JAR3D on RF02997

RF02997 HOLDH RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222233333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334444444444444444444444444444444444444444444444444444444444444
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556
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((((((((.......(((....((((.((((..........))))...))))..)))....)))))))).(((((((......((((............(((.......))).................(((((.....)))))..))))....))))))).....(((((......((((....)))).....)))))..........(((((..................(((...((((((................................)))))).)))..............)))))...........((((............((((.........((....(((...............))).....))))))..)))).................(((((((((................))))))))).((((((.......))))))
>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: 8-16, 57-62
Loop 2IL Column numbers: 18-23, 52-55
Loop 3IL Column numbers: 26-28, 45-49
Loop 4HL Column numbers: 31-42
Loop 5IL Column numbers: 77-84, 150-155
Loop 6J3 Column numbers: 87-100, 112-130, 144-147
Loop 7HL Column numbers: 102-110
Loop 8HL Column numbers: 134-140
Loop 9IL Column numbers: 171-178, 189-195
Loop 10HL Column numbers: 181-186
Loop 11IL Column numbers: 214-233, 286-301
Loop 12IL Column numbers: 235-239, 282-284
Loop 13HL Column numbers: 244-277
Loop 14IL Column numbers: 320-333, 383-386
Loop 15IL Column numbers: 336-346, 379-380
Loop 16IL Column numbers: 347-352, 372-378
Loop 17HL Column numbers: 354-370
Loop 18HL Column numbers: 415-432
Loop 19HL Column numbers: 447-455

Loop 1 Internal loop

Column numbers: 8-16, 57-62

    Scored sequences and counts

    
    AAGUGAAGG*CUGGAU    3

    
    UGAUGAAGA*UUGGAA    3

    
    UUAUGACUG*CAAGAG    2

    
    AAGCGAAGG*CUGGAU    1

    
    AAGUGAAAG*CUGGAU    1

    
    CGUUGAGGG*AAAGAG    1

    
    CGUUGAGGU*AAAGAG    1

    
    UGAUGACGG*CAAGAG    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_41853.1 View motif instance in 3D Basepair signature: cWW-L-tHH-L-tHS-L-cWW-L-L	7.69	-69.40	7	5

Loop 2 Internal loop

Column numbers: 18-23, 52-55

    Scored sequences and counts

    
    AAAUAU*A-UU    5

    
    GUCA-A*U-CC    3

    
    AGU--A*A-CU    2

    
    AGAACA*U-CU    1

    
    AUGU-G*CCCU    1

    
    AUGU-G*CCUU    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_98347.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	46.15	-37.14	6	4
2	Motif group IL_73789.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	38.46	-34.59	7	3
3	Motif group IL_88082.1 View motif instance in 3D Basepair signature: cWW-L-tSS-L-cWW-L	38.46	-48.98	7	4
4	Motif group IL_47108.1 View motif instance in 3D Basepair signature: cWW-L-R-L-tHH-L-cWW	38.46	-54.28	7	5
5	Motif group IL_59302.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	38.46	-55.70	7	3
6	Motif group IL_74957.1 View motif instance in 3D Basepair signature: cWW-L-cHW-L-cWW-L	38.46	-59.05	8	5	cWH basepair with bulged bases
7	Motif group IL_33323.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L-L	38.46	-118.07	7	4
8	Motif group IL_46387.1 View motif instance in 3D Basepair signature: cWW-cWW-L-cWW-L	23.08	-46.67	4	2
9	Motif group IL_76319.5 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	23.08	-53.06	5	3
10	Motif group IL_61341.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	23.08	-53.26	6	2

Loop 3 Internal loop

Column numbers: 26-28, 45-49

    Scored sequences and counts

    
    GUG*CUUCC    5

    
    GUG*CGUCC    4

    
    GAG*CAUCC    2

    
    UAG*CAUCG    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_36516.3 View motif instance in 3D Basepair signature: cWW-cWW-cSH-cWW-L	84.62	24.97	4	2
2	Motif group IL_46387.1 View motif instance in 3D Basepair signature: cWW-cWW-L-cWW-L	84.62	14.71	5	2
3	Motif group IL_63596.11 View motif instance in 3D Basepair signature: cWW-cWS-cSH-tWH-cWW-L	84.62	11.68	3	1	C-loop
4	Motif group IL_89984.3 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	69.23	25.86	5	2
5	Motif group IL_26728.3 View motif instance in 3D Basepair signature: cWW-cSH-R-cSH-cWW-cWW	69.23	14.53	5	2
6	Motif group IL_11415.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	69.23	5.03	5	3
7	Motif group IL_42314.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	61.54	2.49	6	3
8	Motif group IL_61476.2 View motif instance in 3D Basepair signature: cWW-tSH-L-cWW-L	61.54	-15.04	5	2
9	Motif group IL_25463.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	46.15	-12.21	4	2
10	Motif group IL_51387.2 View motif instance in 3D Basepair signature: cWW-cSH-cWW-cWW	38.46	-12.37	1	1

Loop 4 Hairpin loop

Column numbers: 31-42

    Scored sequences and counts

    
    GGGAUAAUCUAC    6

    
    GGGGUAAACUAC    4

    
    GGGAUAAACUAC    3

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

Loop 5 Internal loop

Column numbers: 77-84, 150-155

    Scored sequences and counts

    
    GAAAGUAC*UGGAAA    3

    
    UGAACUAG*UGAG-A    3

    
    GAAAGUAC*GGAA-A    2

    
    UGAACUAG*UGAA-G    2

    
    UGAAUUAG*UGAG-A    1

    
    C-AAGUAG*CGAA-A    1

    
    U-AAGUAG*CGAA-A    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_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	38.46	-7.21	4	3	6x5 Sarcin-Ricin; 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	-12.11	6	3	8x6 Sarcin-Ricin with inserted A; G-bulge
3	Motif group IL_09044.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-L-tHS-cWW	30.77	-30.94	6	3
4	Motif group IL_33886.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-R-L-R-cWW	30.77	-31.61	7	3	Kink-turn with embedded cWW pair
5	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	-13.49	6	4
6	Motif group IL_62654.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-tHS-cWW	15.38	-62.08	6	4	tSH-tHH-tHS
7	Motif group IL_54041.2 View motif instance in 3D Basepair signature: cWW-L-R-L-R-tWH-L-cWW	7.69	-58.21	6	5	tHW-tHW cross-strand stack

Loop 6 3-way junction loop

Column numbers: 87-100, 112-130, 144-147

    Scored sequences and counts

    
    U---UAGAAAGAUC*GAUUGAGUAUA--AAUAAC*GUCG    5

    
    CUU----------U*A----------UGAAUAAC*GUCG    3

    
    CUA-----------*-----------UAAAUAAC*GUCG    2

    
    CU-----------A*U-----------AAAUAAC*GUCG    1

    
    -CAU----------*-----------AGAAUAAU*GU--    1

    
    -CUU----------*-----------AGAAUAAU*GU--    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 J3_98484.1 View motif instance in 3D Basepair signature: 16	23.08	-198.69	12	8

Loop 7 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 8 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 9 Internal loop

Column numbers: 171-178, 189-195

    Scored sequences and counts

    
    UA-GAAGU*GGCAGAA    5

    
    UA-GACGU*AACCAAA    4

    
    CAAGAUGU*AGC-UAG    2

    
    UA-GAUGU*AACCGAA    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_09129.2 View motif instance in 3D Basepair signature: cWW-L-R-tWH-L-R-L-tWW-cWW	69.23	-15.05	8	4
2	Motif group IL_88116.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-L-R-L-R-cWW-cWW	46.15	-17.48	6	5

Loop 10 Hairpin loop

Column numbers: 181-186

    Scored sequences and counts

    
    GCAAGC    7

    
    GCGUGC    5

    
    GCGAGC    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_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	37.89	3	1
2	Motif group HL_86870.2 View motif instance in 3D Basepair signature: cWW-F-F-F	92.31	6.82	3	2
3	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	92.31	5.88	2	2
4	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	9.96	2	1
5	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	53.85	-10.12	3	2
6	Motif group HL_57176.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-13.61	2	1	Pseudoknot geometry with 3' bulge
7	Motif group HL_07886.3 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-16.60	4	2
8	Motif group HL_34617.5 View motif instance in 3D Basepair signature: cWW-tSW-F	53.85	-17.67	2	0	UNCG
9	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	46.15	20.60	2	2
10	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	38.46	9.79	3	2

Loop 11 Internal loop

Column numbers: 214-233, 286-301

    Scored sequences and counts

    
    GAUGAUGAAGCAGCGUAA-G*UAAUACGAGAGGUGGC    3

    
    GUUGCUGAAGCAGCGUAA-G*CAAUAUGAAAGUUGGC    2

    
    GUUGCUGAAGCAGCGUAA-G*CAAUAUGAGAGUUGGC    2

    
    GUUGUUGAAGUAGCGUAA-G*UAAUACGAGAGGUGGC    2

    
    UUUGUUGAAGUAGCGUAAUU*AGUUAUGAAAGUUGGG    1

    
    UUUGUUGAAGUGGCGUAAUU*AAUUAUGAAAGUUGGG    1

    
    GUUGCUGAAGCAGCAUAA-G*UAGUAUGAAAGUUGGC    1

    
    GUUGUUGAAGUAGCGUAA-A*UAAUACGAGAGGUGGC    1

No Matches Found View All Results for this Loop

Loop 12 Internal loop

Column numbers: 235-239, 282-284

    Scored sequences and counts

    
    UCCCU*AAA   11

    
    UCCCU*AUA    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_11415.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	100.00	41.33	4	2
2	Motif group IL_63596.11 View motif instance in 3D Basepair signature: cWW-cWS-cSH-tWH-cWW-L	100.00	38.86	1	1	C-loop
3	Motif group IL_19102.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	100.00	35.26	5	1
4	Motif group IL_10389.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-cWW	100.00	24.74	5	2
5	Motif group IL_25463.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	100.00	17.47	5	2
6	Motif group IL_82741.2 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	100.00	3.76	4	2
7	Motif group IL_44325.1 View motif instance in 3D Basepair signature: cWW-cWH-cWW-L	84.62	17.19	6	2
8	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	84.62	-0.75	4	1	Isolated non-canonical cWW pair
9	Motif group IL_59302.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	84.62	-0.81	4	2
10	Motif group IL_89984.3 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	15.38	-5.64	5	3

Loop 13 Hairpin loop

Column numbers: 244-277

    Scored sequences and counts

    
    UA--AACUCCCUG----AAGUUAUCAUAGUAAUA    2

    
    U-AUAACUCCCUGAUUCAAAGUUU---------A    2

    
    A---AGCUCCCUUACUAAAAGUAA---------U    2

    
    ----------------AAAA--------------    2

    
    UA--AGCUCCCUGAAU-AAAUU--CACAGCAAUA    1

    
    UA--AGCUCCCUGAAU-AAAUUCA--CAGCAAUA    1

    
    UA--AACUCCCUG----AAAUUAUUAUAGUAAUA    1

    
    CA--AACUCCCUGAUUCAAAGUAA--------UG    1

    
    U-ACAACUCCCUGAUUCAAAGUUU---------A    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_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	15.38	-9216.56	17	16	GNRA
2	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	15.38	-9321.97	17	17

Loop 14 Internal loop

Column numbers: 320-333, 383-386

    Scored sequences and counts

    
    CUGUUA---UGCAG*CAUG    6

    
    CUGUUAACGGAAAG*CAUG    3

    
    CUGUUAACAGGAAG*CAUG    2

    
    CUGUUG-CAAAUAA*UAUG    2

No Matches Found View All Results for this Loop

Loop 15 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

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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_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 16 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 17 Hairpin loop

Column numbers: 354-370

    Scored sequences and counts

    
    -----CACGAUAU----    3

    
    ACGUCGUGA----GACA    2

    
    AUGUCGGGA----GACA    2

    
    U----AUUA-------A    2

    
    -----AAAU--------    2

    
    ACGUCGCGA----GACA    1

    
    -----UGAUAC------    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_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	30.77	-158.12	4	3
2	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	30.77	-253.84	3	3
3	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	30.77	-260.70	5	5
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	30.77	-4150.23	4	4
5	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	30.77	-4157.94	4	4	Mini UNCG
6	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	30.77	-4184.17	4	5	Mini UNCG
7	Motif group HL_32346.4 View motif instance in 3D Basepair signature: cWW-F	30.77	-4188.74	4	5
8	Motif group HL_86769.4 View motif instance in 3D Basepair signature: cWW-cWW-cSH-F	23.08	-137.01	5	3
9	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	15.38	-146.41	5	4	tRNA anticodon loop with synthetase
10	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	15.38	-155.73	3	4

Loop 18 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 19 Hairpin loop

Column numbers: 447-455

    Scored sequences and counts

    
    AUAUUUUAU    3

    
    U-AAAC--A    3

    
    --GAAA---    3

    
    AUAUCUUAU    2

    
    UUAUAA-AA    1

    
    --UUAAA--    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_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-43.82	3	2
2	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	53.85	-57.99	3	2
3	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-64.93	3	2
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	53.85	-65.63	3	2
5	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	53.85	-93.46	3	2	tRNA D-loop
6	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.85	-99.84	3	2
7	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	46.15	-37.53	4	2
8	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	46.15	-101.36	3	3	Mini UNCG
9	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	46.15	-114.00	2	2	GNRA
10	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	46.15	-932.03	3	2

Nucleotide numbers Coloring options:

JAR3D Query RF02997-3.98 completed Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.

RF02997 HOLDH RNA

Input Summary

Jump to results for:

Loop 1 Internal loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Hairpin loop

Loop 5 Internal loop

Loop 6 3-way junction loop

Loop 7 Hairpin loop

Loop 8 Hairpin loop

Loop 9 Internal loop

Loop 10 Hairpin loop

Loop 11 Internal loop

Loop 12 Internal loop

Loop 13 Hairpin loop

Loop 14 Internal loop

Loop 15 Internal loop

Loop 16 Internal loop

Loop 17 Hairpin loop

Loop 18 Hairpin loop

Loop 19 Hairpin loop

JAR3D Query RF02997-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold secondary structure.