RNA 3D Hub

JAR3D Query RF03020-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF03020 RT-17 RNA

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345
.((.(((((.....))))).....................((((((((.((......(..((((((((........))))))..))).....))).)..))))))...........).)......
>URS0000D68146_12908_1-87
AGCCUUACCUCUU-GGUAAAA----AAUA-AAUUU--UC-AAAAAGGG-AU-UGGUAG--G-U-----UAAA---------A--UCCGAAG-AUC-C--UGAUAUGAAGUAAAGGCG-AUGA---
>URS0000D6B6DE_12908_1-98
GGCCUUGCCUCUU-GGCAAAAA----ACA-UAACG--UC-AGAAAGGA-GC-UGGUAGGAACGCCCGUUGU-----AUGGGC-UACCGAAC-GCC-C--CGAAUAAGAAAAGCAAAG-CA-----
>URS0000D6C2C7_12908_1-97
GACCUUGCCUCUU-GGCAAAACA--CAAA-GCAGA--GC-CUCAUUUG-GUUUGGUAG--UCCCGA--UAUA------UCGG-GAUCGAAGAACCAG-AGGCGACAUAAGCAAAAAG--------
>URS0000D668D1_12908_1-99
GACCUUGCCUCUU-GGCAAAACA--CAAA-GCAGA--GCCUCUUUUGG-UU-UGGUAG--GUCUGGU-GAUU-----ACCGG-AGUCGAAG-AAUCAGAGGCGACAUAAGCAAAAAG--------
>URS0000D65A2F_12908_1-96
AGCCAUGCCCCUU-GGCAAAACA--CAAAGCAAUG--CC-UCAUUCGU-GU-UGGUAG--UCCCGU--UUUUU-----UCGG-GGUCGAAU-ACU-C--GGAGGUGA----AAUAAG-CAAAA--
>URS0000D6C340_12908_1-94
AGCCGCACCUCAA-GGUGAAA----GAAA-AACGU--UG-GAUGUAGU-GU-UGGUAA--UCGUGC--AAGG------GCAC-GGCUGAAG-ACA-G--AGAGAAAC----AAAAAG-CAGACAA
>URS0000D6C565_12908_1-96
AGCCACACCCAAUAGGUGAAA----AAUC-AACUU--UU-GAUGUAGU-GU-UGGUAA--UCGUGC--AUUUG-----GCAC-GGCUGAAG-ACA-G--AGAAAAAG----UAAAAG-CAGACAA
>URS0000D6C11A_12908_1-95
AGCCACACCCAAU-GGUGAAA----AAUC-AACUU--UU-GAUGUAGU-GU-UGGUAA--UCGUGC--AUUUG-----GCAC-GGCUGAAG-ACA-G--AGAAAAAG----UAAAAG-CAGACAA
>URS0000D6BB23_12908_1-94
AACCGCACCCCAC-GGUGAAA----AAUA-CACUG--AU-AAAGAAGU-GC-UGGUAG--ACAUAC--ACAC------GUAU-GGCCGAAG-GCA-G--GGACUUAG----GAAAAG-CAGACAA
>URS0000D69F35_12908_1-93
AACCGCACCCCAC-GGUGAAAA---AUAC-ACUGA--UU-AAAGAAGU-GC-UGGUAG--ACAUA---CACG-------UAU-GGCCGAAG-GCA-G--GGACUUAG----GAAAAG-CAGACAA
>URS0000D6D162_12908_1-97
AACCGCACCUCAA-GGUGAAA----GAUA-AAGAU--GA-CAGGAAGU-GC-CGGUAG--GUUUGGC-AUAC-----GCCAU-UCUCGACA-GCA-G--GGACUACAG---GAAAAG-CAGACAA
>URS0000D6D2C5_12908_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GCUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D6A2F7_709991_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D6A2F7_12908_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D6A2F7_457424_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D6A2F7_817_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D6A2F7_1121098_1-94
GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
>URS0000D69EC1_12908_1-88
GACCUUGCCGCAU-GGCAAAA----AAUA-AAUAG--CG-UAACGGAU-GC-UGGUAG--G-UU----GAAA--------GA--UUCGACG-GUU-U--CCAAUUAA----GCAAAG-CAGACCC
>URS0000D6AD7F_12908_1-91
AGCCUUGCCGCUU-GGCAAAAA---AUAA-CAAGC--AG-UAACGGGU-GU-CGGUAG--GCCG----GUAA--------CG-GUUCGAAG-GCU-C--CCAAUUAA----GCAAAG-CAGACCC
>URS0000D6B63C_12908_1-101
GACCCCGCCUCAC-GGCGAAAA---AUAA-ACUAA--AA-ACGGAGGU-GU-CAGUAG--ACCGGGU-ACAUA----AUCCG-GGCCGACC-GCA-A--CGACGUUCAAG-AAAAAG-CAGACAA
>URS0000D66E1D_997885_1-100
GACCUCGCCUCAC-GGCGAAAA---AUAA-ACUAA--AA-ACGGAGGU-GU-CAGUAG--ACCGGGU-AAAU-----AUCCG-GGCCGACC-ACA-A--CGACGUUAAAG-AAAAAG-CAGACAA
>URS0000D657A6_12908_1-96
AACCUCGCCUCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGCAU-------CG-GGCCGAAG-GUA-A--CGAGGUCAGAAGAAAAAG-CAGACAA
>URS0000D6C609_12908_1-96
AACCUCGCCCCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGAAU-------CG-GGCCGAAC-GUA-A--CGAGGUCAGAAGAAAAAG-CAGACAA
>URS0000D68EE7_12908_1-95
AACCUCGCCCCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGAAU-------CG-GGCCGAAC-GUA-A--CGAAGUCAGAA-GAAAAG-CAGACAA
>URS0000D670B9_1235787_1-98
GGCCUCACCCCAC-GGUGAAAAA--CAAA-CGACA--GG-CGGGCAGU-GC-CGGUAG--ACGGG---UUUAU------CCC-GGCCGACA-GCA-A--CGAAGCCGGAA-GAAUUG-CAGACCA
>URS0000D6AF49_12908_1-103
GGCCUCACCUCAU-GGUGAAAAA--CAAA-CGAAA--UG-CGGGCAGU-GC-CGGUAG--ACGGGA--CCGAUAA---UCCC-GGCCGACG-GUA-A--CGAAGCAAGAGAAAAUUG-CAGACAC
>URS0000D69A0E_12908_1-95
GGCCUCGCCCGAC-GGCGGAA----AAUA-AACUA--AA-CGAAAGAU-GC-UGGUAG--AUCGUA--AAUUG-----UACG-AGCCGAAC-GCG-U--GAUAAGUA----AAAAAG-CAGACAA
>URS0000D68416_12908_1-95
GGCCUCGCCCGAC-GGCGGAA----AAUA-AACUA--AA-CGAAAGAU-GU-UAGUAG--AUCGUA--GAUUG-----UACG-AGCCGAAC-GCG-U--GAUAAGUA----AAAAAG-CAGACAA
>URS0000D671ED_12908_1-102
GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--UAGGAUAAA---AAAUAG-CAGACAA
>URS0000D681A0_12908_1-102
GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UAGGGUAAA---AAAUAG-CAGACAA
>URS0000D69E01_12908_1-102
GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--UAGGGUAAA---AAAUAG-CAGACAA
>URS0000D66F62_12908_1-102
GUCCUCGCCCCAU-GGCGAUA----CAUA-CACAC--AC-CAAGAUUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UGAACAUUA---AAAAAG-CAGACAA
>URS0000D6CB38_12908_1-102
GUCCUCGCCCCAU-GGCGAUA----CAUA-CACAC--AC-CAAGAUUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UGAACAUUA---AAAAAG-CAGACAC
>URS0000D671D5_12908_1-99
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA-----GAAAG-CAGACAA
>URS0000D696A2_12908_1-103
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAAAGUU-A--GGACAUUUA---GAAAAGCCAGACAA
>URS0000D6B9EC_12908_1-100
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA----GAAAAG-CAGACAA
>URS0000D6686D_12908_1-100
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA----UAAAAG-CAGACAA
>URS0000D6CAC1_12908_1-100
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUCA----UAAAAG-CAGACAA
>URS0000D67BDF_12908_1-100
GGCCUUGCCUCAU-GGCAAAA----CAUA-CACAU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUCA----UAAAAG-CAGACAA
>URS0000D6838E_12908_1-102
GACCUUGCCCCAA-GGCAGAA----AAUU-CACUU--AU-CUAGAUUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--GGACUCUUA---AUUAAG-CAGACAA
>URS0000D6A207_12908_1-102
GGCCUUGCCCCAA-GGCAGAA----AAUA-CACUU--GU-UAAGAUUA-GC-UGGUAG--AUGAUGACAGUAGG--GUCAUCCGGUCGAAA-GUU-A--GGAUUUUAG---AAAAAG-CAGACAA
>URS0000D694D4_12908_1-100
