RNA 3D Hub

JAR3D Query RF02984-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF02984 DUF3800-X RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
((((((...............................................((((((((...............................(((((................)))))...............)))))))).))))))
>URS0000D66C3C_12908/1-95
UUACAA-GUAAA----------------------------------------UCCCUUCCAGAAA---G---GAGA---CCUCUCACGAGGCACUUCACCGCCAUGU-GUAGUGGAGUAUCGUUA--CGAGUAUGGAAGGUAUUGUAA
>URS0000D6C323_12908/1-69
GUAUGA-GUAAG-----------------------------------------U-CGCAAUGAAA---GAAUGAUG----------------UCUCA------GGA-------UGAGA-UUAGGA--CGAGUAAUUACG-GUUCAUAC
>URS0000D68BF5_12908/1-72
AUGCGU-GUAAG-----------------------------------------ACCUGCCCGAAG---CAAUGAAG----------------GCCGA-----GGAG-------UCGGU-ACGGGAG-UGUGUAGGGCAGGC-UCGCAA
>URS0000D65D1C_12908/1-72
ACGCGC-AUAAG-----------------------------------------ACCUGUCCGAGG---CUAUGAUG----------------CCCAU-----GGAC-------UUGGG-AUGGGAG-CGAGUAGGACAGGC-ACGCAC
>URS0000D66678_12908/1-77
UUGCGA-GUAAG-----------------------------------------UCCCUUCCGAAGUAUAAAUGGGUG---------------GCACC-----UUGA-------GGCGA-CCGCGAC-GCAGUAGGAAGGGGUUCGCAA
>URS0000D6A211_12908/1-72
UAGUGA-GUAAG-----------------------------------------UCCCGUUCGAAC---CUAUGAUG----------------CCUGU-----GUUU-------UCAGG-AUGGGA--GAAGUAGAGCGGGGAUCACGG
>URS0000D67D2B_589924/1-93
AGGCGG-GUAAGGUC------GGGGC-------CUACUAU-------GCCCCCCUCCGUCCGAAA---CGAUGAGG----------------CCUCC-----UUGA-------GGAGG-GUGGGAU-GGAGUAGGACGGGG-CCGCCG
>URS0000D6593E_387631/1-71
UAUGGG-GUAAG-----------------------------------------UCCCAC-CGAAA---CGAUGAGG----------------CCUCC-----UUGA-------GGAGG-GUGGGAU-GGAGUAG-GUGGGGUCCCGUU
>URS0000D6CDB1_12908/1-86
-GGGGAGGUAAGGUC------GGCGA---------------------UAGCCCCUCCGGCCGAAA---CGAUGAGG----------------CUCAC-----GUAA-------GUGGG-GUGGGAU-GGAGUAGGCCGGGGCUCCCC-
>URS0000D6CDD9_12908/1-86
UAGGGG-GUAAGGUC------GGC---------GAUA------------GCCCCUCCGUCCGAAA---CGAUGAGG----------------CCCGC-----GUAA-------GCGGG-GUGGGAU-GGAGUAGGAUGGGG-CCCCUU
>URS0000D6728D_12908/1-86
UAGGGG-GUAAGGUC------GGCGA---------------------UAGCCCCUCCGUCCGAAA---CGAUGAGG----------------CCCGC-----GUAA-------GCGGG-GUGGGAU-GGAGUAGGACGGGG-CCCCUU
>URS0000D68278_12908/1-72
CUGCGA-GUAAG-----------------------------------------GCCCGUCCGAGG---CUGUGAUG----------------CCUGC-----GGCU-------GCGGG-AUGGGA--GCAAUAGGACGGGGUUCGCAC
>URS0000D669D9_12908/1-73
UUGCGU-GUAAA----------------------------------------GACCCACCCGAGG---CAAUGAUG----------------CCUGC-----GUAU-------GUAGG-AUGAGG--GUAAUAGGGUGGGCAACGCAA
>URS0000D6AB0D_12908/1-73
AUGCGU-GUAAA----------------------------------------GACCCAUCCGAGG---CAGUGAUG----------------CUCGC-----GUAU-------GCGGG-AUGGGA--GUAAUAGGGUGGGCAACGCAC
>URS0000D68EB1_12908/1-78
UGGUGG-UUAAACCACUAGAA-------------------------------CUCCGCCCC-AAA---GGAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGAC--GA--AGGGGAGGA-CCACCA
>URS0000D69E33_12908/1-78
UUGUGG-UUAAACCACUGGAA-------------------------------CUCCGCCCC-AAA---GGAUGAUG----------------UCCGU-----GGAU-------ACGGA-AUGGGAC-GA---AGGGGAGGA-UCACAU
>URS0000D69D98_12908/1-96
GGGCGG-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----GCCCGC-CGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CUGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D6BC09_12908/1-96
GGGCGG-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----GCCCGC-CGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D66F69_12908/1-84
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCCGCUCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAG-GCGGGUGCCGCCC
>URS0000D6BDFE_12908/1-83
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCC-GCCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAA-CGAGUAGGC-GGGUGCCGCCC
>URS0000D68FCE_12908/1-83
GGGCGG-UUAAAC--------GUCGC---------------------GCGACGGCCC-GCCGAAA---GGAUGAGC----------------CCGCC-----GGAC-------GGCGG-CCGGGAG-CGAGUAGGC-GGGUGCCGCCC
>URS0000D69C8F_12908/1-71
UAGUGA-GUAAG-----------------------------------------UCCUGU-UGAAC---GAAUGACG----------------CCUCA-----GGAAU------GGAGG-UCAGGA--CAAGUAA-ACAGGGUUCACUU
>URS0000D678ED_12908/1-70
UAACGA-GUAAG-----------------------------------------UCCUGC-UGAAA---GGAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAA-GCAGGGUUCGUUU
>URS0000D67FFC_12908/1-70
CAACGA-GUAAG-----------------------------------------UCCUGC-UGAAA---GGAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAA-GCAGGGUUCGUUC
>URS0000D66005_12908/1-70
UAACGA-GUAAG-----------------------------------------UCCU-ACUGAAC---GAAUGACG----------------GCUCA-----GGAU-------UGAGC-UCAGGA--CCAGUAAGUAGGG-GUCGUUA
>URS0000D6631F_12908/1-89
GGGUGG-GUAACC--------GCGGG-------AAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCU-----GGAU-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D6BEEA_12908/1-89
GGGUGG-GUAACC--------GCGGG-------GAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCC-----GGAU-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D6A83A_12908/1-89
GGGUGG-GUAACC--------GCGGG-------GAUA----------CCCGCCUCCUCCCCGAAA---GGGUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCAGAG-CGAGUAGGGGAGGGGCCACCU
>URS0000D67063_12908/1-104
GGGUGG-GUAACU--------GCGGG--CCCGGCGCACG-CCGGGAACCUGCCUCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCGGAGGCGAGUAGGGGAGGGGCCACCU
>URS0000D65BFA_12908/1-102
-GGUGG-GUAACU--------GCGGG--CCCGGCGCACA-CCGGGAACCUGCCUCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-ACCGGAGGCGAGUAGGGGAGGGGCCACC-
>URS0000D6B860_12908/1-97
GGGCGA--UAAU---------UGCGCCCGGU--GCGG-----AGCGGGCGCAUCCCGCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAC-------GGCGG-UCCGGAGGCGAGUAGGGGCGGU-UCGCCC
>URS0000D6A8FE_12908/1-90
GGGCGG-GUAAA----------GCGGA------GGAA---------UCCGCUUCCCUCCCCGAAA---GUAUGAGG----------------CCGCC-----GGAG-------GGCGG-UCCGGAGCCGAGUAGGGGAGGUCCCGCCC
>URS0000D6D1B9_12908/1-72
