop 7HL Column numbers: 51-66
Loop 8IL Column numbers: 111-112, 140-142
Loop 9IL Column numbers: 119-120, 128-133
Loop 10HL Column numbers: 120-128
Loop 11IL Column numbers: 152-154, 168-169
Loop 12HL Column numbers: 157-165
Loop 13IL Column numbers: 185-187, 197-250
Loop 14HL Column numbers: 189-195

Loop 1 Internal loop

Column numbers: 21-22, 98-100 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AU*A-U    4

    
    UG*C-A    4

    
    CG*C-G    3

    
    CU*A-G    3

    
    UA*U-A    3

    
    UC*G-A    3

    
    AC*GCG    2

    
    AC*G-U    2

    
    CA*A-G    2

    
    CA*C-G    2

    
    CC*G-G    2

    
    GA*G-A    2

    
    GG*C-A    2

    
    GU*G-C    2

    
    UU*A-A    2

    
    UC*GGA    1

    
    UG*CCA    1

    
    AA*A-U    1

    
    AC*A-U    1

    
    CU*G-G    1

    
    GA*A-A    1

    
    GA*U-U    1

    
    GU*A-G    1

    
    UU*A-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	87.23	15.08	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	80.85	15.89	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	74.47	12.84	3	1	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	70.21	11.26	3	1
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	68.09	11.66	3	1	Intercalated cWS
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	68.09	6.53	3	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	68.09	-1.85	3	1
8	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	65.96	-2.04	1	1	Single bulged G
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	63.83	7.15	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	63.83	4.25	2	1	Single stack bend

Loop 2 Internal loop

Column numbers: 22-24, 96-98 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-C*G-C    7

    
    A-U*A-U    3

    
    C-U*A-G    3

    
    U-A*U-A    3

    
    U-U*A-A    3

    
    C-U*AAG    2

    
    A-A*G-A    2

    
    A-A*G-C    2

    
    A-U*U-G    2

    
    C-A*U-G    2

    
    G-A*U-C    2

    
    U-C*U-A    2

    
    C-U*ACG    1

    
    C-U*AUG    1

    
    UUA*U-G    1

    
    A-A*A-A    1

    
    A-G*C-U    1

    
    A-U*U-A    1

    
    C-A*C-G    1

    
    C-U*A-A    1

    
    G-G*U-C    1

    
    U-A*C-A    1

    
    U-C*U-G    1

    
    U-G*A-A    1

    
    U-G*A-G    1

    
    U-G*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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	80.85	14.35	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	72.34	10.71	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	70.21	11.68	3	1	Multiple bulged bases
4	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	68.09	2.53	3	1	Major groove intercalation
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	68.09	-1.06	4	1
6	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	65.96	-9.22	2	1	Single bulged G
7	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	63.83	7.40	3	1	Intercalated cWS
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	59.57	6.69	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	59.57	1.13	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	59.57	-1.95	2	1	Single stack bend

Loop 3 Internal loop

Column numbers: 26-29, 91-94 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    C-AA*GG-G    6

    
    C-AU*GG-G    6

    
    A-AU*GG-U    5

    
    U-AU*GG-A    5

    
    C-AG*GG-G    4

    
    G-AU*GG-C    4

    
    C-AC*AG-G    3

    
    G-AA*GG-C    3

    
    A-AA*GG-U    2

    
    C-A-*GG-G    2

    
    GCAU*GG-U    1

    
    U-AU*GGGA    1

    
    UCAA*GG-G    1

    
    UCAU*GG-G    1

    
    A-AA*GG-G    1

    
    U-AA*GG-A    1

    
    A-A-*GG-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_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	93.62	36.77	1	0	Isolated non-canonical cWW pair
2	Motif group IL_85599.2 View motif instance in 3D Basepair signature: cWW-tHS-cWW	93.62	32.69	2	0	Isolated tHS basepair with bulges
3	Motif group IL_44465.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	91.49	48.23	2	0	Isolated non-canonical cWW contact
4	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	91.49	27.59	4	1
5	Motif group IL_10167.6 View motif instance in 3D Basepair signature: cWW-cHW-cWW	91.49	26.08	2	0	Isolated cWH basepair
6	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	87.23	17.05	2	1	Stack and bulge
7	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	82.98	18.15	2	1	Isolated non-canonical cWW pair
8	Motif group IL_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	74.47	0.36	4	2	Isolated non-canonical cWW pair
9	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	74.47	-0.45	3	1	Isolated cWS basepair
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	74.47	-1.29	3	1	Multiple bulged bases

Loop 4 Internal loop

Column numbers: 29-39, 85-91 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AGA--GUA--A*U-GAAAG    3

    
    AGA--GUA--G*U-GGAAG    3

    
    UAA--GUA--U*G-GAAAG    3

    
    UCA--GUA--A*U-GAAAG    2

    
    UGA--CUA--A*U-GAAAG    2

    
    UUA--GUA--A*U-GAAAG    2

    
    --A--GUAA-C*U-GAGGG    2

    
    G----GUA--A*C-GAGGG    2

    
    UGAAUCUACGC*G-AGGAG    1

    
    AAA--GUA--G*U-GAAAG    1

    
    AGA--GUA--C*G-GAAAG    1

    
    AGA--GUA--G*A-GAAAG    1

    
    AGA--GUA--G*C-GAAAG    1

    
    AGA--GUA--G*U-GAAAG    1

    
    AGA--GUA--U*U-GAAAG    1

    
    AGA--GUC--G*U-UAAAG    1

    
    AUA--GUA--G*U-GAACG    1

    
    CAA--GUA--A*U-GAACA    1

    
    CUA--GUA--A*C-GAACA    1

    
    CUA--GUA--A*U-GAACA    1

    
    UAA--GUA--A*U-GAAAG    1

    
    UAA--GUA--C*G-GAAAG    1

    
    UAA--GUA--U*A-GAAAG    1

    
    UAA--GUA--U*U-GAAAG    1

    
    UCA--GUA--G*C-GAAAG    1

    
    UCA--GUA--U*A-GAAAG    1

    
    UGA--AUC---*UAGAGGG    1

    
    UGA--GUA--A*U-AAAAG    1

    
    UGA--GUA--A*U-GAAAG    1

    
    UGA--GUC--A*U-AAAAG    1

    
    UGA--GUC--G*C-AAAAG    1

    
    UUA--GUA--A*U-GGAAG    1

    
    G----GUAA-C*U-GAGGG    1

    
    -----GUAA-C*U-GAGGG    1

    
    G----GUA--G*U-GAGGG    1

    
    U----GUA--U*A-GAA-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	78.72	27.07	3	1	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	76.60	-22.19	5	2	8x6 Sarcin-Ricin with inserted Y; G-bulge
3	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	65.96	-12.39	6	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
4	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	53.19	-20.14	5	3	8x6 Sarcin-Ricin with inserted A; G-bulge
5	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	42.55	-31.06	6	3	tSH-tSH-tHH-tHS
6	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	29.79	-28.20	5	3	Sarcin-Ricin target in LSU H95; G-bulge
7	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	27.66	-29.88	6	3	7x7 Sarcin-Ricin with intercalated A; G-bulge
8	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	27.66	-45.52	4	3	8x7 Sarcin-Ricin; G-bulge
9	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	25.53	-32.36	7	3	8x6 Sarcin-Ricin with bulged A; G-bulge
10	Motif group IL_32016.1 View motif instance in 3D Basepair signature: cWW-tSH-tSH-tSS-tHS-L-R-cWW	12.77	-49.88	6	4	Kink-turn

Loop 5 Internal loop

Column numbers: 40-41, 82-84 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UU*A-A   10

    
    CU*A-G    7

    
    CA*U-G    4

    
    AG*U-U    3

    
    GG*C-C    3

    
    AA*U-U    2

    
    AC*G-U    2

    
    AU*A-U    2

    
    GC*G-C    2

    
    UA*U-A    2

    
    GC*GGU    1

    
    AG*C-U    1

    
    CC*A-G    1

    
    CG*C-G    1

    
    CG*U-A    1

    
    CU*G-G    1

    
    GA*U-C    1

    
    UU*A-U    1

    
    UU*G-A    1

    
    Omitted sequenced and counts

    
    -U*A-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	97.83	18.87	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	93.48	26.06	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	93.48	20.47	2	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	93.48	18.35	3	1	Intercalated cWS
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	93.48	7.22	2	1	Single bulged G
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	89.13	14.27	2	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	89.13	5.94	4	1
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	84.78	17.54	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	11.30	2	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	8.91	4	1

Loop 6 Internal loop

Column numbers: 45-49, 68-78 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AUU--*CAAUG---AAU    4

    
    UGGA-*CUGUG---AUA    3

    
    CAGAA*UGUUG---A--    3

    
    CAGAG*CGAUG---AAG    2

    
    CU---*CGAUG---AAG    2

    
    GCUA-*GGCUGUUAAAC    1

    
    AGAAG*UAGCA---GCU    1

    
    AGAUA*ACAAU---UAU    1

    
    AUGAG*CGAUG---AAG    1

    
    CAGAG*CAAUG---ACG    1

    
    CAGAG*CGCUG---AAG    1

    
    CCGAG*CAAAG---ACG    1

    
    CGGAG*CGCUG---AUG    1

    
    CGGAG*UGCUG---AUG    1

    
    GAGGU*CAAUA---CUC    1

    
    GGGAG*CUGUG---AUC    1

    
    GUGAG*CGAUG---AUC    1

    
    UAGAA*UGAUG---ACA    1

    
    UCGAG*CAAUG---ACA    1

    
    UCGAG*CGACG---ACA    1

    
    UCGAG*UUAUG---AAG    1

    
    UGGAA*UUAUG---AAG    1

    
    UGGAG*CAAUG---AAA    1

    
    UGGAG*CCGUG---AAA    1

    
    UGGAG*CGUUG---AGA    1

    
    UGGAG*CUGUG---AAA    1

    
    AGAU-*CAACA---GCU    1

    
    UGGA-*CGGGG---AAG    1

    
    CAGAA*AGUUG---A--    1

    
    GUU--*CAAUG---AGC    1

    
    UGG--*AGACG---CGU    1

    
    AGAUU*CAG------CU    1

    
    CA---*CAAUG---AAG    1

    
    CA---*CGAAG---AAG    1

    
    CU---*CGAAG---AGG    1

    
    CU---*CGAGG---AGG    1

    
    UG---*CUAAG---AAG    1

    
    Omitted sequenced and counts

    
    U----*CGAUG---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_69229.3 View motif instance in 3D Basepair signature: cWW-L-tSH-L-tHS-cWW-cWW	47.83	-50.72	5	2.5	Kink-turn
2	Motif group IL_70923.9 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-tHS-tHS-cWW	41.30	-83.82	4	2	Kink-turn
3	Motif group IL_01488.3 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-R-tHS-L-cWW	39.13	-908.81	5	3	Kink-turn
4	Motif group IL_94910.1 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-R-R-L-cWW-L	26.09	-850.57	6	4	Kink-turn
5	Motif group IL_74051.1 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-tHS-cWW-L	15.22	-72.48	6	3	Kink-turn
6	Motif group IL_77045.1 View motif instance in 3D Basepair signature: cWW-L-tSW-L-tHW-cWW-L	15.22	-848.95	7	4.5	Kink-turn
7	Motif group IL_78472.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L-L	13.04	-66.71	8.5	5
8	Motif group IL_74957.1 View motif instance in 3D Basepair signature: cWW-L-cHW-L-cWW-L	10.87	-106.96	7.5	6	cWH basepair with bulged bases
9	Motif group IL_77870.1 View motif instance in 3D Basepair signature: cWW-L-R-L-tHS-L-cWW-L-cWW	8.70	-90.90	7	5
10	Motif group IL_99692.2 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-R-R-L-cWW-L-L	8.70	-130.01	6	5	Kink-turn

Loop 7 Hairpin loop

Column numbers: 51-66 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    -------GGGGUGAUG    5

    
    -------GAGUGGAUA    4

    
    CGAA---ACAAAGACG    3

    
    -------GGAGCCAGU    3

    
    UCGU---AUGGGACAU    2

    
    -------GAGUGGAAA    2

    
    UUAAGGAGAAGAACCU    1

    
    UAUUU--AUGGUACAU    1

    
    UUAUU--AAGGAACGU    1

    
    A------AGAUGAGUU    1

    
    A------AGAUGGAUU    1

    
    A------GAAUGAGAU    1

    
    A------GAAUGAGCU    1

    
    A------GUAUGGGCU    1

    
    C------UGUCUGCUA    1

    
    U------AUUUAAGGG    1

    
    U------GGGUCACCA    1

    
    U------UUAAUGGAA    1

    
    U------UUGUCUGCU    1

    
    -------AAACUGUCU    1

    
    -------AACCGUAAU    1

    
    -------AAGAUGGAU    1

    
    -------AGCACAACA    1

    
    -------AGCCGUGAU    1

    
    -------AGCCGUUGU    1

    
    -------AUCUGACUG    1

    
    -------CUGAUGGGG    1

    
    -------GAGUGGAGA    1

    
    -------GAGUUAAGU    1

    
    -------GGAACCAGU    1

    
    -------GGCUGACAG    1

    
    -------UGGAGCACA    1

    
    -------UGGGUCACA    1

    
    -------UGUUAAGGG    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_66853.7 View motif instance in 3D Basepair signature: cWW-cWS-F-cSH	23.40	-63.88	5	4
2	Motif group HL_45175.1 View motif instance in 3D Basepair signature: cWW-cWS-F-F	21.28	-73.59	5	4	tRNA D-loop
3	Motif group HL_04171.7 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F-F-F	14.89	-89.05	6	5
4	Motif group HL_07951.3 View motif instance in 3D Basepair signature: cWW-F-F	12.77	-249.34	5	5	tRNA D-loop
5	Motif group HL_53454.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F-F	8.51	-69.02	5	4
6	Motif group HL_04642.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	6.38	-64.46	6	5	tRNA D-loop
7	Motif group HL_58224.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	6.38	-67.87	6	5
8	Motif group HL_49941.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	6.38	-70.98	6	5	tRNA D-loop
9	Motif group HL_70658.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F-F	6.38	-89.88	7	6
10	Motif group HL_29762.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	4.26	-57.50	7	5

Loop 8 Internal loop

Column numbers: 111-112, 140-142 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GA*U-U    9

    
    AA*U-U    7

    
    CA*U-G    7

    
    GA*U-C    5

    
    AU*A-U    2

    
    GG*CAU    1

    
    AA*G-U    1

    
    AC*G-U    1

    
    AG*C-U    1

    
    AG*U-U    1

    
    CG*C-C    1

    
    GC*C-U    1

    
    GG*C-U    1

    
    GG*G-C    1

    
    GG*U-C    1

    
    GU*A-U    1

    
    UU*G-G    1

    
    UU*U-U    1

    
    Omitted sequenced and counts

    
    -G*C-A    2

    
    -A*U-U    1

    
    --*A-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	90.70	15.72	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	88.37	18.06	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	86.05	12.81	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	79.07	-1.04	1	1	Single bulged G
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	60.47	9.96	4	1	Intercalated cWS
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	60.47	3.71	3	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	60.47	-0.34	3	1
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	55.81	9.29	3	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	55.81	4.36	3	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	55.81	-1.08	5	1

Loop 9 Internal loop

Column numbers: 119-120, 128-133 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GG*A----C    3

    
    UC*GUUUAG    2

    
    AU*G----U    2

    
    UU*A----A    2

    
    UU*GUAUCG    1

    
    AA*A----A    1

    
    AA*U----U    1

    
    AU*C----G    1

    
    AU*G----C    1

    
    CC*A----U    1

    
    CU*G----G    1

    
    GA*U----G    1

    
    GU*A----C    1

    
    UG*U----G    1

    
    UU*A----G    1

    
    UU*G----G    1

    
    Omitted sequenced and counts

    
    U-*-----A    5

    
    C-*-----U    4

    
    A-*-----U    3

    
    A-*U----U    1

    
    AC*-----A    1

    
    AG*-----C    1

    
    AU*-----U    1

    
    C-*A----G    1

    
    CA*-----G    1

    
    CC*-----G    1

    
    GC*-----A    1

    
    GC*-----U    1

    
    GU*-----A    1

    
    U-*G----C    1

    
    UC*-----U    1

    
    C-*-----A    1

    
    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	61.90	-23.47	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	52.38	-13.23	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	38.10	-36.20	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	33.33	-58.22	2	1	Single bulged G
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	28.57	-25.51	3	1	Intercalated cWS
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	23.81	-17.44	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	19.05	-24.00	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	19.05	-40.59	4	1
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	19.05	-44.73	2	1	Single stack bend
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	19.05	-52.24	2	1	Single stack bend

Loop 10 Hairpin loop

Column numbers: 120-128 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    ---GUCA--    6

    
    GCUGGCC-A    3

    
    ---AUCA--    3

    
    CU-CUUU-G    2

    
    UC-CAUA-A    2

    
    U--AGCA-G    2

    
    UUCCUUAAG    1

    
    AAUCUCA-U    1

    
    AUACUUU-A    1

    
    UCCUUAA-A    1

    
    UCUGGUC-A    1

    
    AC-CAUC-U    1

    
    AGUGACC--    1

    
    CCCAUCG--    1

    
    GCCGAUC--    1

    
    UC-CACU-C    1

    
    UU-CUUU-G    1

    
    UU-GACC-G    1

    
    ---CUCAUU    1

    
    C--CUUA-A    1

    
    CC-AUAA--    1

    
    CC-AUUC--    1

    
    CU-CAUA--    1

    
    CU-CAUU--    1

    
    G--UUCU-U    1

    
    U--CGCA-G    1

    
    UC-GGCC--    1

    
    UG-CGGC--    1

    
    UU-CGGC--    1

    
    ---AGCA-G    1

    
    ---GCUC-A    1

    
    ---AUCG--    1

    
    ---AUCU--    1

    
    ---GCUC--    1

    
    ---GUCG--    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	42.55	-18.87	3	2
2	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	29.79	-35.69	3	2
3	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	29.79	-41.28	3	3
4	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	27.66	-72.50	2	2	Mini UNCG
5	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	25.53	-25.06	3	2
6	Motif group HL_78677.1 View motif instance in 3D Basepair signature: cWW-F-F	25.53	-92.23	3	3
7	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	23.40	-50.45	3	2
8	Motif group HL_66103.1 View motif instance in 3D Basepair signature: cWW-F-F	14.89	-79.44	4	3
9	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	12.77	-80.32	5	4
10	Motif group HL_78347.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F	10.64	-57.45	4	3

Loop 11 Internal loop

Column numbers: 152-154, 168-169 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-U*AC   17

    
    A-G*CU    6

    
    G-U*GC    6

    
    A-C*GU    4

    
    A-U*AU    2

    
    G-C*GC    2

    
    U-G*CA    2

    
    AAU*AU    1

    
    UAU*AA    1

    
    UGU*GA    1

    
    UUU*GA    1

    
    A-A*UU    1

    
    G-C*AC    1

    
    G-C*GU    1

    
    Omitted sequenced and counts

    
    G-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_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	97.83	23.09	5	1	Multiple bulged bases
2	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	97.83	21.85	2	1
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	97.83	18.27	3	1	Major groove platform
4	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	91.30	25.27	2	2	Multiple bulged bases
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	21.63	2	1	Intercalated cWS
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	18.18	2	1	Major groove intercalation
7	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	16.76	3	1	Single stack bend
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	14.58	1	1	Single stack bend
9	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	10.44	4	1
10	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	82.61	10.28	2	1

Loop 12 Hairpin loop

Column numbers: 157-165 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GCUGAAU-C    7

    
    U--GAAUAA    6

    
    U--UAAGAG    6

    
    CC-GAAA-G    4

    
    UC-GAAA-G    4

    
    UC-GAAUAG    3

    
    CC-UAAA-G    3

    
    CU-GAAA-G    3

    
    AA-CAAUAA    1

    
    CU-GAAUAA    1

    
    A--AAAUAU    1

    
    C--GAACAG    1

    
    C--GAAUAG    1

    
    G--AAAAAC    1

    
    G--GAAAAC    1

    
    U--AAAUAA    1

    
    U--CAAUAG    1

    
    U--GAACAA    1

    
    -A-CAAA--    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_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	65.96	13.35	2	2
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	57.45	8.27	2	1
3	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	57.45	7.00	3	2
4	Motif group HL_28075.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	55.32	-0.51	3	2
5	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.19	3.27	3	2
6	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	51.06	-2.88	4	2
7	Motif group HL_18565.1 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F	51.06	-15.57	4	2
8	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	51.06	-243.95	2	1	Pseudoknot geometry
9	Motif group HL_87954.2 View motif instance in 3D Basepair signature: cWW-tSW-F	48.94	-13.73	2	2
10	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	46.81	-25.39	3	2

Loop 13 Internal loop

Column numbers: 185-187, 197-250 - View nucleotides in PDB file(s)

    Scored sequences and counts

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

    
    G-A*GGGGCAAUCA-------------------------------------------G    1

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

    
    Omitted sequenced and counts

    
    --U*-----------------------------------------------------A    7

    
    --A*------------------------------------------------------    4

    
    --A*GUCGGGCGUUUCGC---------------------------------------A    3

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

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

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

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

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

    
    --A*GUCGGGCGUUUCAUACCCGAACACCUCAGCGCCCAAAGCGGUGAGUCGGGUCUA    1

    
    --G*UAGGGCGGUCA------------------------------------------A    1

    
    --U*UGGACGUCCA-------------------------------------------G    1

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

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

    
    CGG*-----------------------------------------------------G    1

    
    GGU*-----------------------------------------------------A    1

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

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

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

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

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

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

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

    
    A-A*------------------------------------------------------    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	80.00	-1667.82	2	1	Major groove platform
2	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-137.89	3	1	Major groove intercalation
3	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	20.00	-2138.98	3	2	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2141.92	4	1
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2149.33	4	1	Intercalated cWS
6	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	20.00	-2156.52	3	1	Multiple bulged bases
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2158.79	4	1
8	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2161.85	5	1
9	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2162.03	2	1	Single bulged G
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	20.00	-2164.24	2	1	Single stack bend

Loop 14 Hairpin loop

Column numbers: 189-195 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CGUUCGC    4

    
    UGUCGAA    3

    
    UUUACAU    2

    
    CGUCCUG    1

    
    CGUUCCU    1

    
    UAAUGUA    1

    
    UAUUCAC    1

    
    UCCCCAG    1

    
    UGUCCGU    1

    
    UUUCCCG    1

    
    UUUUGAU    1

    
    AAUUUU-    1

    
    UCUGAU-    1

    
    UAAUA--    1

    
    AAGA---    1

    
    UAAU---    1

    
    UGUU---    1

    
    UUUU---    1

    
    U-AU---    1

    
    Omitted sequenced and counts

    
    A------   10

    
    U------   10

    
    C------    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 HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	24.00	-34.66	4	2
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	24.00	-37.76	3	2
3	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	24.00	-41.87	3	2
4	Motif group HL_08100.1 View motif instance in 3D Basepair signature: cWW-F-F-F	24.00	-55.69	4	2
5	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	24.00	-68.26	3	2	Mini UNCG
6	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	20.00	-48.97	5	3
7	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	20.00	-70.63	3	2	Mini UNCG
8	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	20.00	-424.12	4	3
9	Motif group HL_37369.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F	20.00	-1279.38	4	3
10	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	20.00	-1717.67	3	2	Pseudoknot geometry with 3' bulge