JAR3D on RF02997

RF02997 HOLDH RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222233333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334444444444444444444444444444444444444444444444444444444444444
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
((((((((......(((((((..((((((((..........)))).)))))).)))))...)))))))).((((((.......((((((.((....((((((.......)))))).....))))....((((((.....)))))).)))).....)))))).......((...........................................................................................................................((((((....((..........((((((((.........((((.........((....((.((((........)))))).....)))))))))))))))).....)))))).))((((((((................))))))))..(((((((.....)))))))
>URS0000D67621_12908_1-371
GUUAACUCGUUGAGGGUAGU--AUCUAGUCGGGAUAAACUACGGCAUCGGAA-CUAAAAGAGAGUUAACCUUAUACU-AAGUAGCU-CAU--------------------------------AGAAUAAUCGGUAGAG-GCCGGU--AGCGAA-AGUAUAAUGAU-CUCCCAAGAUGUGGGCAAGCCUAGC-UAGGGAG-GUAUCGAAAACUGUUUGUUGAAGUGGCGUAAUUCUCCCUAUGUA---AGCUCCCUUACUAAAAGUAA---------UACAUAAAGAAUUAUGAAAGUUGGGCAGUAUAAAAAUAAUGACCUGUUG-CAAAUAACGGAUUAUC---CU----CG-----AAAU--------CG-----AGCCGUAUGGUCAGAC--AGACAACUUUAGGGUUAUAUAGAUAGUGC-AAUGAGAUAUAACCUAGUAAC--UUAAA--GUUAC
>URS0000D67ABE_12908_1-375
GUUAACUCGUUGAGGUUAGU--AUCUAGUCGGGAUAAACUACGGCAUCGGAA-CUAAAAGAGAGUUGACCUUAUACC-AAGUAGCU-CUU--------------------------------AGAAUAAUCGGUAGAG-GCCGGU--AGCGAA-AGUAUAAUGAUUCUCCCAAGAUGUGGGCAAGCCUAGC-UAGGGAG-GUAUCGAAAACUGUUUGUUGAAGUAGCGUAAUUCUCCCUGUGUA---AGCUCCCUUACUAAAAGUAA---------UACAUAAAGAGUUAUGAAAGUUGGGCAGUAUAAAAAUAAUGACCUGUUG-CAAAUAACGGAUUAUC---CU----CG-----AAAU--------CG-----AGCCGUAUGGUCAGAC--AGACAACUUUAGGGGUAUAUAGAUAGUGC-AAUGAGAUAUAACCUAGCAACUUAUAA-AAGUUGC
>URS0000D6CCC4_12908_1-431
AUGCUUUAAGUGAAGGGAAAUAUCCGUGUCGGGGUAAACUACGGCUUCCGGA-UUCCUGGAUAGAGCAUCUCAUAGGAAAGUACCGU---UAGAAAGAUCAACUCGUAAUUGAUUGAGUAUA--AAUAACCUCUAGAG-GGAGGUCGCGUGGAAACUAUGAUGAAACUCCUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCAUAA-GCUCCCUGAUGUA--AGCUCCCUGAAU-AAAUU--CACAGCAAUACAUCAAAGUAGUAUGAAAGUUGGCCAGUAUAAA-UAAAUUCCCUGUUAACGGAAAGAGGGUUUGCAAAUC----CGACGUCGUGA----GACACG-----GACCUCAUGGGAAGAA-GAAGCAACUUUAGUGUUAGAGAGAUACUGUUAAUGAGCUCUAACAUGUUCAAAUAUUUUAUUUAAG
>URS0000D68563_12908_1-430
AUGCUUUAAGUGAAAGGAAAUAUCCGUGUCGGGAUAAACUACGGCUUCCGGA-UUCCUGGAUAGAGCAUCUCAUAGGAAAGUACCGU---UAGAAAGAUCAACUCGUAAUUGAUUGAGUAUA--AAUAACCUCUAGAG-GGAGGUCGCGGGAA-ACUAUGAUGAAACUCCUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AGCUCCCUGAAU-AAAUUCA--CAGCAAUACAUCAAAGCAAUAUGAGAGUUGGCCAGUAUAAA-UAAAUUCCCUGUUAACAGGAAGAGGGUUUGCAAAUC----CAAUGUCGGGA----GACACG-----GACCUCAUGGGAAGAA-GAAACAACUCUAGUGUUAGAGAGAUACUGUUAAUGAGCUCUAACAUGUUCAAAUAUCUUAUUUAAG
>URS0000D66989_12908_1-430
AUGCUUUAAGUGAAGGGAAAUAUCCGUGUCGGGGUAAACUACGGCUUCCGGA-UUCCUGGAUAGAGCAUCUCAUAGGAAAGUACCGU---UAGAAAGAUCAACUCGUAAUUGAUUGAGUAUA--AAUAACCUCUAGAG-GGAGGUCGCGUGGAAACUAUGAUGAAACUCCUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AACUCCCUG----AAAUUAUUAUAGUAAUACAUCAAAGCAAUAUGAGAGUUGGCCAGUAUAAA-UAAAUUCCCUGUUAACAGGAAGAGGGUUUGCAAAUC----CAAUGUCGGGA----GACACG-----GACCUCAUGGGAAGAA-GAAACAACUCUAGUGUUAGAGAGAUACUGUUAAUGAGCUCUAACAUGUUCAAAUAUCUUAUUUAAG
>URS0000D66C17_12908_1-429
AUGCUUUAAGUGAAGGGAAAUAUCCGUGUCGGGGUAAACUACGGCUUCCGGA-UUCCUGGAUAGAGCAUCUCAUAGGAAAGUACCGU---UAGAAAGAUCAACUCGUAAUUGAUUGAGUAUA--AAUAACCUCUGGAG-GGAGGUCGCGGGAA-ACUAUGAUGAAACUCCUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AACUCCCUG----AAGUUAUCAUAGUAAUACAUCAAAGCAAUAUGAAAGUUGGCCAGUAUAAA-UAAAUUCCCUGUUAACGGAAAGAGGGUUUGCAAAUC----CGACGUCGUGA----GACACG-----GACCUCAUGGGAAGAA-GAAGCAACUUUAGUGUUAGAGAGAUACUGUUAAUGAGCUCUAACAUGUUCAAAUAUUUUAUUUAAG
>URS0000D66A62_12908_1-430
AUGCUUUAAGCGAAGGGAAAUAUCCGUGUCGGGGUAAACUACGGCUUCCGGA-UUCCUGGAUAGAGCAUCUCAUAGGAAAGUACCGU---UAGAAAGAUCAACUCGUAAUUGAUUGAGUAUA--AAUAACCUCUAGAG-GGAGGUCGCGUGGAAACUAUGAUGAAACUCCUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AACUCCCUG----AAGUUAUCAUAGUAAUACAUCAAAGCAAUAUGAAAGUUGGCCAGUAUAAA-UAAAUUCCCUGUUAACGGAAAGAGGGUUUGCAAAUC----CGACGUCGCGA----GACACG-----GACCUCAUGGGAAGAA-GAAACAACUUUAGUGUUAGAGAGAUACUGUUAAUGAGCUCUAACAUGUUCAAAUAUUUUAUUUAAG
>URS0000D6AC53_12908_1-397
GUAGUGUUGAUGAAGAGGUCA-ACCGUGUCGGGAUAAUCUACGGCGUCCGGU-CCCUUGGAAACAUUACCUUACUGUGAACUAGCACUU----------UGGGAAA---CCA----------UGAAUAACCUCUAGAG-GGAGGUCGUGUGAG-ACAGUAAUGAAACUCCUA-GACGUGGGCAAGCCUAACCAAAGGAG-CAAUCGAAAACUCGAUGAUGAAGCAGCGUAA-GCUCCCUGAUAU-ACAACUCCCUGAUUCAAAGUUU---------AUAUUAAAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGCGG-AUUGCAA-CCGAAA-------CACGAUAU------UAGUAGGCCGCAUGGGAAGAUAGAUACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGAUACUU-AAAC--AAGUAU
>URS0000D676BD_12908_1-397
GUAGUGUUGAUGAAGAGGUCA-ACCGUGUCGGGAUAAUCUACGGCGUCCGGU-CCCUUGGAAACAUUGCCUUACUGUGAACUAGCACUU----------UGGGAAA---CCA----------UGAAUAACCUCUAGAG-GGAGGUCGUGUGAG-ACAGUAAUGAAACUCCUA-GACGUGGGCAAGCCUAACCAAAGGAG-CAAUCGAAAACUCGAUGAUGAAGCAGCGUAA-GCUCCCUGAUAU-AUAACUCCCUGAUUCAAAGUUU---------AUAUUAAAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGCGG-AUUGCAA-CCGAAA-------CACGAUAU------UAGUAGGCCGCAUGGGAAGAUAGAUACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGAUACUU-AAAC--AAGUAU
>URS0000D6AF65_12908_1-397
GUAGUGUUGAUGAAGAGGUCA-ACCGUGUCGGGAUAAUCUACGGCGUCCGGU-CCCUUGGAAACAUUACCUUACUGUGAACUAGCACUU----------UGGGAAA---CCA----------UGAAUAACCUCUAGAG-GGAGGUCGUGUGAG-ACAGUAAUGAAACUCCUA-GACGUGGGCAAGCCUAACCAAAGGAG-CAAUCGAAAACUCGAUGAUGAAGCAGCGUAA-GCUCCCUGAUAU-AUAACUCCCUGAUUCAAAGUUU---------AUAUUAAAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGCGG-AUUGCAA-CCGAAA-------CACGAUAU------UAGUAGGCCGCAUGGGAAGAUAGAUACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGAUACUU-AAAC--AAGUAU
>URS0000D696E4_12908_1-393
AUGAUGUUGAUGACGGAAGAACACCGUGUCGGGAUAAUCUACGGCGUCCGGU-CUUCAAGAGACAUCAUCUUACUGUGAAUUAGUCCUA-----------GAGAAA---UC-----------UAAAUAACCUCGAGAGGCGGGGUCGGAUGAG-ACAGUAAUGAAACUCCUA-GACGUGGGCGAGCCUAACCAAAGGAGUCAGUCGAAAACUCGUUGUUGAAGUAGCGUAA-ACUCCCUGAUACA--AACUCCCUGAUUCAAAGUAA--------UGUAUCAAAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGUGG-AUUGUAA-CCGAAA-------UGAUAC--------GAGUAGGCCACAUGGGAAGAU-GAAACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGACACC--GAAA---GGUGU
>URS0000D67502_12908_1-366
AUAAUAUUUAUGACUGAAUGU-GCUGAGUCGGGAUAAUCUACGGCAUCCGGCCCUUCAAGAGAUAUUAUCUUACUGUGAACUAGUCCU-----------AGAGAAA---UCU-----------AAAUAACCUCGAGAGACGGGGUCGGAUGAA-GCAGUAAUGAAACUCCUA-GAUGUGGGCAAGCCUAACCGAAGGAGUCGAUCGAAAACUCGUUGUUGAAGUAGCGUAA-GCUCCCUGAU-----------------AAAA---------------AUCAUAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGUGG-AUUGUAA-UC----GAU----AUUA-------AUC-----GGCCACAUGGGAAGAU-GAAACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGAUACC--GAAA---GGUAU
>URS0000D66E00_12908_1-366
AUAAUAUUUAUGACUGAAUGU-GCUGAGUCGGGAUAAUCUACGGCAUCCGGCCUUUCAAGAGAUAUUAUAUUACUGUGAACUAGUCCUA-----------GAGAAA---UC-----------UAAAUAACCUCGAGAGACGGGGUCGGAUGAA-GCAGUAAUGAAACUCCUA-GAUGUGGGCAAGCCUAACCGAAGGAGUCGAUCGAAAACUCGUUGUUGAAGUAGCGUAA-GCUCCCUGAU-----------------AAAA---------------AUCAUAGUAAUACGAGAGGUGGCGAGUAUAAA-UAAAUUUCCUGUUA---UGCAGUGG-AUUGUAA-UC----GAU----AUUA-------AUC-----GGCCACAUGGGAAGAU-GAAACAUCUCUGGUCUUGUAGAGAUAGCAU-AUUGAGCUACAAGAUGAUACC--GAAA---GGUAU

There are no chains in PDB that we map to Rfam family RF02997.

Jump to results for:

Loop 1IL Column numbers: 8-15, 58-62
Loop 2IL Column numbers: 19-20, 52-54
Loop 3IL Column numbers: 21-24, 50-51
Loop 4IL Column numbers: 27-28, 45-47
Loop 5HL Column numbers: 31-42
Loop 6IL Column numbers: 76-84, 150-156
Loop 7J3 Column numbers: 87-88, 124-129, 145-147
Loop 8IL Column numbers: 89-91, 122-123
Loop 9IL Column numbers: 92-97, 115-121
Loop 10HL Column numbers: 102-110
Loop 11HL Column numbers: 134-140
Loop 12IL Column numbers: 170-294, 404-406
Loop 13IL Column numbers: 299-304, 393-399
Loop 14IL Column numbers: 305-316, 391-392
Loop 15IL Column numbers: 323-333, 383-384
Loop 16IL Column numbers: 336-346, 379-380
Loop 17IL Column numbers: 347-352, 372-378
Loop 18IL Column numbers: 353-355, 370-371
Loop 19HL Column numbers: 358-367
Loop 20HL Column numbers: 415-432
Loop 21HL Column numbers: 448-454

Loop 1 Internal loop

Column numbers: 8-15, 58-62

    Scored sequences and counts

    
    AAGUGAAG*UGGAU    3

    
    UGAUGAAG*UGGAA    3

    
    CGUUGAGG*AAGAG    2

    
    UUAUGACU*AAGAG    2

    
    AAGCGAAG*UGGAU    1

    
    AAGUGAAA*UGGAU    1

    
    UGAUGACG*AAGAG    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_70923.9 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-tHS-tHS-cWW	100.00	46.05	4	1	Kink-turn
2	Motif group IL_69229.3 View motif instance in 3D Basepair signature: cWW-L-tSH-L-tHS-cWW-cWW	100.00	40.52	5	2	Kink-turn
3	Motif group IL_01488.3 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-R-tHS-L-cWW	84.62	32.46	5	2	Kink-turn
4	Motif group IL_74051.1 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-tHS-cWW-L	53.85	-14.83	5	2	Kink-turn
5	Motif group IL_77045.1 View motif instance in 3D Basepair signature: cWW-L-tSW-L-tHW-cWW-L	38.46	-6.83	6	4	Kink-turn
6	Motif group IL_94910.1 View motif instance in 3D Basepair signature: cWW-tSS-tSH-L-R-R-L-cWW-L	23.08	-8.01	5	3	Kink-turn
7	Motif group IL_78472.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L-L	23.08	-21.40	7	4
8	Motif group IL_41853.1 View motif instance in 3D Basepair signature: cWW-L-tHH-L-tHS-L-cWW-L-L	7.69	-42.22	6	4

Loop 2 Internal loop

Column numbers: 19-20, 52-54

    Scored sequences and counts

    
    AA*A-U    5

    
    UC*U-C    3

    
    GU*A-C    2

    
    UG*CCC    1

    
    UG*CCU    1

    
    GA*U-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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	76.92	9.28	2	1	Major groove platform
2	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-3.60	4	1
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-3.75	4	1	Intercalated cWS
4	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	38.46	-4.42	4	1	Multiple bulged bases
5	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-5.26	2	1	Single stack bend
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-9.73	2	1
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-11.58	3	1	Major groove intercalation
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-12.54	2	1	Single stack bend
9	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-14.00	5	1
10	Motif group IL_61258.15 View motif instance in 3D Basepair signature: cWW-L-cWW	38.46	-15.39	2	1	Single bulged C

Loop 3 Internal loop

Column numbers: 21-24, 50-51

    Scored sequences and counts

    
    UAUC*GG    5

    
    A-AC*GG    3

    
    U-GC*GG    2

    
    --AU*GA    2

    
    ACAC*GG    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_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	60.58	1	0	Major groove intercalation
2	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	37.48	2	1
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	32.88	2	0	Major groove platform
4	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	28.18	3	0	Single stack bend
5	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	92.31	14.34	1	0	Major groove platform
6	Motif group IL_82107.4 View motif instance in 3D Basepair signature: cWW-cWW	84.62	32.52	1	1	Multiple bulged bases
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	84.62	26.18	3	1
8	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	84.62	22.32	4	1	Intercalated cWS
9	Motif group IL_51454.3 View motif instance in 3D Basepair signature: cWW-cSH-cWW	76.92	-8.48	1	1	Minor groove platform
10	Motif group IL_95583.2 View motif instance in 3D Basepair signature: cWW-L-cWW	61.54	-12.00	2	1	Minor groove platform, major groove intercalation

Loop 4 Internal loop

Column numbers: 27-28, 45-47

    Scored sequences and counts

    
    UG*CUU    5

    
    AG*CAU    4

    
    UG*CGU    4

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_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	60.30	2	0	Single stack bend
2	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	60.02	2	0	Major groove platform
3	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	59.36	2	0	Major groove platform
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	54.55	3	1	Intercalated cWS
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	54.04	2	0	Major groove intercalation
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	53.59	3	1
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	48.57	3	0
8	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	48.40	2	1	Multiple bulged bases
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	47.75	2	0	Single stack bend
10	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	45.48	3	1

Loop 5 Hairpin loop

Column numbers: 31-42

    Scored sequences and counts

    
    GGGAUAAUCUAC    6

    
    GGGGUAAACUAC    4

    
    GGGAUAAACUAC    3

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_38649.1 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F-F-F	46.15	-7.20	5	5

Loop 6 Internal loop

Column numbers: 76-84, 150-156

    Scored sequences and counts

    
    GGAAAGUAC*UGGAAAC    3

    
    GUGAACUAG*UGAG-AC    3

    
    GGAAAGUAC*GGAA-AC    2

    
    GUGAACUAG*UGAA-GC    2

    
    GUGAAUUAG*UGAG-AC    1

    
    CC-AAGUAG*CGAA-AG    1

    
    CU-AAGUAG*CGAA-AG    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_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	38.46	-7.13	5	3	8x6 Sarcin-Ricin with bulged A; G-bulge
2	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	30.77	-34.34	6	4	8x6 Sarcin-Ricin with inserted A; G-bulge
3	Motif group IL_78349.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L-L	15.38	-27.69	7	4
4	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	15.38	-51.65	4	3	7x6 Sarcin-Ricin; G-bulge
5	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	15.38	-60.61	4	4	8x7 Sarcin-Ricin; G-bulge
6	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	7.69	-67.16	7	5	7x6 Sarcin-Ricin with UU cWW pair; G-bulge

Loop 7 3-way junction loop

Column numbers: 87-88, 124-129, 145-147

    Scored sequences and counts

    
    CU*AAAUAA*UCG    3

    
    CU*GAAUAA*UCG    3

    
    Omitted sequenced and counts

    
    U-*-AAUAA*UCG    5

    
    -C*GAAUAA*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
1	Motif group J3_12003.2 View motif instance in 3D Basepair signature: 9	100.00	63.30	6	2
2	Motif group J3_67856.4 View motif instance in 3D Basepair signature: 12	50.00	-2.46	7.5	2
3	Motif group J3_01052.1 View motif instance in 3D Basepair signature: 13	50.00	-5.00	6.5	3

Loop 8 Internal loop

Column numbers: 89-91, 122-123

    Scored sequences and counts

    
    Omitted sequenced and counts

    
    --U*A-    5

    
    U--*-U    3

    
    A--*-U    2

    
    AU-*-A    1

    
    UU-*-A    1

    
    ---*--    1

No Matches Found View All Results for this Loop

Loop 9 Internal loop

Column numbers: 92-97, 115-121

    Scored sequences and counts

    
    AGAAAG*UGAGUAU    5

    
    Omitted sequenced and counts

    
    ------*-------    8

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#	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	100.00	97.38	2	0	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	100.00	35.68	5	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	100.00	30.43	4	1	8x6 Sarcin-Ricin with inserted Y; G-bulge
4	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	100.00	24.18	6	2	8x6 Sarcin-Ricin with bulged A; G-bulge
5	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	100.00	18.24	6	2	7x7 Sarcin-Ricin with intercalated A; G-bulge
6	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	100.00	17.10	6	2	tSH-tSH-tHH-tHS
7	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	100.00	9.30	6	3	8x6 Sarcin-Ricin with inserted A; G-bulge
8	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	9.20	4	2	8x7 Sarcin-Ricin; G-bulge
9	Motif group IL_87284.1 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tWH-tHS-cWW	100.00	2.66	5	2	tSH-tHW-tWH-tHS
10	Motif group IL_09044.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-L-tHS-cWW	100.00	1.39	5	3

Loop 10 Hairpin loop

Column numbers: 102-110

    Scored sequences and counts

    
    ACUCGUAAU    5

    
    AGAAA---U    3

    
    GGAAA---C    3

    
    Omitted sequenced and counts

    
    ---------    2

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	54.55	20.32	2	0
2	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	54.55	11.30	2	0
3	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	54.55	-0.03	3	1
4	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	54.55	-11.58	2	0
5	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	54.55	-26.07	4	2
6	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	54.55	-32.65	3	1
7	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	54.55	-33.01	2	0
8	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	54.55	-46.34	2	0	Pseudoknot geometry
9	Motif group HL_97917.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	54.55	-52.96	4	2
10	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	54.55	-56.49	3	1

Loop 11 Hairpin loop

Column numbers: 134-140

    Scored sequences and counts

    
    UAGAG-G    9

    
    GAGAGAC    2

    
    GAGAGGC    1

    
    UGGAG-G    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	21.35	2	2
2	Motif group HL_89893.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	92.31	28.73	2	1
3	Motif group HL_55195.3 View motif instance in 3D Basepair signature: cWW-F	76.92	5.51	1	1
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	76.92	4.41	2	1
5	Motif group HL_99040.1 View motif instance in 3D Basepair signature: F-F-F-F-F-F	76.92	1.91	2	2
6	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	76.92	-0.74	2	2
7	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	69.23	12.65	2	1
8	Motif group HL_20811.4 View motif instance in 3D Basepair signature: cWW-cWS-F	69.23	-7.92	3	2	tRNA D-loop
9	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	15.38	-22.93	3	2	Pseudoknot geometry
10	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	15.38	-25.59	3	2	Pseudoknot geometry with 3' bulge

Loop 12 Internal loop

Column numbers: 170-294, 404-406

    Scored sequences and counts

    
    CUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AACUCCCUG----AAGUUAUCAUAGUAAUACAUCAAAGCAAUAUGAA*UUA    2

    
    CUA-GACGUGGGCAAGCCUAACCAAAGGAG-CAAUCGAAAACUCGAUGAUGAAGCAGCGUAA-GCUCCCUGAUAU-AUAACUCCCUGAUUCAAAGUUU---------AUAUUAAAGUAAUACGAG*CUG    2

    
    CUA-GAUGUGGGCAAGCCUAACCGAAGGAGUCGAUCGAAAACUCGUUGUUGAAGUAGCGUAA-GCUCCCUGAU-----------------AAAA---------------AUCAUAGUAAUACGAG*CUG    2

    
    CUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCAUAA-GCUCCCUGAUGUA--AGCUCCCUGAAU-AAAUU--CACAGCAAUACAUCAAAGUAGUAUGAA*UUA    1

    
    CUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AGCUCCCUGAAU-AAAUUCA--CAGCAAUACAUCAAAGCAAUAUGAG*CUA    1

    
    CUA-GAAGUGGGCGUGCCUGGCAGAAGGAGUAGGUCGAAAACUGGUUGCUGAAGCAGCGUAA-GCUCCCUGAUGUA--AACUCCCUG----AAAUUAUUAUAGUAAUACAUCAAAGCAAUAUGAG*CUA    1

    
    CUA-GACGUGGGCGAGCCUAACCAAAGGAGUCAGUCGAAAACUCGUUGUUGAAGUAGCGUAA-ACUCCCUGAUACA--AACUCCCUGAUUCAAAGUAA--------UGUAUCAAAGUAAUACGAG*CUG    1

    
    CUA-GACGUGGGCAAGCCUAACCAAAGGAG-CAAUCGAAAACUCGAUGAUGAAGCAGCGUAA-GCUCCCUGAUAU-ACAACUCCCUGAUUCAAAGUUU---------AUAUUAAAGUAAUACGAG*CUG    1

    
    CCAAGAUGUGGGCAAGCCUAGC-UAGGGAG-GUAUCGAAAACUGUUUGUUGAAGUAGCGUAAUUCUCCCUGUGUA---AGCUCCCUUACUAAAAGUAA---------UACAUAAAGAGUUAUGAA*UUA    1

    
    CCAAGAUGUGGGCAAGCCUAGC-UAGGGAG-GUAUCGAAAACUGUUUGUUGAAGUGGCGUAAUUCUCCCUAUGUA---AGCUCCCUUACUAAAAGUAA---------UACAUAAAGAAUUAUGAA*UUA    1

No Matches Found View All Results for this Loop

Loop 13 Internal loop

Column numbers: 299-304, 393-399

    Scored sequences and counts

    
    GGCGAG*UAGAUAC    3

    
    GGCCAG*A-GAAAC    3

    
    GGCGAG*U-GAAAC    3

    
    GGCCAG*A-GAAGC    2

    
    GGGCAG*C--AGAC    2

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_82292.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	61.54	3.65	5	3
2	Motif group IL_49767.8 View motif instance in 3D Basepair signature: cWW-cWW-tWH-L-tHS-cWW	46.15	-20.48	4	3	UAA/GAN with extra cWW
3	Motif group IL_87284.1 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tWH-tHS-cWW	46.15	-22.61	6	3	tSH-tHW-tWH-tHS
4	Motif group IL_06136.2 View motif instance in 3D Basepair signature: cWW-tHS-cWW-tHS-tSH-tSH-cWW	46.15	-24.36	4	3	Quadruple sheared
5	Motif group IL_01038.1 View motif instance in 3D Basepair signature: cWW-tWH-L-R-tHS-cWW	46.15	-25.57	4	3	UAA/GAN with extra stack
6	Motif group IL_44438.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	23.08	-15.20	8	4
7	Motif group IL_78349.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L-L	23.08	-21.33	5	4
8	Motif group IL_71294.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	23.08	-21.85	5	3	Double sheared; A in syn; two near cWW pairs
9	Motif group IL_88116.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-L-R-L-R-cWW-cWW	23.08	-30.58	5	4
10	Motif group IL_09044.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-L-tHS-cWW	23.08	-32.38	5	4

Loop 14 Internal loop

Column numbers: 305-316, 391-392

    Scored sequences and counts

    
    UAUAAA-UAAAU*GA   11

    
    UAUAAAAAUAAU*GA    2

No Matches Found View All Results for this Loop

Loop 15 Internal loop

Column numbers: 323-333, 383-384

    Scored sequences and counts

    
    UUA---UGCAG*CA    6

    
    UUAACGGAAAG*CA    3

    
    UUAACAGGAAG*CA    2

    
    UUG-CAAAUAA*UA    2

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_27393.10 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L-R	46.15	-49.24	9	5
2	Motif group IL_32056.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-tWH-R-L-R-L	15.38	-71.24	7	5

Loop 16 Internal loop

Column numbers: 336-346, 379-380

    Scored sequences and counts

    
    GGUUUGCAAAU*AC    5

    
    G-AUUGCAA-C*GC    3

    
    G-AUUGUAA-U*GC    2

    
    GAUUAUC---C*GC    2

    
    G-AUUGUAA-C*GC    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_55917.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	38.46	-31.40	8	4
2	Motif group IL_58960.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-tWW-L-R-L	23.08	-70.50	9	5
3	Motif group IL_25412.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	15.38	-91.62	8	4	Major groove intercalation

Loop 17 Internal loop

Column numbers: 347-352, 372-378

    Scored sequences and counts

    
    C----C*G-----G    5

    
    CGAAA-*-UAGUAG    3

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

    
    U----C*G-----A    2

    
    CGAAA-*-GAGUAG    1

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#	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 View motif instance in 3D Basepair signature: cWW-cWW	69.23	-86.97	2	2	Multiple bulged bases
2	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-115.61	3	1	Stack and bulge
3	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-144.28	3	1
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-149.77	3	1	Intercalated cWS
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-152.78	2	1	Major groove intercalation
6	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	69.23	-153.31	3	1	Multiple bulged bases
7	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-153.78	2	1	Major groove platform
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-169.03	3	1
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-181.96	1	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	69.23	-205.24	2	1

Loop 18 Internal loop

Column numbers: 353-355, 370-371

    Scored sequences and counts

    
    GAC*AC    3

    
    AAU*AC    2

    
    AU-*AU    2

    
    Omitted sequenced and counts

    
    ---*--    4

    
    G--*-C    2

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	64.39	2	0	Single stack bend
2	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	61.02	4	0
3	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	59.33	1	0	Single stack bend
4	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	57.34	3	0	Multiple bulged bases
5	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	53.78	2	0	Major groove platform
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	48.62	2	0	Major groove intercalation
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	47.52	3	1
8	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	45.27	4	1	Intercalated cWS
9	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	44.76	3	0	Stack and bulge
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	13.82	5	1

Loop 19 Hairpin loop

Column numbers: 358-367

    Scored sequences and counts

    
    -CACGAUAU-    3

    
    CGGGA----G    2

    
    CGUGA----G    2

    
    -AAAU-----    2

    
    -AUUA-----    2

    
    -UGAUAC---    1

    
    CGCGA----G    1

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#	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 View motif instance in 3D Basepair signature: cWW-F	61.54	-46.76	3	2	Mini UNCG
2	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	53.85	-33.54	2	2
3	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	53.85	-40.72	2	1
4	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-41.11	2	2
5	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	46.15	-49.78	4	2
6	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	38.46	-39.52	4	2
7	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	38.46	-43.73	3	1
8	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	38.46	-45.96	4	2
9	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	38.46	-53.26	3	2
10	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	38.46	-54.81	3	2

Loop 20 Hairpin loop

Column numbers: 415-432

    Scored sequences and counts

    
    GAGAUAGCAU-AUUGAGC    6

    
    GAGAUACUGUUAAUGAGC    5

    
    UAGAUAGUGC-AAUGAGA    2

No Matches Found View All Results for this Loop

Loop 21 Hairpin loop

Column numbers: 448-454

    Scored sequences and counts

    
    UAUUUUA    3

    
    -AAAC--    3

    
    -GAAA--    3

    
    UAUCUUA    2

    
    UAUAA-A    1

    
    -UUAAA-    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_75660.5 View motif instance in 3D Basepair signature: cWW-F	61.54	6.45	2	1
2	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	61.54	-2.64	3	1
3	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-21.86	3	1
4	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	53.85	-39.01	3	2
5	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	46.15	-4.79	3	2
6	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	46.15	-11.31	3	3
7	Motif group HL_47787.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	46.15	-50.82	3	2
8	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	46.15	-76.83	4	3
9	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	46.15	-94.88	2	1	GNRA
10	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	38.46	-32.43	3	1	tRNA D-loop