UAGUGA-AUAAA-----------------------------------------UCCUGUUCGAAA---UGAUGAUG----------------CCUGC-----AUUA-------GUGGG-UUAGGA--AAAGUAGAACAGGUAUCACAG
>URS0000D668EC_12908/1-73
CAGUGA-GUAAG-----------------------------------------UCCCUCUUGAAAA--GAAUGAGG----------------CUAC------UUUGGU------GUGG--UGUGAC-GAAGUAAAGAGGGCUUCACUC
>URS0000D65A59_12908/1-84
AGGUGA-CUAAUG--------CCC---------AUAA------------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D6A2DC_12908/1-84
AGGUGA-CUAAUG--------CCC---------AUAA------------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GUGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D675F0_12908/1-84
AGGUGA-CUAAUG--------CCC---------AUCAA-----------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGA-GAUUCACCA
>URS0000D6B36B_12908/1-85
AGGUGA-CUAAUG--------CCC---------AUCAA-----------GGGGUCUUUCCCGAAA---GAAUGAUG----------------CCCGU-----GGAU-------GCGGG-AUGGGA--CAAGUAGGGGGAGAUUCACCA
>URS0000D68B80_12908/1-72
UGGUGA-GUAAG-----------------------------------------GCUC-CCAGAAA---GAAUGAUG----------------UCCGU-----GGAC-------GCGGG-AUGGGAU-CAAGUAAGGGGAGGUUCACCA
>URS0000D6CEA6_868131/1-71
AAGUGA-GUAAG-----------------------------------------UCCC-CCAGAAA---GGAUGAUG----------------UCCAC-----GUAU-------GUGGA-GUGGGA--CGAGUACGGUGGGGUUCACUU
>URS0000D67A2C_12908/1-80
AGGUGA-GUAAG-----------------------------------------UCCU-CCCGAAA---UAAUGAUGAUG-------------CCAUGAC---UAAUU----GACAGGG-GUGGGAG-CAAGUAGGGGAGGGUUCAGCU
>URS0000D6C25E_12908/1-72
UGGUGA-GUAAG-----------------------------------------UCCU-CCCGAAA---GGAUGAUG----------------CCAUG-----UUGA-------CAUGG-GUGGGAG-CGAGUAGGGAAGGGUUCACCA
>URS0000D69A07_12908/1-75
UAGUGUUGUAAG-----------------------------------------ACCCUUCUGAAAA--GGAUGAUG----------------CCACC-----GAUU-------GGUGG-ACGUGAC-GAAGUAAGGAGGGGUUCACUA
>URS0000D66B3A_12908/1-75
UAGUGUUGUAAG-----------------------------------------ACCCUCCUGAAAA--GGAUGAUG----------------CCACC-----CAUU-------GGUGG-ACGUGAC-GAAGUAUGGAGGGGGUCACUA
>URS0000D66553_12908/1-75
UAGUGUUGUAAG-----------------------------------------UCCCUUCCGAAAA--GGAUGAUG----------------CCACC-----AAUU-------GGUGG-ACGUGAC-GAAGUACGAAGGGGUUCACUA
>URS0000D6B639_12908/1-78
UAGUGUUGUAAGAGU--------------------------------------UCCCUCCUGAAAA--GGAUGAUG----------------CUGCC-----UAUU-------GGCAG-GCGUGAC-GAAGUAGGGUGGGGUUCACUA
>URS0000D667A3_12908/1-74
UCGUGG-GUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----GUGA-------GGUGG-GUGGGAC-AAAGUAGGAGAGGGGCCACUU
>URS0000D68C85_12908/1-74
UGGUGA-AUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----UUGA-------GGUGG-GUGGGAC-AAAGUAGGAAAGGGAUCACAA
>URS0000D6ABC4_12908/1-74
UAGUGA-GUAAG-----------------------------------------UCCUUUCCGAAAC--GGAUGAGG----------------CCACC-----AUGA-------GGUGG-GUGGGAC-AAAGUAGGAAAGGGUUCACUU
>URS0000D67076_12908/1-74
UAGUGA-GUAAG-----------------------------------------ACCUUUCUGAAAC--GGAUGAGG----------------CCACC-----UUGA-------GGUGG-GCGGGAC-AAAGUAGGAAAGGGUUCACGU
>URS0000D69096_12908/1-74
CUGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAC--GGAUGAGG----------------CUACC-----UUGA-------GGUAG-AUGGGAC-AAAGUAGGGAAGGGUUCACAC
>URS0000D6CA26_368407/1-74
UAGUGA-GUAAA-----------------------------------------UCCUUCCUGAAAA--GGAUGAGG----------------CCGCC-----UUGA-------GGCGG-GUGGGAC-AAAGUAAGGAAGGGGUCACUA
>URS0000D658E7_12908/1-74
UUGUGA-GUAAA-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----UUGA-------GGCGG-GUGGGAC-AAAGUAGGGAAGGGGUCACGU
>URS0000D6CDCF_12908/1-75
UAGUGUUGUAAG-----------------------------------------UCCUUCCUGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAAGGAAGGGUUCACUA
>URS0000D6B65C_12908/1-75
UAGUGUUGUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAAGGAAGGGUUCACUA
>URS0000D668F4_12908/1-75
UAGUGCUGUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAGG----------------CCGCC-----CUGA-------GGCGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUA
>URS0000D6C134_28892/1-74
CAGCGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----GUAA-------GGUGG-GUGGGAC-GAAGUAGGGAAGGGUUCACUG
>URS0000D67465_12908/1-74
UAGUGA-GUAAG-----------------------------------------UCCUUCCC-AAAAA-GGAUGAUG----------------CCACC-----UUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUG
>URS0000D68B04_12908/1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAC--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-AAAGUAGGGAAGGGUUCACUG
>URS0000D6D3FC_12908/1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUA----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACGU
>URS0000D6C442_12908/1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGGUCACUA
>URS0000D66EEE_12908/1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUU
>URS0000D6BF74_12908/1-74
CAGUGA-GUAAG-----------------------------------------UCCUUCCCGAAAA--GGAUGAUG----------------CCACC-----CUGA-------GGUGG-AUGGGAC-GAAGUAGGGAAGGGUUCACUA
>URS0000D6A168_12908/1-74
ACGUGA-GUAAG-----------------------------------------UCCUUUCCGAAAC--GAAUGAUG----------------CUACC-----UUGA-------GGUAG-GUGGGAC-AAAGUAGGGAAGGGGUCACAU
>URS0000D68283_12908/1-72
GAGCGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----CAUG-------AGCAG-GUGGGA--CGAUUAGAGAGGGGUUCACCA
>URS0000D66BE9_12908/1-72
GAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----CAUG-------AGCAG-GUGGGA--CGAUUAGAGAGGGGUUCACCA
>URS0000D67888_12908/1-72
UAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----UAUU-------AGCAG-GUGGGA--CAAUUAGAGAGGGGUUCACUA
>URS0000D69DB6_12908/1-72
AAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAA---GGAUGAUG----------------CUGCU-----UAUU-------AGCAG-GUGGGA--CAAUUAGAGAGGGGUUCACUA
>URS0000D6AECF_12908/1-73
AGGUGA-GUAAG-----------------------------------------UCCCUCUCGAAAA--GAAUGAGG----------------CCGCC-----AAUU-------GGCGG--GGGGAC-GAAGUAGAGAGGGGUUCACUA
>URS0000D67AAD_12908/1-75
UAGUGCUGUAAG-----------------------------------------UCCCUCUCGAAAA--GAAUGAGG----------------CCGCC-----AAUU-------GGCGG-GUGGGAC-GAAGUAGAGAGGGGUUCGCUA
>URS0000D6909D_12908/1-74
GAGUGA-GUAAG-----------------------------------------UCCCUCUCGAAAA--GGAUGAGG----------------CCGCC-----AAUU-------AGCGG-GUGGGAC-GAAGUAGAGAGGGGGUCGCUA
>URS0000D67DE1_12908/1-74
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAAA--GAAUGAGG----------------CCUAU-----GGAA-------GUAGG-AUGGAAG-CGAGUAGGGCAGGGUUUACCA
>URS0000D6B01C_12908/1-73
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAA---GAAUGAGG----------------CCUAC-----GGAA-------GUAGG-AUGGGAG-CGAGUAGGGCAGGGUUUACCA
>URS0000D6C3DB_12908/1-73
UGGUAA-GUAAG-----------------------------------------ACCUGCCCGAAA---GAAUGAGG----------------CCUAU-----GGAA-------GUAGG-AUGGGAG-CGAGUAGGGCAGGAUUUACCA
>URS0000D6892D_12908/1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCUGAAA---GGAUGAUG----------------UCCAC-----GUAG-------GUGGA-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D67E45_12908/1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGC-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D66E2B_12908/1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGU-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCA
>URS0000D6CFB4_12908/1-72
UGGUGA-GUAAG-----------------------------------------UCCU-UCCGAAA---GGAUGAUG----------------CCUGU-----GGAC-------GCAGG-AUGGGAG-CGAGUAGGAAAGGGUUCACCG
>URS0000D69350_12908/1-73
UGGUGA-GUAAG-----------------------------------------UCUUGCCCGAAA---GGAUGAGG----------------CCUGU-----GGAG-------ACAGG-AUGGGAG-CGAGUAGGGCAAGGUUCACCA
>URS0000D6D265_868131/1-71
CAGUGA-GUAAG-----------------------------------------UCCU-UUCGAAA---GAAUGAGG----------------CCCGU-----GGAC-------ACGGG-GUGGGA--CAAGUAGGAAUGGGUUCACCU
>URS0000D6ABC6_12908/1-71
AGGUGA-GUAAG-----------------------------------------UCCU-UCUGAAA---GAAUGAGG----------------CCCGU-----GGAU-------ACGGG-GUGGGA--UGAGUAAGAAAGGGUUCACCU
>URS0000D681B1_12908/1-72
AAGUGA-GUAAG-----------------------------------------UCCUCCCUGAAA---GAAUGAGG----------------CUGCC-----GGAU-------GGUGG-AUGGGA--CAAGUAAGAGAGGGUUCACGA
>URS0000D69953_323259/1-72
AAGUGA-GUAAG-----------------------------------------UCCUCCCUGAAA---GAAUGAGG----------------CUGCC-----GGAU-------GGUGG-AUGGAA--CAAGUAAGAGAGGGUUCACGA
>URS0000D6CD98_12908/1-72
CUGCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUGAUG---------------CCCGC------ACUU--------GUGGAAUGGGA--GUACUAUGAUAGGGGUCGCAG
>URS0000D6D0E7_12908/1-72
UUGCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUGAUG----------------CCCGC-----GCUU-------GUGGG-AUGGGA--GUAUUAGAAUAGGGAUCGCGA
>URS0000D670E1_12908/1-72
UCUCGA-GUAAG-----------------------------------------UCCUAUCCGAGG---CAAUAAUG----------------CCCGC-----GCUU-------GUGGG-AUGGGA--GCAUUAGGAUAGGGGUCGCGU
>URS0000D6C2BA_12908/1-72
CAGCGA-GUAAG-----------------------------------------UCCUAUUCGAAC---CAAUGAUG----------------CCUGC-----AUUA-------GUGGG-AUGGGA--GAACUAGGGUAGGGGUCGCUU
>URS0000D6BC49_12908/1-72
UAGCGA-GUAAA-----------------------------------------GCCUAUCCGAAA---CAAUGAUG----------------CCUGC-----AUUA-------GUGGG-UUAGGA--GGAUUAGGAUAGGGGUCGCUU

There are no chains in PDB that we map to Rfam family RF02984.

Jump to results for:

  • Loop 1IL Column numbers: 6-54, 141-143
  • Loop 2IL Column numbers: 61-93, 118-134
  • Loop 3HL Column numbers: 97-114

Loop 1 Internal loop

Column numbers: 6-54, 141-143 
    Scored sequences and counts

    
    A-GUAAG-----------------------------------------U*GUU   30

    
    A-GUAAG-----------------------------------------U*GGU    6

    
    G-UUAAAC--------GUCGC---------------------GCGACGG*UGC    3

    
    UUGUAAG-----------------------------------------U*GUU    3

    
    A-GUAAG-----------------------------------------A*GUU    3

    
    G-UUAAA------------CGUCGCGUGCUAUUUUCGCGCGACG----G*UGC    2

    
    G-GUAACC--------GCGGG-------GAUA----------CCCGCCU*GGC    2

    
    A-CUAAUG--------CCC---------AUCAA-----------GGGGU*AUU    2

    
    A-CUAAUG--------CCC---------AUAA------------GGGGU*AUU    2

    
    CUGUAAG-----------------------------------------U*GUU    2

    
    U-GUAAA----------------------------------------GA*CAA    2

    
    A-GUAAA-----------------------------------------U*GGU    2

    
    A-GUAAG-----------------------------------------G*GUU    2

    
    A-GUAAG-----------------------------------------U*GAU    2

    
    G-GUAACU--------GCGGG--CCCGGCGCACA-CCGGGAACCUGCCU*GGC    1

    
    G-GUAACU--------GCGGG--CCCGGCGCACG-CCGGGAACCUGCCU*GGC    1

    
    A--UAAU---------UGCGCCCGGU--GCGG-----AGCGGGCGCAUC*U-U    1

    
    G-GUAAGGUC------GGGGC-------CUACUAU-------GCCCCCC*G-C    1

    
    G-GUAAA----------GCGGA------GGAA---------UCCGCUUC*UCC    1

    
    G-GUAACC--------GCGGG-------AAUA----------CCCGCCU*GGC    1

    
    AGGUAAGGUC------GGCGA---------------------UAGCCCC*GCU    1

    
    G-GUAAGGUC------GGC---------GAUA------------GCCCC*G-C    1

    
    G-GUAAGGUC------GGCGA---------------------UAGCCCC*G-C    1

    
    G-UUAAACCACUAGAA-------------------------------CU*A-C    1

    
    G-UUAAACCACUGGAA-------------------------------CU*A-U    1

    
    UUGUAAGAGU--------------------------------------U*GUU    1

    
    A-GUAAA----------------------------------------UC*UAU    1

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

    
    UUGUAAG-----------------------------------------A*GUU    1

    
    A-AUAAA-----------------------------------------U*UAU    1

    
    A-AUAAG-----------------------------------------U*GAU    1

    
    A-GUAAA-----------------------------------------G*GGU    1

    
    A-GUAAG-----------------------------------------A*AUU    1

    
    A-GUAAG-----------------------------------------U*CUU    1

    
    G-GUAAG-----------------------------------------U*GGC    1

    
    G-GUAAG-----------------------------------------U*GUC    1

    
    A-GUAAG-----------------------------------------U*-GU    1

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

    
    U-GUAAG-----------------------------------------A*C-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_74957.1

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

51.14 -1106.49 5 2

cWH basepair with bulged bases

2

Motif group IL_43622.1

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

40.91 -1671.61 4.5 2

3

Motif group IL_82706.1

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

7.95 -1426.73 8 4

4

Motif group IL_52743.1

Basepair signature:
cWW-tSW-L-cSW-L-cWW-L

4.55 -1537.16 7 3

5

Motif group IL_88082.1

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

4.55 -1611.46 6 4

6

Motif group IL_38186.6

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

4.55 -1994.90 6 2

7

Motif group IL_64842.1

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

2.27 -1020.26 7 5

8

Motif group IL_37603.1

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

1.14 -920.89 8 5

9

Motif group IL_51191.1

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

1.14 -1460.02 7 5

10

Motif group IL_25412.1

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

1.14 -1779.19 8 4

Major groove intercalation

Loop 2 Internal loop

Column numbers: 61-93, 118-134 
    Scored sequences and counts

    
    CGAAA---CGAUGAGG----------------C*G-GUGGGAU-GGAGUAG    5

    
    CGAAA---GAAUGAUG----------------C*G-AUGGGA--CAAGUAG    4

    
    CGAAAA--GGAUGAUG----------------C*G-AUGGGAC-GAAGUAG    3

    
    CGAAAC--GGAUGAGG----------------C*G-GUGGGAC-AAAGUAG    3

    
    CGAAA---GGAUGAGC----------------C*G-CCGGGAG-CGAGUAG    3

    
    CGAAA---GGAUGAUG----------------C*G-AUGGGAG-CGAGUAG    3

    
    CGAAA---GGGUGAGG----------------C*G-ACCAGAG-CGAGUAG    3

    
    CGAAA---GUAUGAGG----------------C*G-ACCGGAGGCGAGUAG    2

    
    CGAAA---GAAUGAGG----------------C*G-AUGGGAG-CGAGUAG    2

    
    CGAAA---GGAUGAUG----------------C*G-GUGGGA--CAAUUAG    2

    
    CGAAA---GGAUGAUG----------------C*G-GUGGGA--CGAUUAG    2

    
    UGAAA---GGAUGACG----------------G*C-UCAGGA--CCAGUAA    2

    
    AGAAA---G---GAGA---CCUCUCACGAGGCA*UAUCGUUA--CGAGUAU    1

    
    CGAAGUAUAAAUGGGUG---------------G*A-CCGCGAC-GCAGUAG    1

    
    CGAAA---UAAUGAUGAUG-------------C*G-GUGGGAG-CAAGUAG    1

    
    C-AAAAA-GGAUGAUG----------------C*G-AUGGGAC-GAAGUAG    1

    
    CGAAA---GUAUGAGG----------------C*G-UCCGGAGCCGAGUAG    1

    
    CGAAA---GUAUGAGG----------------C*G-UCCGGAGGCGAGUAG    1

    
    CGAAAA--GAAUGAGG----------------C*G-AUGGAAG-CGAGUAG    1

    
    CGAAAA--GAAUGAGG----------------C*G-GUGGGAC-GAAGUAG    1

    
    CGAAAA--GGAUGAGG----------------C*G-AUGGGAC-GAAGUAA    1

    
    CGAAAA--GGAUGAGG----------------C*G-AUGGGAC-GAAGUAG    1

    
    CGAAAA--GGAUGAGG----------------C*G-GUGGGAC-AAAGUAG    1

    
    CGAAAA--GGAUGAGG----------------C*G-GUGGGAC-GAAGUAG    1

    
    CGAAAA--GGAUGAUA----------------C*G-AUGGGAC-GAAGUAG    1

    
    CGAAAA--GGAUGAUG----------------C*G-ACGUGAC-GAAGUAC    1

    
    CGAAAA--GGAUGAUG----------------C*G-GUGGGAC-GAAGUAG    1

    
    CGAAAC--GAAUGAUG----------------C*G-GUGGGAC-AAAGUAG    1

    
    CGAAAC--GGAUGAGG----------------C*G-AUGGGAC-AAAGUAG    1

    
    CGAAAC--GGAUGAUG----------------C*G-AUGGGAC-AAAGUAG    1

    
    CGAGG---CAAUGAUG---------------CC*GAAUGGGA--GUACUAU    1

    
    UGAAAA--GGAUGAGG----------------C*G-AUGGGAC-GAAGUAA    1

    
    UGAAAA--GGAUGAGG----------------C*G-GUGGGAC-AAAGUAA    1

    
    UGAAAA--GGAUGAUG----------------C*G-ACGUGAC-GAAGUAA    1

    
    UGAAAA--GGAUGAUG----------------C*G-ACGUGAC-GAAGUAU    1

    
    UGAAAA--GGAUGAUG----------------C*G-GCGUGAC-GAAGUAG    1

    
    UGAAAC--GGAUGAGG----------------C*G-GCGGGAC-AAAGUAG    1

    
    AGAAA---GAAUGAUG----------------U*G-AUGGGAU-CAAGUAA    1

    
    CGAAA---GGAUGAGC----------------C*G-CCGGGAA-CGAGUAG    1

    
    CGAAA---GGAUGAGC----------------C*G-CUGGGAG-CGAGUAG    1

    
    CGAAA---GGAUGAGG----------------C*G-AUGGGAG-CGAGUAG    1

    
    CGAAA---GGAUGAUG----------------C*G-GUGGGAG-CGAGUAG    1

    
    CGAAAA--GAAUGAGG----------------C*G--GGGGAC-GAAGUAG    1

    
    CGAAG---CAAUGAAG----------------G*U-ACGGGAG-UGUGUAG    1

    
    CGAGG---CUAUGAUG----------------C*G-AUGGGAG-CGAGUAG    1

    
    UGAAA---GGAUGAUG----------------U*A-AUGGGAG-CGAGUAG    1

    
    UGAAAA--GAAUGAGG----------------C*G--UGUGAC-GAAGUAA    1

    
    AGAAA---GGAUGAUG----------------U*A-GUGGGA--CGAGUAC    1

    
    CGAAA---CAAUGAUG----------------C*G-UUAGGA--GGAUUAG    1

    
    CGAAA---GAAUGAGG----------------C*G-GUGGGA--CAAGUAG    1

    
    CGAAA---UGAUGAUG----------------C*G-UUAGGA--AAAGUAG    1

    
    CGAAC---CAAUGAUG----------------C*G-AUGGGA--GAACUAG    1

    
    CGAAC---CUAUGAUG----------------C*G-AUGGGA--GAAGUAG    1

    
    CGAGG---CAAUAAUG----------------C*G-AUGGGA--GCAUUAG    1

    
    CGAGG---CAAUGAUG----------------C*G-AUGAGG--GUAAUAG    1

    
    CGAGG---CAAUGAUG----------------C*G-AUGGGA--GUAUUAG    1

    
    CGAGG---CAGUGAUG----------------C*G-AUGGGA--GUAAUAG    1

    
    CGAGG---CUGUGAUG----------------C*G-AUGGGA--GCAAUAG    1

    
    UGAAA---GAAUGAGG----------------C*G-AUGGAA--CAAGUAA    1

    
    UGAAA---GAAUGAGG----------------C*G-AUGGGA--CAAGUAA    1

    
    UGAAA---GAAUGAGG----------------C*G-GUGGGA--UGAGUAA    1

    
    UGAAA---GAAUGAUG----------------U*A-UUAGGA--CGAGUAA    1

    
    UGAAC---GAAUGACG----------------C*G-UCAGGA--CAAGUAA    1

    
    UGAAC---GAAUGACG----------------G*C-UCAGGA--CCAGUAA    1

    
    C-AAA---GGAUGAUG----------------C*G-AUGGGAC--GA--AG    1

    
    C-AAA---GGAUGAUG----------------U*A-AUGGGAC-GA---AG    1
No Matches Found View All Results for this Loop

Loop 3 Hairpin loop

Column numbers: 97-114 
    Scored sequences and counts

    
    C-----GGAC-------G   10

    
    C-----UUGA-------G   10

    
    C-----CUGA-------G    8

    
    U-----GGAU-------G    6

    
    C-----GUAA-------G    4

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

    
    C-----AAUU-------G    3

    
    C-----AUUA-------G    3

    
    C-----GGAU-------G    3

    
    C-----GUAU-------G    3

    
    U-----GGAC-------G    3

    
    C-----GCUU-------G    2

    
    U-----CAUG-------A    2

    
    U-----GGAA-------G    2

    
    U-----GGAU-------A    2

    
    U-----UAUU-------A    2

    
    CACCGCCAUGU-GUAGUG    1

    
    GAC---UAAUU----GAC    1

    
    A-----GGAAU------G    1

    
    ------UUUGGU------    1

    
    A-----GGAG-------U    1

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

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

    
    C-----CAUU-------G    1

    
    C-----GAUU-------G    1

    
    C-----GGAA-------G    1

    
    C-----GGAG-------G    1

    
    C-----GGCU-------G    1

    
    C-----GUAG-------G    1

    
    C-----GUGA-------G    1

    
    C-----UAUU-------G    1

    
    G-----UUGA-------C    1

    
    U-----GGAC-------A    1

    
    U-----GGAC-------U    1

    
    U-----GGAG-------A    1

    
    U-----GUUU-------U    1

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

    
    ------ACUU--------    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_56334.1

Basepair signature:
cWW-F

89.77 -212.07 2 1

Mini UNCG

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

84.09 -105.08 2 2

3

Motif group HL_93535.1

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

81.82 -111.76 2 2

4

Motif group HL_56131.2

Basepair signature:
cWW-F-F

78.41 -111.96 3 2

5

Motif group HL_48417.5

Basepair signature:
cWW-F-F

63.64 -2.33 2 2

6

Motif group HL_57875.1

Basepair signature:
cWW-F-F

63.64 -110.73 2 2

7

Motif group HL_75660.5

Basepair signature:
cWW-F

63.64 -113.67 2 2

8

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

63.64 -121.64 3 2

tRNA D-loop

9

Motif group HL_13963.3

Basepair signature:
cWW-F-F

62.50 -122.18 4 2

10

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

60.23 -9.21 2 2

Coloring options: