JAR3D on RF03020

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 1HL Column numbers: 9-15
Loop 2IL Column numbers: 48-50, 94-95
Loop 3IL Column numbers: 51-58, 87-93
Loop 4IL Column numbers: 58-63, 82-87
Loop 5HL Column numbers: 66-79

Loop 1 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 View motif instance in 3D Basepair signature: cWW-F-F-F	96.83	41.88	2	1
2	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	92.06	29.97	2	1	Mini UNCG
3	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	90.48	32.83	3	2
4	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	82.54	27.18	2	2
5	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	82.54	13.68	3	2	Pseudoknot geometry with 3' bulge
6	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	71.43	15.39	2	1
7	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	71.43	-3.26	2	2
8	Motif group HL_86870.2 View motif instance in 3D Basepair signature: cWW-F-F-F	69.84	29.38	2	1
9	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	65.08	-5.69	1	1	Mini UNCG
10	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	58.73	2.70	2	2	tRNA D-loop

Loop 2 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 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	17.74	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	60.32	9.54	2	1	Multiple bulged bases
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	58.73	7.77	3	1	Intercalated cWS
4	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	57.14	8.73	3	2	Multiple bulged bases
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	36.51	-6.45	2	1	Single bulged G
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	34.92	5.54	4	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	34.92	-0.24	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	34.92	-7.50	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.75	3.17	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.75	-1.31	2	1	Single stack bend

Loop 3 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D 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 View motif instance in 3D Basepair signature: cWW-L-R-tSW-tHH-cSH-tWH-tHS-cWW	17.46	-8.74	4	3	8x7 Sarcin-Ricin; G-bulge

Loop 4 Internal loop

Column numbers: 58-63, 82-87

    Scored sequences and counts

    
    G--AUG*CCGGUC   13

    
    G--GCC*G-GUUC    6

    
    G--ACC*G-GGCC    5

    
    G--ACC*G-GGUU    4

    
    G--ACU*A-GGUU    4

    
    A--UCG*C-GGCU    3

    
    G--ACU*G-GGUU    3

    
    G--GUU*A-AGUC    3

    
    A--ACU*A-GGUU    2

    
    G--ACA*U-GGCC    2

    
    G--ACC*G-GGUC    2

    
    G--ACG*C-GGCC    2

    
    G--AUC*G-AGCC    2

    
    GGAACG*C-UACC    1

    
    A--AUC*GAAGUU    1

    
    A--AUU*AAAGGU    1

    
    G--AUG*CCAGUC    1

    
    G--ACG*C-GGUU    1

    
    G--GCC*G-GCUC    1

    
    G--GUC*G-AGUC    1

    
    G--GUU*U-UCUC    1

    
    G--UCC*G-GAUC    1

    
    G--UCC*G-GGUC    1

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

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

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

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_11344.2 View motif instance in 3D Basepair signature: cWW-cSS-L-cWW	44.44	-12.45	5	3	180 degree turn
2	Motif group IL_05192.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW-L	42.86	-11.03	6	3
3	Motif group IL_68909.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	28.57	-20.87	4	3
4	Motif group IL_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	20.63	-41.29	5	3	6x5 Sarcin-Ricin; G-bulge
5	Motif group IL_64231.5 View motif instance in 3D Basepair signature: cWW-cWW-L-R-L-cWW	17.46	-60.95	4	3
6	Motif group IL_48444.6 View motif instance in 3D Basepair signature: cWW-L-R-cWW-cWW	15.87	-34.48	6	3
7	Motif group IL_51479.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	15.87	-83.14	5	3
8	Motif group IL_23774.1 View motif instance in 3D Basepair signature: cWW-L-R-L-tHS-cWW	11.11	-125.69	6	4	UAA/GAN variation
9	Motif group IL_13404.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW-cWW	9.52	-92.12	5	3	Tandem non-canonical cWW pairs
10	Motif group IL_61242.1 View motif instance in 3D Basepair signature: cWW-cWW-L-R-L-R-cWW	7.94	-39.33	7	4

Loop 5 Hairpin loop

Column numbers: 66-79

    Scored sequences and counts

    
    C--ACCU------G    8

    
    ---GUAA-------    7

    
    GACAAUAAG--GUC    3

    
    GACAAUAGG--GUC    3

    
    GACAAUGG---GUC    3

    
    GGCAAUGG---GUC    3

    
    C--AUUUG-----G    2

    
    ---UGAAU------    2

    
    GAAAAUUAACUUUC    1

    
    GAAAGCAAAAUUUC    1

    
    GAAAGUUAAGAUUC    1

    
    GAAAGUUAAUUUUC    1

    
    GACAAAAGG--GUC    1

    
    GACAGUAGG--GUC    1

    
    AC-UCAUUC---GU    1

    
    ACCCAUU----UGU    1

    
    ACUCAUU----UGU    1

    
    A--CCGAUAA---U    1

    
    AACAAU-----GUU    1

    
    CGUUGU-----AUG    1

    
    GU-ACAUA----AU    1

    
    C--CAAACA----G    1

    
    GC-AUAC-----GC    1

    
    GC-AUCU-----GC    1

    
    GU-AAAU-----AU    1

    
    GU-GAUU-----AC    1

    
    A--AAUUG-----U    1

    
    A--GAUUG-----U    1

    
    U--UUUUU-----U    1

    
    A--GAAA------U    1

    
    A--UAUA------U    1

    
    C--AAGG------G    1

    
    C--ACAC------G    1

    
    ---UGCAU------    1

    
    ---UUUAU------    1

    
    ---CACG-------    1

    
    ---CGAG-------    1

    
    ---GAAA-------    1

    
    ---GCAA-------    1

    
    ---UAAA-------    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	36.51	-142.82	3	2
2	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	31.75	-2136.45	3	2	Mini UNCG
3	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	30.16	-116.36	4	3
4	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	30.16	-173.09	4	3
5	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	25.40	-96.81	3	2
6	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	22.22	-3097.57	3	3	Mini UNCG
7	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	20.63	-151.73	4	3
8	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	20.63	-813.98	4	3
9	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	19.05	-229.30	2	2	GNRA
10	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	19.05	-2112.63	4	3

Nucleotide numbers Coloring options:

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

RF03020 RT-17 RNA

Input Summary

Jump to results for:

Loop 1 Hairpin loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Internal loop

Loop 5 Hairpin loop

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