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: 26-39, 85-94
Loop 4IL Column numbers: 40-41, 82-84
Loop 5HL Column numbers: 46-77
Loop 6IL Column numbers: 111-112, 140-142
Loop 7HL Column numbers: 119-133
Loop 8IL Column numbers: 152-154, 168-169
Loop 9HL Column numbers: 157-165
Loop 10HL Column numbers: 183-252

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: 26-39, 85-94 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    G-AAGA--GUA--G*U-GGAAGG-C    3

    
    A-AUGA--CUA--A*U-GAAAGG-U    2

    
    C-AUCA--GUA--A*U-GAAAGG-G    2

    
    C-A--A--GUAA-C*U-GAGGGG-G    2

    
    C-AG----GUA--A*C-GAGGGG-G    2

    
    U-AUGAAUCUACGC*G-AGGAGG-A    1

    
    U-AUGA--AUC---*UAGAGGGGGA    1

    
    UCAAGA--GUA--A*U-GAAAGG-G    1

    
    UCAUCA--GUA--G*C-GAAAGG-G    1

    
    A-AAAA--GUA--G*U-GAAAGG-U    1

    
    A-AAGA--GUA--A*U-GAAAGG-G    1

    
    A-AAGA--GUA--A*U-GAAAGG-U    1

    
    A-AUAA--GUA--U*G-GAAAGG-U    1

    
    A-AUUA--GUA--A*U-GAAAGG-U    1

    
    A-AUUA--GUA--A*U-GGAAGG-U    1

    
    C-AAGA--GUA--C*G-GAAAGG-G    1

    
    C-AAGA--GUA--G*C-GAAAGG-G    1

    
    C-AAGA--GUA--G*U-GAAAGG-G    1

    
    C-AAGA--GUA--U*U-GAAAGG-G    1

    
    C-AAGA--GUC--G*U-UAAAGG-G    1

    
    C-AAUA--GUA--G*U-GAACGG-G    1

    
    C-ACAA--GUA--A*U-GAACAG-G    1

    
    C-ACUA--GUA--A*C-GAACAG-G    1

    
    C-ACUA--GUA--A*U-GAACAG-G    1

    
    C-AUCA--GUA--U*A-GAAAGG-G    1

    
    C-AUGA--GUA--A*U-AAAAGG-G    1

    
    C-AUGA--GUA--A*U-GAAAGG-G    1

    
    C-AUUA--GUA--A*U-GAAAGG-G    1

    
    G-AUAA--GUA--C*G-GAAAGG-C    1

    
    G-AUAA--GUA--U*G-GAAAGG-C    1

    
    G-AUGA--GUC--A*U-AAAAGG-C    1

    
    G-AUGA--GUC--G*C-AAAAGG-C    1

    
    U-AAGA--GUA--G*A-GAAAGG-A    1

    
    U-AUAA--GUA--A*U-GAAAGG-A    1

    
    U-AUAA--GUA--U*A-GAAAGG-A    1

    
    U-AUAA--GUA--U*G-GAAAGG-A    1

    
    U-AUAA--GUA--U*U-GAAAGG-A    1

    
    C-AG----GUAA-C*U-GAGGGG-G    1

    
    A-A-----GUAA-C*U-GAGGGG-G    1

    
    C-AG----GUA--G*U-GAGGGG-G    1

    
    GCAU----GUA--U*A-GAA-GG-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_34470.3 View motif instance in 3D Basepair signature: cWW-cSH-cWW-tHH-tWH-tHS-cWW-tSH-R-cWW-L	78.72	26.78	4	2	9x8 Sarcin-Ricin with GA cWW pair; G-bulge
2	Motif group IL_70670.1 View motif instance in 3D Basepair signature: cWW-R-L-R-L-R-L-R-L-R-L-R-tWH-L-R-L	17.02	-34.55	8	5	9x9 Sarcin-Ricin with pseudoknotted region; G-bulge

Loop 4 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 5 Hairpin loop

Column numbers: 46-77 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UU----------GGGGUGAUGCCAAUG---AA    4

    
    GGA---------GGAGCCAGUCCUGUG---AU    3

    
    AGAAGUCGU---AUGGGACAUGUGUUG---A-    2

    
    AGGUGUUAAGGAGAAGAACCUCCAAUA---CU    1

    
    AGAAGCGAA---ACAAAGACGCUGAUG---AC    1

    
    AGAAGUAUUU--AUGGUACAUAAGUUG---A-    1

    
    AGAAGUUAUU--AAGGAACGUGUGUUG---A-    1

    
    CGAGGCGAA---ACAAAGACGCCAAUG---AC    1

    
    CGAGGCGAA---ACAAAGACGCCGACG---AC    1

    
    AGAGGU------AUUUAAGGGCCGAUG---AA    1

    
    CGAGGA------GUAUGGGCUCUUAUG---AA    1

    
    CUA---------GGCUGACAGGGGCUGUUAAA    1

    
    GAUAAU------UUGUCUGCUAACAAU---UA    1

    
    GGAAGU------GGGUCACCACUUAUG---AA    1

    
    GGAGAA------AGAUGAGUUUCCGUG---AA    1

    
    GGAGAA------GAAUGAGCUUCAAUG---AA    1

    
    GGAGAU------UUAAUGGAAUCUGUG---AU    1

    
    GGAGGA------GAAUGAGAUCCGUUG---AG    1

    
    UGAGGA------AGAUGGAUUCCGAUG---AA    1

    
    AGAGG-------AGCCGUGAUCCGCUG---AA    1

    
    AGAGG-------AGCCGUUGUCCAAUG---AC    1

    
    AGAGG-------UGUUAAGGGCCGAUG---AA    1

    
    CGAGU-------UGGAGCACAACAAAG---AC    1

    
    GAAGA-------AUCUGACUGCUAGCA---GC    1

    
    GGAGA-------AAGAUGGAUUCUGUG---AA    1

    
    GGAGA-------UGGGUCACAUUGCUG---AU    1

    
    GGAGG-------AACCGUAAUCCGCUG---AU    1

    
    UGAGG-------CUGAUGGGGCCGAUG---AU    1

    
    GAU---------AAACUGUCUGCAACA---GC    1

    
    GAUUAC------UGUCUGCUAACAG------C    1

    
    GGA---------GGAACCAGUCCGGGG---AA    1

    
    GG----------AGCACAACAAAGACG---CG    1

    
    UU----------GGGGUGAUGCCAAUG---AG    1

    
    A-----------GAGUGGAUAACAAUG---AA    1

    
    A-----------GAGUGGAUAACGAAG---AA    1

    
    G-----------GAGUUAAGUGCUAAG---AA    1

    
    U-----------GAGUGGAAAACGAUG---AA    1

    
    U-----------GAGUGGAAAGCGAUG---AA    1

    
    U-----------GAGUGGAGAACGAGG---AG    1

    
    U-----------GAGUGGAUAACGAAG---AG    1

    
    ------------GAGUGGAUAACGAUG---A-    1

No Matches Found View All Results for this Loop

Loop 6 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 7 Hairpin loop

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

    Scored sequences and counts

    
    C---GUCA------U    4

    
    GGCUGGCC-A----C    3

    
    UCU-CUUU-GUUUAG    2

    
    UUC-CAUA-A----A    2

    
    AU--AGCA-G----U    2

    
    A---GUCA------U    2

    
    U---AUCA------A    2

    
    UUU-CUUU-GUAUCG    1

    
    CUUCCUUAAG----G    1

    
    AAUACUUU-A----A    1

    
    GAAUCUCA-U----G    1

    
    GUCUGGUC-A----C    1

    
    UUCCUUAA-A----G    1

    
    AAC-CAUC-U----U    1

    
    AGCCGAUC------C    1

    
    AUC-CACU-C----G    1

    
    CAGUGACC------G    1

    
    CCCCAUCG------G    1

    
    UUU-GACC-G----G    1

    
    A---CUCAUU----U    1

    
    ACC-AUAA------A    1

    
    AU--CGCA-G----C    1

    
    AUU-CGGC------U    1

    
    CC--CUUA-A----U    1

    
    GCC-AUUC------A    1

    
    GCU-CAUA------U    1

    
    GUG-CGGC------A    1

    
    UCU-CAUU------U    1

    
    UG--UUCU-U----G    1

    
    C---GCUC-A----G    1

    
    U---AGCA-G----C    1

    
    UUC-GGCC-------    1

    
    A---GUCG------U    1

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

    
    U---AUCG------A    1

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

    
    U---GCUC------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_78347.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F	27.66	-84.69	5	3
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	27.66	-129.25	4	3
3	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	27.66	-775.23	4	3
4	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	25.53	-88.63	3	2
5	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	25.53	-142.78	5	3
6	Motif group HL_56676.1 View motif instance in 3D Basepair signature: cWW-F-F	25.53	-190.87	5	3
7	Motif group HL_71391.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	23.40	-188.81	5	3
8	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	23.40	-782.53	4	3	Pseudoknot geometry
9	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	23.40	-834.89	4	3
10	Motif group HL_47787.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	21.28	-159.78	4	3

Loop 8 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 9 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 10 Hairpin loop

Column numbers: 183-252 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAG    3

    
    GAA-UUUGUCGAAAU----------------------------------------------------UUC    3

    
    UA--UAUUUACAUU-----------------------------------------------------AAA    2

    
    GA--AACGUUCGCAGUCGGGCGUUUCAUACCCGAACACCUCAGCGCCCAAAGCGGUGAGUCGGGUCUACA    1

    
    GGG-AUUGUCCGUAGGGGCAAUCA-------------------------------------------GCA    1

    
    GU--GCCGUUCCUUUAGGGCGGUCA------------------------------------------ACA    1

    
    GA--UUCGUCCUGAUGGACGUCCA-------------------------------------------GCA    1

    
    AAG-GCUCCCCAGGC----------------------------------------------------CUU    1

    
    GA--GGUUUCCCGAGC---------------------------------------------------CUU    1

    
    UA--UAUAUUCACAUU---------------------------------------------------AAA    1

    
    UA--UUUAAUGUA------------------------------------------------------UAA    1

    
    UC--AUUUUUGAU------------------------------------------------------UAA    1

    
    AGCGGAUGUU---------------------------------------------------------GCU    1

    
    AUG-GUUAAUA--------------------------------------------------------ACC    1

    
    AUGGUUAAGA---------------------------------------------------------ACC    1

    
    UC--UUAAUUUU-------------------------------------------------------AAA    1

    
    UU--UUUCUGAU-------------------------------------------------------UAA    1

    
    UCA-AAUAAU---------------------------------------------------------CGG    1

    
    UC--UUUUUU---------------------------------------------------------AAA    1

    
    UA--UUU-AU---------------------------------------------------------CCA    1

    
    CUA-GAA------------------------------------------------------------UAG    1

    
    AA--UCA------------------------------------------------------------UUU    1

    
    CA--GCG------------------------------------------------------------CCG    1

    
    CGG-UGC-------------------------------------------------------------CG    1

    
    GA--UUU------------------------------------------------------------AUU    1

    
    UC--CUU------------------------------------------------------------GUA    1

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

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

    
    UU--UAA------------------------------------------------------------AAA    1

    
    UU--UUA------------------------------------------------------------AGA    1

    
    AA--UCA-------------------------------------------------------------UU    1

    
    AU--AAA-------------------------------------------------------------GU    1

    
    UU--CAA-------------------------------------------------------------UA    1

    
    UUA-ACA--------------------------------------------------------------G    1

    
    AU--GCU--------------------------------------------------------------U    1

    
    GA--CCU--------------------------------------------------------------C    1

    
    GC--UUU--------------------------------------------------------------U    1

    
    GU--AUU--------------------------------------------------------------C    1

    
    UA--AAU--------------------------------------------------------------G    1

    
    ----AUU---------------------------------------------------------------    1

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

    
    ----UUA---------------------------------------------------------------    1

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

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	17.02	-3189.77	6	5
2	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	14.89	-2483.22	6	5
3	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	12.77	-1838.12	5	4
4	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	12.77	-4049.32	6	6
5	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	12.77	-5364.07	6	6
6	Motif group HL_77436.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	10.64	-1210.74	5	4	T-loop related
7	Motif group HL_25967.2 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F	10.64	-2457.49	7	5
8	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	10.64	-3144.40	6	4
9	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	10.64	-3155.57	6	4
10	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	10.64	-4055.91	7	6