AGCCUUGCCUCAU-GGCAGA-----ACAU-ACACU--AA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAAAGG--GUCAUCCAGUCGAAU-GUU-A--GGACAUAA----AAAAAG-CAGACAA
>URS0000D6C873_12908_1-86
UGCCUUGGCUCAU-GCCAAAACA--UAAC-AAACU--UC-AACGCUGU-AU-UAGUAG--ACGC----CGAG--------GC-GGUUGAAA-AUU-C--AGCA----------AAAA-CAAACAU
>URS0000D6ABFC_12908_1-95
CGCCCUGCCACUU-GGCAAAAUA--UAAA-AAUAC--AA-UGAACUAU-AU-UAGUAA--AUUUGA--GAAA------UCAAAAGGUGAAA-GUU-U--AGUUUG------UAAAUG-CAUACAA
>URS0000D66DAF_12908_1-92
UGCCCUGCCACUU-GGCAAAAUA--UAAA-AAUUA--UU-UGAACUGU-UU-UGGUAA--AUCCU---GCAA-------AGGAAGUUGAAG-AAU-C--AGUUU-------GAAGUG-CAUACAA
>URS0000D68438_12908_1-95
UACCUUGCCACAU-GGCAAAAC---ACAA-AAAUU--UA-UUAACUGU-AU-UAGUAG--ACUUGAACAAU-----GUUCAA-GGUUGAAG-AUU-C--GGUUA-------UAUUAG-CAUACAC
>URS0000D6B951_12908_1-99
UACCUUGCCUCUA-GGCAAAAC---AUAU-CAAUU--CU-GAAGCUGU-AU-UAGUAG--ACUUUGAAAGCAAAAUUUCAAA-GGUUGAAA-AUU-C--GGCA--------AACGAG-CAUACAA
>URS0000D6CB95_12908_1-95
UACCGUGCCACUU-GGCAAAACA--UCAA-AAACACCAA-AGAACCGU-AU-UAGUAG--ACCCGGC-AUCU-----GCCGG-GGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAA
>URS0000D6B51A_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D6B51A_742740_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D6B51A_657313_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D677C6_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGCC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D69C0A_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-AUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D6A1E3_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUUA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D69754_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D6C89F_12908_1-90
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUG--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D695C3_12908_1-94
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--CA-UGGACUGU-AU-UAGUAG--GUUGCACUCAUU----UGUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D65A8A_12908_1-94
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--CA-UGGACUGU-AU-UAGUAG--GUUGCACCCAUU----UGUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D6BAA7_12908_1-94
UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--UA-UGGACUGU-AU-UAGUAG--GUUGUAC-UCAUUC---GUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
>URS0000D67C59_12908_1-96
CACCGUGCCACUU-GGCAAAACAUUCAAA-AAUUC--AA-UAGGCUGU-UU-UGGUAA--ACUGCC--CAAACA----GGCA-GGUUGAAG-AAU-C--GGCU--------UUAGUG-CAUACAA
>URS0000D6B22E_12908_1-99
UGCCUUGCCACAU-GGCAAAACA--UAAC-AAUUC--AA-UAUCCUGU-GU-UAGUAG--ACUUUGAAAGUUAAGAUUCAAA-GGUUGAAC-GCU-U--GGGG---------GAUUG-CAUACAC
>URS0000D65DE4_12908_1-101
GACAGCCCCCGAAAGGGGGAAGU--UAAA-AAUAA--AA-UUUGUCGU-AU-UGGUAG--ACUUUGAAAGUUAAUUUUCAAA-GGUUGAAG-AUU-C--GGCU--------GAUGUG-CAUACAA
>URS0000D68472_12908_1-101
GACAGCCCCCGAAAGGGGGAAGU--UAAA-AAUAA--AU-UUGGUCGU-GU-UGGUAA--ACUUUGAAAAUUAACUUUCAAA-GGUUGAAG-AUU-C--GGCU--------GAUGUG-CAUACAA

There are no chains in PDB that we map to Rfam family RF03020.

Jump to results for:

  • Loop 1IL Column numbers: 2-3, 117-119
  • Loop 2J3 Column numbers: 3-5, 19-41, 105-117
  • Loop 3HL Column numbers: 9-15
  • Loop 4IL Column numbers: 46-47, 97-100
  • Loop 5IL Column numbers: 47-48, 95-97
  • Loop 6IL Column numbers: 48-50, 94-95
  • Loop 7IL Column numbers: 51-58, 87-93
  • Loop 8IL Column numbers: 58-61, 86-87
  • Loop 9IL Column numbers: 62-63, 82-85
  • Loop 10HL Column numbers: 68-77

Loop 1 Internal loop

Column numbers: 2-3, 117-119 
    Scored sequences and counts

    
    AC*G-C   36

    
    GC*G-C   20

    
    UC*G-C    2

    
    GC*GCC    1

    
    GC*A-C    1

    
    GC*G-A    1

    
    Omitted sequenced and counts

    
    AC*G--    2
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_84476.1

Basepair signature:
cWW-cWW

98.36 16.26 3 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

96.72 7.16 4 1

Major groove platform

3

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

91.80 0.67 3 1

Single bulged G

4

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

34.43 6.56 2 1

5

Motif group IL_42771.1

Basepair signature:
cWW-cWW

34.43 6.32 5 1

Multiple bulged bases

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

34.43 5.81 3 1

Intercalated cWS

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

34.43 3.42 2 1

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

34.43 2.55 2 1

Major groove intercalation

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

34.43 -1.35 3 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

34.43 -2.70 2 1

Single stack bend

Loop 2 3-way junction loop

Column numbers: 3-5, 19-41, 105-117 
    Scored sequences and counts

    
    CCU*AAAGA--UGAC-GAACG--CU-C*UAAG---GCAAAG    6

    
    CCG*AAAC---AUCA-AAAUA--CA-U*-------UCAGUG    6

    
    CCU*AAA----CAUA-CACAU--AG-U*UAAA---AAAUAG    3

    
    CCU*AAAA---AUAA-ACUAA--AG-G*UCAGAAGAAAAAG    2

    
    CCU*AUA----CAUA-CACAC--AC-C*AUUA---AAAAAG    2

    
    CCA*AAA----AAUC-AACUU--UU-G*AAG----UAAAAG    2

    
    CCU*GAA----AAUA-AACUA--AA-C*GUA----AAAAAG    2

    
    CCG*AAAC---AUCA-AAAUU--CA-U*-------UCAGUG    2

    
    CCU*AAACA--CAAA-GCAGA--GCCU*CAUAAGCAAAAAG    1

    
    CCU*AAAAA--CAAA-CGAAA--UG-C*CAAGAGAAAAUUG    1

    
    CCU*AAACA--CAAA-GCAGA--GC-C*CAUAAGCAAAAAG    1

    
    CCU*AAAAA--CAAA-CGACA--GG-C*CCGGAA-GAAUUG    1

    
    CCC*AAAA---AUAA-ACUAA--AA-A*UUCAAG-AAAAAG    1

    
    CCU*AAA----AAUA-AAUUU--UC-A*UGAAGUAAAGGCG    1

    
    CCU*AAAA----ACA-UAACG--UC-A*AAGAAAAGCAAAG    1

    
    CCU*AAAA---AUAA-ACUAA--AA-A*UUAAAG-AAAAAG    1

    
    CCU*AAAA---AUAA-ACUAA--AG-G*UCAGAA-GAAAAG    1

    
    CCA*AAACA--CAAAGCAAUG--CC-U*UGA----AAUAAG    1

    
    CCG*AAA----GAUA-AAGAU--GA-C*ACAG---GAAAAG    1

    
    CCG*AAAA---AUAC-ACUGA--UU-A*UAG----GAAAAG    1

    
    CCG*AAACA--UCAA-AAACACCAA-A*-------UCAGUG    1

    
    CCG*AAACAUUCAAA-AAUUC--AA-U*-------UUAGUG    1

    
    CCU*AAA----CAUA-CACUU--UA-G*UUUA---GAAAAG    1

    
    CCU*AAAA---AUAA-CAAGC--AG-U*UAA----GCAAAG    1

    
    CCU*GAA----AAUA-CACUU--GU-U*UUAG---AAAAAG    1

    
    CCU*GAA----AAUU-CACUU--AU-C*CUUA---AUUAAG    1

    
    CCC*AAAUA--UAAA-AAUAC--AA-U*G------UAAAUG    1

    
    CCG*AAA----AAUA-CACUG--AU-A*UAG----GAAAAG    1

    
    CCG*AAA----GAAA-AACGU--UG-G*AAC----AAAAAG    1

    
    CCU*AAA----AAUA-AAUAG--CG-U*UAA----GCAAAG    1

    
    CCU*AAA----CAUA-CACAU--UA-G*UCA----UAAAAG    1

    
    CCU*AAA----CAUA-CACUU--UA-G*UCA----UAAAAG    1

    
    CCU*AAA----CAUA-CACUU--UA-G*UUA----GAAAAG    1

    
    CCU*AAA----CAUA-CACUU--UA-G*UUA----UAAAAG    1

    
    CAG*GAAGU--UAAA-AAUAA--AA-U*-------GAUGUG    1

    
    CAG*GAAGU--UAAA-AAUAA--AU-U*-------GAUGUG    1

    
    CCC*AAAUA--UAAA-AAUUA--UU-U*-------GAAGUG    1

    
    CCU*AAA----CAUA-CACUU--UA-G*UUA-----GAAAG    1

    
    CCU*GA-----ACAU-ACACU--AA-G*UAA----AAAAAG    1

    
    CCG*AAAC---AUCA-AAAUG--CA-U*-------UCAGUG    1

    
    CCG*AAAC---AUCA-AAAUU--UA-U*-------UCAGUG    1

    
    CCG*AAAC---AUUA-AAAUA--CA-U*-------UCAGUG    1

    
    CCU*AAAC---ACAA-AAAUU--UA-U*-------UAUUAG    1

    
    CCU*AAAC---AUAU-CAAUU--CU-G*-------AACGAG    1

    
    CCU*AAACA--UAAC-AAUUC--AA-U*--------GAUUG    1

    
    CCU*AAACA--UAAC-AAACU--UC-A*---------AAAA    1
No Matches Found View All Results for this Loop

Loop 3 Hairpin loop

Column numbers: 9-15 
    Scored sequences and counts

    
    CACUU-G   21

    
    CUCAU-G    9

    
    CCCAU-G    5

    
    CUCUU-G    5

    
    CCCAC-G    3

    
    CCCUU-G    3

    
    CCGAAAG    2

    
    CACAU-G    2

    
    CCCAA-G    2

    
    CCGAC-G    2

    
    CUCAA-G    2

    
    CUCAC-G    2

    
    CCAAUAG    1

    
    CCAAU-G    1

    
    CGCAU-G    1

    
    CGCUU-G    1

    
    CUCUA-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_53890.2

Basepair signature:
cWW-F-F-F

96.83 41.88 2 1

2

Motif group HL_56334.1

Basepair signature:
cWW-F

92.06 29.97 2 1

Mini UNCG

3

Motif group HL_56131.2

Basepair signature:
cWW-F-F

90.48 32.83 3 2

4

Motif group HL_48417.5

Basepair signature:
cWW-F-F

82.54 27.18 2 2

5

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

82.54 13.68 3 2

Pseudoknot geometry with 3' bulge

6

Motif group HL_75660.5

Basepair signature:
cWW-F

71.43 15.39 2 1

7

Motif group HL_81100.2

Basepair signature:
cWW

71.43 -3.26 2 2

8

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

69.84 29.38 2 1

9

Motif group HL_48778.2

Basepair signature:
cWW-F

65.08 -5.69 1 1

Mini UNCG

10

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

58.73 2.70 2 2

tRNA D-loop

Loop 4 Internal loop

Column numbers: 46-47, 97-100 
    Scored sequences and counts

    
    UG*C--G   14

    
    AU*A--G    7

    
    GG*U--C    6

    
    GG*A--C    5

    
    CG*C--G    4

    
    AG*G--A    3

    
    AG*G--G    3

    
    CU*A--U    3

    
    AG*A--C    2

    
    GA*U--G    2

    
    GG*C--C    2

    
    UG*C--A    2

    
    UU*A--G    2

    
    UU*A--U    2

    
    UG*AGAG    1

    
    UU*G-AG    1

    
    GA*U--C    1

    
    GG*C--U    1

    
    UA*U--A    1

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

Motif group IL_84476.1

Basepair signature:
cWW-cWW

77.78 3.34 3 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

73.02 8.22 2 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

53.97 -2.41 3 1

Multiple bulged bases

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

53.97 -4.43 4 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

41.27 -6.09 3 1

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

41.27 -11.13 2 1

Major groove intercalation

7

Motif group IL_31462.6

Basepair signature:
cWW-L-cWW

36.51 -30.34 1 1

Single bulged A

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

28.57 -13.74 3 1

9

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

25.40 -16.70 1 1

Single bulged G

10

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

17.46 -14.20 2 1

Single stack bend

Loop 5 Internal loop

Column numbers: 47-48, 95-97 
    Scored sequences and counts

    
    GU*U-C   21

    
    UA*U-A   14

    
    GU*A-A    7

    
    GA*U-U    6

    
    GU*A-G    6

    
    AU*G-U    2

    
    AU*U-U    2

    
    GG*UCA    1

    
    UG*CAG    1

    
    GA*C-C    1

    
    GG*C-C    1

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

Motif group IL_84476.1

Basepair signature:
cWW-cWW

82.54 6.31 3 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

77.78 7.66 3 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

38.10 1.29 3 1

Multiple bulged bases

4

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

30.16 -11.79 2 1

Single bulged G

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

28.57 -7.26 3 1

Major groove intercalation

6

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

28.57 -9.08 3 1

7

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

26.98 -1.27 4 1

Intercalated cWS

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

26.98 -1.81 3 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

26.98 -8.31 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

26.98 -13.50 2 1

Single stack bend

Loop 6 Internal loop

Column numbers: 48-50, 94-95 
    Scored sequences and counts

    
    U-A*UU   17

    
    A-G*UU   14

    
    U-G*CA    9

    
    ACG*CU    6

    
    U-A*UA    3

    
    U-G*CU    3

    
    U-G*CG    2

    
    U-G*UU    2

    
    U-U*AU    2

    
    A-G*CC    1

    
    G-A*UC    1

    
    G-G*CC    1

    
    G-U*AU    1

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

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 17.74 2 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

60.32 9.54 2 1

Multiple bulged bases

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

58.73 7.77 3 1

Intercalated cWS

4

Motif group IL_84476.1

Basepair signature:
cWW-cWW

57.14 8.73 3 2

Multiple bulged bases

5

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

36.51 -6.45 2 1

Single bulged G

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

34.92 5.54 4 1

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

34.92 -0.24 3 1

Major groove intercalation

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

34.92 -7.50 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

31.75 3.17 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

31.75 -1.31 2 1

Single stack bend

Loop 7 Internal loop

Column numbers: 51-58, 87-93 
    Scored sequences and counts

    
    C-UGGUAG*CGAAC-G   10

    
    C-UGGUAG*CGAAG-G    9

    
    U-UAGUAG*UGAAA-G    6

    
    U-UGGUAA*UGAAG-A    6

    
    U-UAGUAG*CGAAA-G    5

    
    C-UAGUAG*CGAAA-G    3

    
    U-UAGUAG*UGAAA-A    3

    
    C-AAGUAG*CGAAA-G    2

    
    C-CGGUAG*CGACA-G    2

    
    U-UGGUAG*CGAAG-A    2

    
    UUUGGUAG*CGAAGAA    1

    
    C-AAGUAG*CGAAAAG    1

    
    C-CGGUAG*CGACG-G    1

    
    C-UAGUAG*CGAAU-G    1

    
    C-UGGUAG*CGAAA-G    1

    
    C-UGGUAG*CGACG-G    1

    
    U-CAGUAG*CGACC-A    1

    
    U-CAGUAG*CGACC-G    1

    
    U-CGGUAG*CGAAG-G    1

    
    U-UAGUAA*UGAAA-G    1

    
    U-UAGUAG*CGAAC-G    1

    
    U-UAGUAG*UGAAC-G    1

    
    U-UAGUAG*UGAAG-A    1

    
    U-UGGUAG*CGAAU-A    1

    
    U-UGGUAG*UGAAG-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_26307.2

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

98.41 52.58 2 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

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

95.24 28.55 5 2

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

3

Motif group IL_61286.1

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

88.89 18.34 5 2

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

4

Motif group IL_16458.4

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

63.49 12.60 4 2

Sarcin-Ricin target in LSU H95; G-bulge

5

Motif group IL_04346.10

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

44.44 -1.28 4 3

8x7 Sarcin-Ricin; G-bulge

6

Motif group IL_29198.2

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

41.27 -4.31 5 3

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

7

Motif group IL_41756.4

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

33.33 -18.39 7 4

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

8

Motif group IL_88269.4

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

25.40 -14.00 4 3

6x5 Sarcin-Ricin; G-bulge

9

Motif group IL_47346.2

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

22.22 -35.04 6 4

tSH-tSH-tHH-tHS

10

Motif group IL_65594.1

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

17.46 -8.74 4 3

8x7 Sarcin-Ricin; G-bulge

Loop 8 Internal loop

Column numbers: 58-61, 86-87 
    Scored sequences and counts

    
    G--A*UC   16

    
    G--G*UC   13

    
    G--A*UU   12

    
    G--A*CC   11

    
    A--A*UU    3

    
    A--U*CU    3

    
    G--U*UC    2

    
    GGAA*CC    1

    
    A--A*GU    1

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

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

98.41 19.29 3 1

Major groove platform

2

Motif group IL_84476.1

Basepair signature:
cWW-cWW

98.41 16.76 3 2

Multiple bulged bases

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

73.02 7.91 2 1

Intercalated cWS

4

Motif group IL_42771.1

Basepair signature:
cWW-cWW

71.43 9.51 3 1

Multiple bulged bases

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

69.84 5.37 2 1

6

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

69.84 4.09 2 1

Major groove intercalation

7

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

69.84 0.18 1 1

Single bulged G

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

53.97 6.61 3 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

31.75 -2.05 2 1

Single stack bend

10

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

31.75 -2.67 2 1

Single stack bend

Loop 9 Internal loop

Column numbers: 62-63, 82-85 
    Scored sequences and counts

    
    UG*CCGG   13

    
    CC*G-GG   12

    
    CC*G-GU    6

    
    CG*C-GG    6

    
    CU*A-GG    6

    
    CU*G-GG    3

    
    UC*G-AG    3

    
    UU*A-AG    3

    
    CA*U-GG    2

    
    UC*GAAG    1

    
    UG*CCAG    1

    
    UU*AAAG    1

    
    CC*G-GA    1

    
    CC*G-GC    1

    
    CG*C-UA    1

    
    UU*U-UC    1

    
    Omitted sequenced and counts

    
    -U*A--U    2
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

78.69 36.66 3 1

Intercalated cWS

2

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

78.69 33.82 3 1

3

Motif group IL_82107.4

Basepair signature:
cWW-cWW

78.69 21.81 3 1

Multiple bulged bases

4

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

78.69 18.24 3 1

5

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

77.05 60.48 2 0

Major groove intercalation

6

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

77.05 48.12 2 0

Major groove platform

7

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

73.77 49.48 2 0

Major groove platform

8

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

73.77 39.97 1 0

Single stack bend

9

Motif group IL_10569.1

Basepair signature:
cWW-L-cWW

73.77 31.22 3 1

10

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

73.77 14.05 1 1

Single stack bend

Loop 10 Hairpin loop

Column numbers: 68-77 
    Scored sequences and counts

    
    -ACCU-----    8

    
    -GUAA-----    7

    
    CAAUGG---G    6

    
    CAAUAAG--G    3

    
    CAAUAGG--G    3

    
    -AUUUG----    2

    
    -UGAAU----    2

    
    -GAAA-----    2

    
    AAAUUAACUU    1

    
    AAGCAAAAUU    1

    
    AAGUUAAGAU    1

    
    AAGUUAAUUU    1

    
    CAAAAGG--G    1

    
    CAGUAGG--G    1

    
    -CCGAUAA--    1

    
    -CAAACA---    1

    
    -UCAUUC---    1

    
    CCAUU----U    1

    
    UCAUU----U    1

    
    -AAUUG----    1

    
    -ACAUA----    1

    
    -GAUUG----    1

    
    -UGCAU----    1

    
    -UUUAU----    1

    
    -UUUUU----    1

    
    CAAU-----G    1

    
    UUGU-----A    1

    
    -AAAU-----    1

    
    -AAGG-----    1

    
    -ACAC-----    1

    
    -AUAC-----    1

    
    -AUCU-----    1

    
    -CACG-----    1

    
    -CGAG-----    1

    
    -GAUU-----    1

    
    -GCAA-----    1

    
    -UAAA-----    1

    
    -UAUA-----    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_48778.2

Basepair signature:
cWW-F

42.86 -60.25 2 2

Mini UNCG

2

Motif group HL_13189.1

Basepair signature:
cWW-F-F

41.27 -49.83 4 3

3

Motif group HL_56131.2

Basepair signature:
cWW-F-F

39.68 -33.82 4 3

4

Motif group HL_70782.2

Basepair signature:
cWW-F

36.51 -53.11 4 3

5

Motif group HL_56334.1

Basepair signature:
cWW-F

36.51 -64.72 2 2

Mini UNCG

6

Motif group HL_32346.4

Basepair signature:
cWW-F

30.16 -66.81 2 2

7

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

28.57 -66.10 3 2

8

Motif group HL_93535.1

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

23.81 -69.07 3 2

9

Motif group HL_48417.5

Basepair signature:
cWW-F-F

22.22 -31.81 2 2

10

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

20.63 -82.67 3 3

Coloring options: