JAR3D on RF02921

RF02921 RT-14 RNA

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112
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((((((((((..(((.......(.(((...(((((........)))))))).).....)))))))).))))).....................(.(((((....................))))))..............((((((((((...(((......(((..........))).....))).))).).)))).))
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>URS0000D6A192_12908_1-142
CUCUACCAC-AUAGUC--AGAUGCCGG---CAGCC-UGAGU--GGCUGCCUCCCAGU-ACAAG--G-UAG----GUAAAGGAC-UACGU-UUCC-GCGCC------AUA-----------GGCGAAAAACU-AAAACA--GCGCACACAC---CGAUAGUA-GG---AAUAU----CC-GAAUUCC-GUG-U-GUGC---
>URS0000D6A142_12908_1-142
CUCUACCAC-AUAGUC--AGAUGCUGA---UAGCC-UAAGU--GGCUAUCUCCCAGU-ACAAG--G-UAG----GUAAAGGAC-UACGUUUCCG-CGCC-------AUA------------GGCGAAAAACUAAAACA--GCGCACACAC---CGAUAGUAGG----AAUAU----AC-GAAUUCC-GUG-U-GUGC---
>URS0000D69338_12908_1-158
CUUUGCCAUCUUCGUC--AGAAGUUGU---CAACU-CAAG---GGUUGGCAUCCAGC-ACAGUUGG-UGA-----UAAAGGGG-UCUGUUUCCU-UGCCCUGCC--AUAU------GGCGCGGCAAAAAAU-CUACGUAGCUGCGAAUGC---CGACAAUA-GG---UAAAU----CC-GAACUCC-GCAAA-GCGC-AG
>URS0000D6757A_12908_1-143
CUCUACCUUCGUGGUC--AGAUGUUAU---AAACU-CAAG---GGUUUAUAUCCAGU-ACAGAAGG---G-----UAAAGGAU-CUUGUUUCCG-UUGC-------GAUA-----------GCAAAAAAAUA---CUAUUUAGCACAAGC---CGAGAGUA-UC---GAUAUU---GA-GAAAUCC-GCA---GUGCUU-
>URS0000D6B9C4_293826_1-146
CAUUUUCAU---CGCC--AGAAG-GCA--AGAUUCCCAAG--GGAGCUUGC-ACAGU-GC--AUGG-AAAA----U-AAGGGG-UCCAUUUCCC-UGCCU------AAA-----------AGGCAAAAAAAUAUAUUG--CUAUGGAAAU---AGCUAGUAGGU---UUAUUC---UC-GAAGAGU-AUUAC-ACAU-AG
>URS0000D67851_12908_1-141
CUCUC----AUUGGCC--AGAUAUUUA---UUACU-UAAG---GGUAAUAUUUCAGU-GC-A-----GAGAGAA-UAAAGGAU-UCCAUUUCCU-UGC--------AUUUA-----------GCAAAAAAU-AUAUUUGGAUAUGAAUGC---CGGAAGUAAGA---AUAAUA---UCCGAACCAC-GCAAU-GC-----
>URS0000D6A898_12908_1-147
CUCUACUCUCACAGCC--AGAUG-UUG---CAGACUCAAG--GGUCUGCAU-CCAGC-GCAGGGAG---G----AUAAAGGAG-CCUAUCUCCU-UGCC-------GCAU-----------GGCAGAAAAGUAAAUUG--UUAUGGAUGC---CGAUAGUA-GCC--ACAA----GGC-CAAUUCC-GCAAC-ACAU-AA
>URS0000D6B9E4_12908_1-143
CUCUC-----GCGGCC--AGAUG-UUG---CAGACUCAAG--GGUCUGCAU-CCAGU-GC-G-----GAGAGAA-UAAAGGAG-UCCAUCUCCA-UGCC-------GAAA-----------GGCAAAAAAG-UAAAAUUUUUAUGGAUGC---CGACAGUA-GCC--GCAA----GGC-CAACUCC-GCAAC-ACAU-AA
>URS0000D6CF82_12908_1-141
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAAUGUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D6CF82_1262790_1-141
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAAUGUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D6AD79_12908_1-140
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUAUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAU-GUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D6688C_12908_1-140
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-GUGC-------UCUC-----------GCAAAAAAAU-GUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D68E6A_12908_1-140
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAU-GUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D68E6A_742740_1-140
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAU-GUAAUG-GGCAUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GC-----
>URS0000D6C164_12908_1-145
CUCUGCCUU-CAAGUC--AGAUG-CUG---CAGACCUAAUG-GGUGUGCAG-UCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUCUCCU-UUGC-------UCUC-----------GCAAAAAAAU-GUAAUGGGCAUUGAAUGC---CGGUAGUA-GU---AUAA-----GC-GAAUCCC-GCAAU-GCUC-UG
>URS0000D68716_12908_1-145
CUCUACCUUCUAAGUC--AGAUG-UUG---UAUACCUACCG-GGUAUACUU-CCAGU-AC-AGAGG-U-G-----UAAAGGAU-UCCGUUUCCU-UGCU-------GUAU-----------AGCAAAAAGU-AAAUC---AUGUGACUGC---CGGCGGUA-GA---GAAAAU---UC-GAGGCUC-GCAAU-GCAC-AU
>URS0000D673CB_1198630_1-139
CUCUC-----AUUGUC--AGAAG-UGA---UAUUCUUAAG--GGAAUAUCU-CCAGU-AC-A-----GAGAGAA-UAAAGGGG-UUCAUCUCCC-UGCC-------GACAA----------GGCAAAAAACUGAAUUG--CUAUGAAAGC---AUCUAGUA-G----GACA------C-GAACGAU-GCU-ACGCAU-AG
>URS0000D6BD4C_12908_1-142
----CUCUCCAAAGUC--AGAUG-CUA---UAAUCUCAAG--GGAUUUUAG-CCAGC-AC-AGAGA-G-G----AUAAAGGGG-UCUGCUUCCG-UGCC-------GACAA----------GGCAAAAAACAAGAUGAAGCUGUGCCUGC---CGUUAGUA-G----AUCC------C-GAACGCC-GCAAA-GCAC-AG
>URS0000D68EDC_459349_1-142
UUCCAUUA--UAAUAAUCAGAAU-UUA---CUCUG-UACG---CAAAGUAA-AU-GU-AAAAAAGG-GAA---A-UCCAGAGC-UUCAU-CCAG-UUCUC------UAAAA---------GAGACAAAAAG--AAAG---UGAGUUUAUU---GCUGAGUA-GU---UAAA-----UC-AAAAAGC-AGU-A-AACU-CU

There are no chains in PDB that we map to Rfam family RF02921.

Jump to results for:

Loop 1IL Column numbers: 5-6, 66-68
Loop 2IL Column numbers: 10-13, 61-62
Loop 3IL Column numbers: 15-23, 53-59
Loop 4IL Column numbers: 23-25, 51-53
Loop 5IL Column numbers: 27-31, 48-49
Loop 6HL Column numbers: 35-44
Loop 7IL Column numbers: 94-96, 125-126
Loop 8HL Column numbers: 100-121
Loop 9IL Column numbers: 142-143, 197-199
Loop 10IL Column numbers: 146-147, 192-194
Loop 11IL Column numbers: 147-148, 190-192
Loop 12IL Column numbers: 150-154, 186-188
Loop 13IL Column numbers: 156-163, 178-184
Loop 14HL Column numbers: 165-176

Loop 1 Internal loop

Column numbers: 5-6, 66-68

    Scored sequences and counts

    
    AA*U-U   89

    
    GC*G-U    8

    
    AC*G-U    6

    
    AU*A-C    3

    
    CU*A-G    3

    
    AU*U-U    2

    
    GU*A-C    2

    
    UA*U-A    2

    
    AA*UUU    1

    
    AG*U-U    1

    
    AU*A-U    1

    
    AU*G-G    1

    
    CC*G-G    1

    
    GC*G-A    1

    
    GC*G-C    1

    
    GG*C-C    1

    
    UA*U-U    1

    
    UC*G-A    1

    
    UG*C-A    1

    
    UG*C-U    1

    
    UU*G-A    1

    
    Omitted sequenced and counts

    
    C-*--G    5

    
    AC*G--    2

    
    --*---    2

    
    AA*--U    1

    
    CC*G--    1

    
    --*U-U    1

    
    AG*---    1

    
    GC*---    1

    
    U-*--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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	96.88	27.62	3	2	Multiple bulged bases
2	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	95.31	19.20	2	1	Major groove platform
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	92.97	21.60	1	1	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	91.41	18.10	4	1
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	90.63	4.80	2	1	Single bulged G
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	86.72	18.89	4	1	Intercalated cWS
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	85.94	10.29	3	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	85.94	4.92	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	85.16	12.37	3	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	85.16	7.58	5	1

Loop 2 Internal loop

Column numbers: 10-13, 61-62

    Scored sequences and counts

    
    AAUU*AG    8

    
    AAUU*AA    7

    
    -UAA*UU    7

    
    -AAU*AA    5

    
    ACAU*AA    3

    
    AUUU*AG    3

    
    -AUA*AA    3

    
    -CUU*UA    3

    
    AAAU*AA    2

    
    -CUU*CU    2

    
    -UAA*AG    2

    
    AAAA*AU    1

    
    AAAU*AG    1

    
    AAGC*AA    1

    
    AGAG*UA    1

    
    AUAA*AU    1

    
    AUUU*AA    1

    
    CACA*AG    1

    
    CGUG*AG    1

    
    CUUC*AG    1

    
    UACG*AA    1

    
    UUUU*AG    1

    
    UUUU*UA    1

    
    -AAA*AA    1

    
    -AAA*AU    1

    
    -AAA*GU    1

    
    -AAA*UA    1

    
    -ACG*AA    1

    
    -CAA*AC    1

    
    -CGA*AU    1

    
    -UAA*AA    1

    
    -UCA*AG    1

    
    -UGU*UU    1

    
    Omitted sequenced and counts

    
    -UAU*-A   16

    
    -CAA*-A   12

    
    -CAU*-A    9

    
    AUAA*-A    3

    
    -UAU*-U    3

    
    -CAA*-U    2

    
    -CGU*-A    2

    
    -CUU*-A    2

    
    AUAU*--    2

    
    AUAG*-A    1

    
    AUUG*-A    1

    
    CAAA*-A    1

    
    CUAA*-A    1

    
    UUUU*-A    1

    
    UUUU*-G    1

    
    -ACC*-A    1

    
    -AUA*-A    1

    
    -AUA*-C    1

    
    -AUU*-A    1

    
    -CAA*-C    1

    
    -GCA*-C    1

    
    -GCG*-G    1

    
    -GUA*-A    1

    
    -GUG*-A    1

    
    -UAA*-C    1

    
    -UAG*-C    1

    
    -UGC*-A    1

    
    -UUU*-A    1

    
    GCAA*--    1

    
    -AAU*--    1

    
    -ACU*--    1

    
    -AUA*--    1

    
    ---A*--    1

    
    ---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_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	92.54	24.57	4	1	Intercalated cWS
2	Motif group IL_82107.4 View motif instance in 3D Basepair signature: cWW-cWW	91.04	36.37	2	0	Multiple bulged bases
3	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	89.55	35.72	3	0	Major groove intercalation
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	89.55	27.15	4	1
5	Motif group IL_42626.2 View motif instance in 3D Basepair signature: cWW-cWW	73.13	1.12	4	1
6	Motif group IL_76709.2 View motif instance in 3D Basepair signature: cWW-L-cWW-L	68.66	17.09	4	0
7	Motif group IL_56987.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.19	3.08	4	1
8	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	59.70	-1.82	3	0	Multiple bulged bases
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	55.22	2.46	2	1	Single stack bend
10	Motif group IL_00881.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	52.24	-11.21	4	1

Loop 3 Internal loop

Column numbers: 15-23, 53-59

    Scored sequences and counts

    
    CU--AGAUU*ACAAU-G   24

    
    UC--AGAUU*ACAGU-A   10

    
    UC--AGAUG*UCAGU-A    8

    
    UU--CGAUG*CCAAU-A    7

    
    UC--AGAUG*CCAGU-A    6

    
    CC--AGAUG*CCAGU-G    4

    
    CG--AGAUU*ACAGU-G    4

    
    UG--AGAUU*ACAGU-A    4

    
    UC--AGACU*GCAAGGA    3

    
    CC--AGAUA*UCAGU-G    3

    
    CC--AGAUU*ACAGA-G    3

    
    CC--AGAUU*ACAGC-G    3

    
    CG--AGAUU*ACAGA-G    3

    
    UC--AGAAG*CCAGU-A    3

    
    CACCUGAUU*AGCAUAG    2

    
    CU--AGAUA*UCAAU-G    2

    
    UC--AGAAG*CCAGC-A    2

    
    UC--AGACU*GCGAA-G    2

    
    UC--AGAUU*ACAGC-A    2

    
    UG--AGAUG*CCAGU-A    2

    
    -A--AGAGU*AAAUUA-    2

    
    CCAGUGGGG*CGAGA-G    1

    
    UAUCAGAUA*AGAGU-A    1

    
    UUCGAGAUU*ACAGU-G    1

    
    UUUCAGAUG*CCAGU-A    1

    
    UUUCAGAUU*ACAGU-A    1

    
    UUUGAGAUU*ACAGU-A    1

    
    AAUCAGAAU*AU-GU-A    1

    
    CC--AGAUU*ACAGUAG    1

    
    CU--AGAUU*ACAAUUG    1

    
    CA--GGAUU*ACAAU-G    1

    
    CC--AGAAG*ACAGA-G    1

    
    CC--AGAAG*ACAGC-G    1

    
    CC--AGAAG*ACAGU-G    1

    
    CC--AGAAG*CCAGU-G    1

    
    CC--AGAAG*UCAGU-G    1

    
    CC--AGAAU*ACAGU-G    1

    
    CC--AGAAU*AGAGU-G    1

    
    CC--AGAUA*UCAGC-G    1

    
    CC--AGAUG*AGAGU-G    1

    
    CC--AGAUG*CCAGC-G    1

    
    CG--AGAAG*ACAGU-G    1

    
    CU--AGGUA*UCAAU-G    1

    
    CU--CGAUU*ACAAU-G    1

    
    UC--AGAAG*ACAGA-A    1

    
    UC--AGAAG*GCAGA-A    1

    
    UC--AGACU*ACAGC-A    1

    
    UC--AGAUA*ACAGA-A    1

    
    UC--AGAUG*CCAGC-A    1

    
    UC--AGAUU*AUAGC-A    1

    
    UC--AGCAU*ACCGU-A    1

    
    UC--GGAAU*ACAGU-A    1

    
    UG--AGAGU*AGAGG-G    1

    
    UG--AGAUG*CCGGU-A    1

    
    UG--AGAUU*ACAGU-G    1

    
    UG--AGAUU*ACGGU-A    1

    
    UG--CGAUU*ACAGU-G    1

    
    UU--AGAUG*CCAAU-A    1

    
    UU--AGAUU*ACAAU-A    1

    
    UU--AGAUU*ACAGU-A    1

    
    UU--AGCAG*CCAGU-A    1

    
    UU--AGGUA*UCAAA-U    1

    
    UU--UGAUG*CCAAU-A    1

    
    -A--AGGGU*AAAUUA-    1

    
    UU--AGGUA*UCAA--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_71294.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	4.20	-56.84	7	4	Double sheared; A in syn; two near cWW pairs
2	Motif group IL_34822.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	2.10	-52.06	7	5
3	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	1.40	-67.91	6	5	7x6 Sarcin-Ricin; G-bulge
4	Motif group IL_58126.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-L-R-L-cWW	0.70	-27.05	6	4
5	Motif group IL_12745.1 View motif instance in 3D Basepair signature: cWW-tWH-tWH-tHW-tHW-cWW	0.70	-43.82	8	5	tWH-tWH-tHW-tHW
6	Motif group IL_78349.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW-L-L	0.70	-55.18	8	5
7	Motif group IL_23038.1 View motif instance in 3D Basepair signature: cWW-L-R-tWH-L-R-L-cWW-cWW	0.70	-65.25	8	6
8	Motif group IL_22564.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	0.70	-66.43	9	6
9	Motif group IL_57188.5 View motif instance in 3D Basepair signature: cWW-tWW-L-tWW-cWW-cSH	0.70	-76.23	6	5	Kink-turn related
10	Motif group IL_76308.6 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tHS-cWW-cWW	0.70	-79.16	8	4	tSH-tWH-tHS-cWW

Loop 4 Internal loop

Column numbers: 23-25, 51-53

    Scored sequences and counts

    
    U-A*U-A   67

    
    G-U*U-C    9

    
    G-C*G-U    7

    
    G-U*G-C    5

    
    U-U*A-G    5

    
    G-C*G-A    4

    
    U-G*U-A    4

    
    U-U*A-A    4

    
    GCU*UCC    3

    
    GUU*AUC    3

    
    G-A*U-C    3

    
    G-G*U-C    3

    
    GUU*UUC    2

    
    A-A*U-U    2

    
    A-G*C-U    2

    
    A-U*U-U    2

    
    U-G*C-A    2

    
    AUU*UUU    1

    
    GCC*UCC    1

    
    GCG*CGA    1

    
    GGC*GUU    1

    
    A-G*CUA    1

    
    A-U*AUA    1

    
    G-C*GCC    1

    
    G-U*UUC    1

    
    A-C*G-U    1

    
    A-G*U-U    1

    
    G-C*G-C    1

    
    G-C*G-G    1

    
    G-G*C-A    1

    
    G-U*A-C    1

    
    G-U*A-U    1

    
    U-C*G-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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	87.41	13.89	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	86.71	10.21	4	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	84.62	18.37	2	1	Multiple bulged bases
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	72.73	11.15	2	1	Intercalated cWS
5	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	69.93	9.41	4	1
6	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	68.53	-0.78	3	1	Stack and bulge
7	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	68.53	-6.09	1	1	Single bulged G
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	67.13	0.84	3	1	Major groove intercalation
9	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	67.13	-0.47	4	1
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	61.54	1.54	2	1	Single stack bend

Loop 5 Internal loop

Column numbers: 27-31, 48-49

    Scored sequences and counts

    
    A---U*AU   74

    
    G---C*GC   11

    
    U---A*UA   11

    
    G---C*AC    5

    
    A---U*GU    4

    
    G---U*AC    4

    
    A---C*GU    3

    
    C---A*UG    3

    
    G---U*AU    3

    
    G---U*GC    3

    
    U---G*CA    3

    
    G---G*CC    2

    
    U---A*UU    2

    
    UUAUA*UA    1

    
    A--AA*UU    1

    
    A--AC*GU    1

    
    A--AG*UU    1

    
    A--CA*UA    1

    
    U--AA*UU    1

    
    A---A*UU    1

    
    A---G*CU    1

    
    A---U*AG    1

    
    A---U*UU    1

    
    C---A*UA    1

    
    C---U*GG    1

    
    G---A*UC    1

    
    U---C*GG    1

    
    U---U*AA    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	95.10	15.70	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	93.71	26.00	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	93.01	21.25	3	1	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	86.71	19.05	4	1
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	86.01	13.07	3	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	85.31	6.56	4	1
7	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	85.31	1.93	1	1	Single bulged G
8	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	84.62	18.77	4	1	Intercalated cWS
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	83.92	13.16	1	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	83.92	8.99	1	1	Single stack bend

Loop 6 Hairpin loop

Column numbers: 35-44

    Scored sequences and counts

    
    U-UAAG---G   48

    
    U-UACG---G   30

    
    CCUAAUG-GG    9

    
    U-CAAG---G    9

    
    U-UAUG---G    8

    
    C-UACG---G    4

    
    CUCAAG--GG    3

    
    U-UACG---A    3

    
    CCUACCG-GG    2

    
    GAUACG--UC    2

    
    C-UAAGU--G    2

    
    U-CAUG---G    2

    
    U-UAGG---G    2

    
    GGUCAAGGCU    1

    
    AACACGC-GG    1

    
    AUCAAG--GU    1

    
    CCCAAG--GG    1

    
    CCCACG--GG    1

    
    CUUAAG--GG    1

    
    UCUACG--GG    1

    
    UUCACG--GG    1

    
    C-UGAGU--G    1

    
    UC-AAC--GA    1

    
    C-CAAG---G    1

    
    C-UAAG---G    1

    
    C-UACG---A    1

    
    C-UAUG---G    1

    
    G-UACG---C    1

    
    U-GAAA---A    1

    
    U-UAGG---A    1

    
    U-UCCC---A    1

    
    --UAAC---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 HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	71.33	0.24	3	2
2	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	71.33	-19.30	2	2
3	Motif group HL_56676.1 View motif instance in 3D Basepair signature: cWW-F-F	70.63	-19.75	2	2
4	Motif group HL_99040.1 View motif instance in 3D Basepair signature: F-F-F-F-F-F	70.63	-69.58	2	2
5	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	50.35	-14.22	2	2
6	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	45.45	-19.19	3	2
7	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	38.46	-10.51	2	2
8	Motif group HL_34617.5 View motif instance in 3D Basepair signature: cWW-tSW-F	37.76	-19.22	2	1	UNCG
9	Motif group HL_55195.3 View motif instance in 3D Basepair signature: cWW-F	34.27	-36.91	2	2
10	Motif group HL_32392.1 View motif instance in 3D Basepair signature: cWW-F-F	34.27	-37.95	3	2

Loop 7 Internal loop

Column numbers: 94-96, 125-126

    Scored sequences and counts

    
    U-U*UA   62

    
    A-U*UA   30

    
    U-U*AA   16

    
    A-U*AA    8

    
    G-U*CA    6

    
    C-U*AA    5

    
    C-G*AA    2

    
    C-U*UA    2

    
    G-U*AA    2

    
    G-U*AC    2

    
    UGU*CA    1

    
    C-C*GA    1

    
    G-C*GA    1

    
    U-C*GA    1

    
    U-G*AA    1

    
    U-G*CA    1

    
    U-G*UA    1

    
    U-U*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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	74.13	3.02	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	21.68	-4.64	4	2	Multiple bulged bases
3	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	19.58	-20.05	4	1	Major groove intercalation
4	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	19.58	-24.72	4	1
5	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	16.08	-10.20	3	1	Multiple bulged bases
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	16.08	-12.32	3	1	Intercalated cWS
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	14.69	-13.60	4	1
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	14.69	-21.42	3	1	Single stack bend
9	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	14.69	-23.13	5	1
10	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	14.69	-24.86	2	1	Single bulged G

Loop 8 Hairpin loop

Column numbers: 100-121

    Scored sequences and counts

    
    A------AUU-----------U   26

    
    -------UCUC-----------    7

    
    A------UUU-----------U    6

    
    AAAU---GUAA-------GUUU    5

    
    GG-----GACUA--------CC    5

    
    -------AAUUA----------    5

    
    -------AAUUC----------    5

    
    --------UAAG----------    5

    
    -------UAUUAAAU-------    4

    
    UU-----UCUAA--------AA    3

    
    -------GACAA----------    3

    
    -------GCAAA----------    3

    
    A------AUG-----------U    3

    
    -------GUA------------    3

    
    -------AUAAAA---------    2

    
    -------GAUAA----------    2

    
    C------AUA-----------G    2

    
    -------GAAA-----------    2

    
    -------AUA------------    2

    
    AUUUACUAAUAC---AGUAAAA    1

    
    GCGCCAGCUUGU---CUGGC-C    1

    
    AAAUUGCAAAA----GCAA-CA    1

    
    GCGAUCUAUUUU---GGA--CC    1

    
    GCGCAUUGUUC----AAUGC-C    1

    
    GC-AAGAUCUA----UCUU--C    1

    
    AAAA---GUAAAG-----UUUU    1

    
    CUGCC--AUAU------GGCGC    1

    
    GGGUG--GUGA------CACCU    1

    
    CAUA---GUGAU------UAUG    1

    
    AAAA---GAAA-------UUUU    1

    
    AAAA---GCAA-------UUUU    1

    
    AAAA---GGAA-------UUUU    1

    
    AAAA---GUAA-------UUUU    1

    
    AAAA---GUAAC------UU-U    1

    
    AAAU---GUAA-------AUUU    1

    
    CUUG---GUGA-------CAAG    1

    
    UGCA---GCGA-------UGCG    1

    
    -------AAGAAAAAAA-----    1

    
    A------AGUAAAAG------U    1

    
    -------AUGAAAAU-------    1

    
    -------UAUAAAUU-------    1

    
    -------UUAGAAUU-------    1

    
    A------AUAAA---------A    1

    
    C------UAAAA---------G    1

    
    -------GAUGA---------A    1

    
    -------GCAAAA---------    1

    
    -------UGAAAU---------    1

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

    
    C------GAAA----------G    1

    
    C------GAGA----------G    1

    
    C------GCAA----------G    1

    
    U------UUAA----------A    1

    
    -------ACUAU----------    1

    
    -------AUUUA----------    1

    
    -------GAAAA----------    1

    
    -------GAAUA----------    1

    
    -------UUGAA----------    1

    
    A-------AUA----------U    1

    
    A------AUA-----------U    1

    
    A------GUU-----------U    1

    
    C------AAG-----------C    1

    
    U------AAA-----------A    1

    
    -------AUUU-----------    1

    
    -------GAUA-----------    1

    
    -------GCAU-----------    1

    
    -------GUAU-----------    1

    
    -------UCUU-----------    1

    
    -------UUAA-----------    1

    
    -------UUUG-----------    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	48.25	-2100.93	2	1
2	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	45.45	-1735.90	4	2
3	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	43.36	-461.73	3	2
4	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	43.36	-1735.15	2	2	Mini UNCG
5	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	42.66	-64.93	3	2
6	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	42.66	-1747.55	2	2	Mini UNCG
7	Motif group HL_32346.4 View motif instance in 3D Basepair signature: cWW-F	41.26	-1745.28	2	2
8	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	39.16	-440.10	4	3
9	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	37.76	-835.23	3	2	tRNA D-loop
10	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	37.06	-2113.84	4	2

Loop 9 Internal loop

Column numbers: 142-143, 197-199

    Scored sequences and counts

    
    UA*U-A   50

    
    CA*U-G   15

    
    AA*U-U   13

    
    AG*C-U    8

    
    AU*A-U    8

    
    UG*C-A    5

    
    GG*C-C    4

    
    UU*A-A    3

    
    AG*U-U    2

    
    GA*U-C    2

    
    GC*G-C    2

    
    AA*UUU    1

    
    AG*CUU    1

    
    CA*UAG    1

    
    GA*UGU    1

    
    AA*UA-    1

    
    AC*G-U    1

    
    AU*C-U    1

    
    CG*C-G    1

    
    GA*U-U    1

    
    GG*C-U    1

    
    GU*A-C    1

    
    GU*AU-    1

    
    UG*U-A    1

    
    Omitted sequenced and counts

    
    CA*---    6

    
    GA*---    5

    
    CG*C--    3

    
    -G*CUU    1

    
    CA*--G    1

    
    UG*C--    1

    
    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	22.28	2	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	99.20	29.41	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	99.20	25.70	3	1	Multiple bulged bases
4	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	97.60	9.56	4	1
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	96.80	23.03	2	1	Intercalated cWS
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	96.80	14.97	3	1	Major groove intercalation
7	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	96.00	8.30	1	1	Single bulged G
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	95.20	15.89	2	1	Single stack bend
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	95.20	11.69	2	1	Single stack bend
10	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	94.40	21.97	4	1

Loop 10 Internal loop

Column numbers: 146-147, 192-194

    Scored sequences and counts

    
    AU*A-U   29

    
    UU*A-A   20

    
    AC*G-U   16

    
    AA*U-G    8

    
    UA*U-A    8

    
    GC*G-C    6

    
    CU*A-G    5

    
    AA*C-G    4

    
    AU*G-U    4

    
    CA*U-G    4

    
    UG*UAG    3

    
    AG*U-U    3

    
    CG*C-G    3

    
    GA*C-A    3

    
    GC*G-U    3

    
    GU*A-C    3

    
    AA*A-G    2

    
    GA*A-A    2

    
    AA*ACG    1

    
    AA*A-U    1

    
    AA*U-U    1

    
    AC*U-G    1

    
    AU*G-A    1

    
    CA*G-G    1

    
    CC*A-G    1

    
    GA*U-A    1

    
    GU*C-C    1

    
    UG*-AA    1

    
    UG*-AG    1

    
    UG*C-A    1

    
    UU*G-A    1

    
    Omitted sequenced and counts

    
    CA*--G    1

    
    CG*--A    1

    
    UU*--A    1

    
    A-*--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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	89.21	15.00	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	80.58	19.35	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	80.58	14.73	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	76.98	-2.41	2	1	Single bulged G
5	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	74.82	7.14	3	1	Major groove intercalation
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	74.82	0.49	4	1
7	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	74.10	11.63	3	1	Intercalated cWS
8	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	73.38	11.00	4	1
9	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	73.38	5.99	2	1	Single stack bend
10	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	73.38	2.11	2	1	Single stack bend

Loop 11 Internal loop

Column numbers: 147-148, 190-192

    Scored sequences and counts

    
    UA*U-A   36

    
    CA*U-G   24

    
    UU*A-A    9

    
    AU*AAU    8

    
    UG*C-A    8

    
    AG*C-U    7

    
    AC*G-U    4

    
    UA*U-G    4

    
    AU*AAC    3

    
    GA*G-U    3

    
    GG*C-C    3

    
    AA*UAA    2

    
    AG*CAC    2

    
    AA*U-A    2

    
    GU*A-U    2

    
    AA*GAA    1

    
    AA*UAC    1

    
    AG*UAC    1

    
    AU*AAA    1

    
    CU*AAA    1

    
    CU*AAU    1

    
    UG*CAA    1

    
    AA*U-G    1

    
    AG*U-U    1

    
    AU*G-U    1

    
    CU*A-G    1

    
    GA*U-U    1

    
    GA*UA-    1

    
    GC*G-C    1

    
    UA*A-A    1

    
    UC*G-A    1

    
    UC*G-G    1

    
    UG*C-C    1

    
    UG*U-G    1

    
    UU*G-A    1

    
    Omitted sequenced and counts

    
    GA*U--    2

    
    A-*G-U    1

    
    AA*A--    1

    
    UG*C--    1

    
    -G*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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	94.89	25.25	2	1	Major groove platform
2	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	93.43	30.10	2	1	Multiple bulged bases
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	89.78	22.42	2	1	Intercalated cWS
4	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	86.13	18.92	3	1	Major groove intercalation
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	86.13	14.31	4	1
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	85.40	21.88	4	1
7	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	85.40	21.05	2	1	Single stack bend
8	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	85.40	16.58	2	1	Single stack bend
9	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	85.40	8.00	3	1	Stack and bulge
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	83.21	9.19	4	1

Loop 12 Internal loop

Column numbers: 150-154, 186-188

    Scored sequences and counts

    
    A---U*A-U   40

    
    C---C*C-G   19

    
    G---U*A-U   18

    
    G---U*A-C   17

    
    C---G*C-G    9

    
    GCGAC*AAC    4

    
    G---U*AUA    3

    
    C---A*U-G    3

    
    U---A*U-A    3

    
    U---U*G-A    3

    
    A--AU*GGU    2

    
    A---G*U-U    2

    
    U---G*C-A    2

    
    AUAAC*AAU    1

    
    AUUAA*AAU    1

    
    GUAAA*AAC    1

    
    A-UAA*CAU    1

    
    G--CC*GCA    1

    
    U-UAA*A-A    1

    
    U---U*UAA    1

    
    A---U*A-G    1

    
    C---C*U-G    1

    
    C---U*C-G    1

    
    G---G*C-C    1

    
    G---G*C-U    1

    
    G---U*C-C    1

    
    G---U*G-A    1

    
    G---U*U-C    1

    
    U---A*U-G    1

    
    U---G*U-U    1

    
    U---U*C-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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	90.21	-0.83	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	88.11	8.83	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	72.73	2.11	3	1	Multiple bulged bases
4	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	66.43	-25.06	1	1	Single bulged G
5	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	58.74	-8.58	3	1	Stack and bulge
6	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	55.94	-2.14	4	1	Intercalated cWS
7	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	53.85	-0.65	3	1
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	53.85	-8.39	2	1	Major groove intercalation
9	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	53.15	-14.66	3	1
10	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	52.45	-14.16	2	1	Single stack bend

Loop 13 Internal loop

Column numbers: 156-163, 178-184

    Scored sequences and counts

    
    UUAGUA-A*U-GAAUA   16

    
    UUAGUA-C*G-GAAUA   16

    
    GUAGUA-G*C-GAAUC    7

    
    UUAGUAGG*CAGAAUA    6

    
    UUAGUA-G*C-GAAGG    6

    
    UUAGUA-G*U-GAAUA    6

    
    CUAGUA-A*U-GAAAG    4

    
    UGAGUA-G*C-GAAAA    4

    
    UUAGUA-G*C-GAAAA    4

    
    CCGGUAGG*C-GAAAG    3

    
    AUAGUA-G*C-GAAUU    3

    
    CUAGUA-G*C-GAAAG    3

    
    CUAGUA-G*C-GAACG    3

    
    UUAGUA-A*U-GAAAA    3

    
    UUUGUA-G*C-GAAGA    3

    
    UUAGUA-A*UCGAACA    2

    
    UUAGUAAA*U-GAAUA    2

    
    CCAGUA-G*C-GAGAG    2

    
    CUGGUA-G*C-GAACG    2

    
    UUAGUA-A*U-GAAAG    2

    
    UUAGUA-G*U-GAAAA    2

    
    UUAGUA-U*A-GAAUA    2

    
    AAAGUACC*GUGAAAU    1

    
    CUGGUAGC*GUGAACG    1

    
    CUGGUAGU*AUGAAUG    1

    
    GAAGUAAG*CCGAACC    1

    
    UAAGUAAG*CUGAAAA    1

    
    UAAGUAGG*UAGAACU    1

    
    UUAGUAAA*UUGAAUA    1

    
    UUAGUAAG*UAGAAUG    1

    
    UUAGUAGA*UAGAAAA    1

    
    UUAGUAGA*UUGAAUA    1

    
    UUAGUAGG*CUGAAUA    1

    
    AUAGUA-A*UGAAAUU    1

    
    AUAGUAGG*C-GAAUU    1

    
    CUAGUAGG*C-GAAGA    1

    
    CUGGUAGG*C-GAACG    1

    
    UUAGUA-A*UGGAAUA    1

    
    UUAGUA-G*UAGAAAA    1

    
    UUAGUAGG*C-GAAAA    1

    
    ACAAUA-G*C-GAACU    1

    
    ACAGUA-G*C-CAACU    1

    
    AGAGUA-U*A-GAAAU    1

    
    AUAGUA-A*U-GAACU    1

    
    AUAGUA-G*C-CAAUU    1

    
    AUAGUA-G*C-GAACU    1

    
    AUGGUA-G*C-GAAGU    1

    
    CAAGUA-A*U-GAAAG    1

    
    CCAGUA-A*U-GAAAG    1

    
    CCAGUA-G*C-AACCG    1

    
    CCGGUA-G*C-GAAAG    1

    
    CUGGUA-G*C-GAAAG    1

    
    CUGGUA-G*C-GAAGG    1

    
    GCGGUA-G*C-GAGGC    1

    
    UGAGUA-G*C-AAAAA    1

    
    UUAGUA-A*-GGAAUA    1

    
    UUAGUA-A*A-GAAUA    1

    
    UUAGUA-A*U-GAGGA    1

    
    UUAGUA-G*C-AAAGG    1

    
    UUAGUA-G*C-GAACG    1

    
    UUAGUA-G*C-GAAGA    1

    
    UUAGUA-G*C-GAAUA    1

    
    UUAGUA-G*U-GAAAG    1

    
    UUAGUA-U*G-GAAUA    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_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	90.91	49.90	4	1	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
2	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	83.92	46.27	3	1	7x6 Sarcin-Ricin; 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	73.43	17.86	6	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	72.03	7.90	5	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	62.24	-0.20	4	2	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	39.16	-12.29	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	25.87	-8.09	6	3	8x6 Sarcin-Ricin with inserted Y; G-bulge
8	Motif group IL_65594.1 View motif instance in 3D Basepair signature: cWW-L-R-tSW-tHH-cSH-tWH-tHS-cWW	23.08	-16.15	5	3	8x7 Sarcin-Ricin; G-bulge
9	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	20.98	-33.74	7	4	tSH-tSH-tHH-tHS
10	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	17.48	-31.73	7	4	8x6 Sarcin-Ricin with bulged A; G-bulge

Loop 14 Hairpin loop

Column numbers: 165-176

    Scored sequences and counts

    
    ---GAAA-----   11

    
    ---AAAU-----    9

    
    ---AUAA-----    7

    
    ---AAAAU----    5

    
    ---GAAAA----    5

    
    ---AAAA-----    5

    
    ---AAUU-----    5

    
    ---UAA------    5

    
    ---GAGA-----    4

    
    ---UAAA-----    4

    
    ---UUUG-----    4

    
    AUUAUAU--AAU    3

    
    ---AAUAU----    3

    
    ---UAUA-----    3

    
    ---AAA------    3

    
    ---AUG------    3

    
    AU-UUUAU--AU    2

    
    UAUUAG---AUA    2

    
    A--AAA-----U    2

    
    C--UAA-----G    2

    
    CUUGAAACAAAG    1

    
    CUUGAAACAAGG    1

    
    AAGAAAUU-CUU    1

    
    UGAUGAU--UCG    1

    
    AGAUUU---UCU    1

    
    UAAUAA---UUA    1

    
    UAUUAA---AUA    1

    
    AA-UAUA---UU    1

    
    C--AAAUUU--G    1

    
    CA-AUUU---UG    1

    
    CUU-GC---AAG    1

    
    UU-GAAA---AA    1

    
    UU-UAAA---AA    1

    
    UU-UUAU---AA    1

    
    ---CUAAAAA--    1

    
    A--AGUAU---U    1

    
    U--UUUUU---A    1

    
    ---AAAAUG---    1

    
    ---AUAAUA---    1

    
    ---AUAUAC---    1

    
    ---GAAAAU---    1

    
    ---GAAUAA---    1

    
    ---GAUAUU---    1

    
    ---UGUAUU---    1

    
    ---UUAUUC---    1

    
    A--AAAU----U    1

    
    A--AAGA----U    1

    
    A--GAAA----U    1

    
    C--ACAA----G    1

    
    C--AUUG----G    1

    
    C--GCAA----G    1

    
    C--GUAU----G    1

    
    C--UUUU----G    1

    
    U--GAAA----A    1

    
    U--GUAU----G    1

    
    U--UCCG----A    1

    
    ---AUUU----U    1

    
    ---CAUAU----    1

    
    ---GUUAA----    1

    
    ---UAAAU----    1

    
    C--UUA-----G    1

    
    U--AAA-----A    1

    
    ---AAUA-----    1

    
    ---AGAA-----    1

    
    ---AUCC-----    1

    
    ---GAAG-----    1

    
    ---GACA-----    1

    
    ---GCUU-----    1

    
    ---GUAA-----    1

    
    ---UAUU-----    1

    
    ---UUAA-----    1

    
    ---UUCG-----    1

    
    ---UUCU-----    1

    
    ---UUUU-----    1

    
    ---CAA------    1

    
    ---UUU------    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	47.55	-1140.15	2	1
2	Motif group HL_38168.1 View motif instance in 3D Basepair signature: cWW-F	47.55	-1143.65	3	2
3	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	41.96	-256.29	2	2	Mini UNCG
4	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	41.26	-50.56	2	1
5	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	39.86	-183.78	2	2	Mini UNCG
6	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	36.36	-53.29	3	3
7	Motif group HL_32346.4 View motif instance in 3D Basepair signature: cWW-F	32.87	-260.39	3	2
8	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	31.47	-40.12	3	3
9	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	29.37	-50.86	3	2
10	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	28.67	-180.54	3	3

Nucleotide numbers Coloring options:

JAR3D Query RF02921-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF02921 RT-14 RNA

Input Summary

Jump to results for:

Loop 1 Internal loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Internal loop

Loop 5 Internal loop

Loop 6 Hairpin loop

Loop 7 Internal loop

Loop 8 Hairpin loop

Loop 9 Internal loop

Loop 10 Internal loop

Loop 11 Internal loop

Loop 12 Internal loop

Loop 13 Internal loop

Loop 14 Hairpin loop

JAR3D Query RF02921-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.