JAR3D on RF03073

RF03073 RT-19 RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901
....((((((((............))).))))).....((....))............................((((((.....(((..(...(......)...))))....))))).).
>URS0000D665BD_12908_1-112
AUUACCGUCGGCCACGA--UCUAAGCCAGACGGC-A-UGCCACGGCCAGAU---CCGAAAAUGCAACACGAGCACGCGGCCGGUAGAU--GAACCCAUCCAGCCACAUCGACAGCCGCGCA
>URS0000D65871_12908_1-94
ACUACCUCCCGCA--CG---GGAAGCGAGGAGGC-ACAGCCCCGGCCAGUU---CCGAAAAUCAAA-CCGAGAAGGCGGCCGGUAGA---------------CGCA-UCGAAAGCCGC-CA
>URS0000D6A46D_12908_1-94
ACUACCUCCCGCGU-----GGGAAGCGAGGAGGCCC-AGCCCCGGCCAGUU---CCGAAAAUCAAA-CCGAGAAGGCGGCCGGUAGA---------------CGCA-UCGAAAGCCGC-CA
>URS0000D6B60E_1203540_1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B60E_205913_1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B60E_12908_1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D66F8F_12908_1-107
ACUGCCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_12908_1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_411481_1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D6B57C_1263059_1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUAGGC--GAACCCAUCCAGCACCGUCGAACGCCGG-CA
>URS0000D67BFC_12908_1-109
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCAGUAGACCCGAACCCAUCCAGCACCGUCGGCAGCCGG-CA
>URS0000D665C9_12908_1-107
ACUACCCUCCACG-CCA---GCCAGUGAGAGGGC-A-AGCCACGGCCCAG----CCGAAAAUCAAA-CCGAGCACCCGGCCGGUACCC--GAACCCCUCCAGCAACAGGGAACGCCGG-CA
>URS0000D693BF_12908_1-106
ACUACCCUCCGUCA-----UGCCAACGAGAGGGC-A-CGCCUCGGCCCAG----CCGAAAAUCAAA-CCGAGCACGCGGCCGGUAGAC--GACCCACGCCAGCACCGUCGAACGCCGC-CA
>URS0000D6C28D_12908_1-100
ACUACCCUCCGCU-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGGC----------CAAGAUGAGCCGAACGCCGC-CA
>URS0000D6B350_12908_1-97
ACUACCCUCCGCC-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGAC------------CCCAA-GUCGAACGCCGC-CA
>URS0000D658F7_12908_1-98
ACUACCCUCCGCC-------GCCCGCGAGAGGGC-C-AGCCACGGCAACCUAAGCCGAAAAUCAAA-CCAAGCACGCGACCGGUAGGC------------CCCAUGGCCGAACGCCGC-CA
>URS0000D685C7_12908_1-97
ACUACCCUCCGCCUUGG-GGAUAUGCGAGAGGGC-U-UGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGAACGCGACCGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D69B86_565040_1-98
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGGCUGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D6B4A9_12908_1-98
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGGCUGGUAGCA--------------CAU-UGCGAACGCCGC-CA
>URS0000D67B95_12908_1-101
ACUACCCUCCGCUUUCGGGGACACGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAAAGCCGC-CA
>URS0000D6C904_12908_1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCAAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAACGCCGC-CA
>URS0000D6BD80_12908_1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGACCGGUAGGC------------CAUAAGGCCGAACGCCGC-CA
>URS0000D676AC_12908_1-101
ACUACCCUCCGCUUUCGGGGAUAUGCGAGAGGGC-A-AGCCUCGGCCAUG----CCGAAAAUCGAA-UCAAGCACGCGACCGGUAGGC------------CACAUGGCCGAACGCCGC-CA

There are no chains in PDB that we map to Rfam family RF03073.

Jump to results for:

Loop 1IL Column numbers: 9-10, 27-29
Loop 2HL Column numbers: 12-25
Loop 3HL Column numbers: 40-45
Loop 4IL Column numbers: 75-76, 118-120
Loop 5IL Column numbers: 80-86, 109-114
Loop 6IL Column numbers: 88-91, 106-107
Loop 7IL Column numbers: 91-95, 102-106
Loop 8HL Column numbers: 95-102

Loop 1 Internal loop

Column numbers: 9-10, 27-29

    Scored sequences and counts

    
    CC*GAG   22

    
    CG*CAG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full 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	100.00	0	Single stack bend
2	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	99.88	0	Single stack bend
3	Motif group IL_31462.6 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	99.84	0	Single bulged A
4	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	99.44	2
5	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	96.90	2	Multiple bulged bases
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	93.60	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	87.35	3
8	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	86.50	1	Stack and bulge
9	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	81.15	2	Major groove platform
10	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	75.32	3	Major groove platform

Loop 2 Hairpin loop

Column numbers: 12-25

    Scored sequences and counts

    
    CG-CCA---GCCAG    9

    
    CUUUCGGGGAUAUG    5

    
    CC-------GCCCG    2

    
    CUUUCGGGGACACG    1

    
    CCUUGG-GGAUAUG    1

    
    CCACGA--UCUAAG    1

    
    CA--CG---GGAAG    1

    
    CGU-----GGGAAG    1

    
    UCA-----UGCCAA    1

    
    CU-------GCCCG    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_93438.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	39.13	-90.27	5	4
2	Motif group HL_85434.1 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F-F-F	39.13	-96.97	7	5
3	Motif group HL_67407.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	39.13	-730.48	5	5
4	Motif group HL_66853.7 View motif instance in 3D Basepair signature: cWW-cWS-F-cSH	13.04	-97.39	5	5
5	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	13.04	-3356.93	3	3	Pseudoknot geometry
6	Motif group HL_50860.2 View motif instance in 3D Basepair signature: cWW-F-cWH-F-F-F-F	8.70	-125.65	5	4
7	Motif group HL_87553.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	8.70	-171.51	3	3
8	Motif group HL_37369.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F	8.70	-254.71	4	4
9	Motif group HL_07951.3 View motif instance in 3D Basepair signature: cWW-F-F	8.70	-1201.84	5	5	tRNA D-loop
10	Motif group HL_58224.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	4.35	-76.03	6	5

Loop 3 Hairpin loop

Column numbers: 40-45

    Scored sequences and counts

    
    CCACGG   13

    
    CCUCGG    8

    
    CCCCGG    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_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	57.99	1	1
2	Motif group HL_34617.5 View motif instance in 3D Basepair signature: cWW-tSW-F	100.00	52.39	1	0	UNCG
3	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	100.00	29.77	3	2
4	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	100.00	21.41	2	2
5	Motif group HL_99040.1 View motif instance in 3D Basepair signature: F-F-F-F-F-F	100.00	9.67	3	2
6	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	91.30	34.34	1	1
7	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	91.30	14.70	2	2
8	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	91.30	-2.48	2	2
9	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	65.22	14.50	2	1	Pseudoknot geometry
10	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	56.52	1.21	3	2

Loop 4 Internal loop

Column numbers: 75-76, 118-120

    Scored sequences and counts

    
    CG*C-C   11

    
    CC*G-C    9

    
    GG*C-C    2

    
    CG*CGC    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_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	95.65	9.85	3	1	Major groove platform
2	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	95.65	2.84	3	2	Multiple bulged bases
3	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	13.04	-4.48	2	1	Multiple bulged bases
4	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-5.56	3	1
5	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-5.73	5	1	Intercalated cWS
6	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-8.83	2	1
7	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-12.93	2	1
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-14.05	2	1	Single stack bend
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-15.44	2	1	Single stack bend
10	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	13.04	-24.59	2	1	Stack and bulge

Loop 5 Internal loop

Column numbers: 80-86, 109-114

    Scored sequences and counts

    
    CCGGUAG*CGAACG   12

    
    CCAGUAG*CGAACG    3

    
    CCGGUAG*CGAAAG    3

    
    CUGGUAG*CGAACG    2

    
    CCAGUAG*CGGCAG    1

    
    CCGGUAC*GGAACG    1

    
    CCGGUAG*CGACAG    1

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

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	57.00	1	1	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	95.65	10.48	7	3	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	86.96	24.47	4	2	Sarcin-Ricin target in LSU H95; G-bulge
4	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	69.57	-0.48	4	3	8x7 Sarcin-Ricin; G-bulge
5	Motif group IL_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	69.57	-1.22	4	2	6x5 Sarcin-Ricin; G-bulge
6	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	21.74	-12.73	6	4	8x6 Sarcin-Ricin with inserted A; G-bulge
7	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	17.39	-24.23	6	4	tSH-tSH-tHH-tHS
8	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	13.04	-12.90	4	3	7x7 Sarcin-Ricin with intercalated A; G-bulge
9	Motif group IL_06136.2 View motif instance in 3D Basepair signature: cWW-tHS-cWW-tHS-tSH-tSH-cWW	13.04	-14.14	5	2	Quadruple sheared
10	Motif group IL_65594.1 View motif instance in 3D Basepair signature: cWW-L-R-tSW-tHH-cSH-tWH-tHS-cWW	13.04	-14.50	4	3	8x7 Sarcin-Ricin; G-bulge

Loop 6 Internal loop

Column numbers: 88-91, 106-107

    Scored sequences and counts

    
    C--G*CG    5

    
    CCCG*CG    4

    
    C--G*CA    1

    
    U--G*CA    1

    
    Omitted sequenced and counts

    
    C---*GG    5

    
    A---*-U    3

    
    ----*A-    2

    
    C---*AG    1

    
    C---*-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 IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	31.28	2	2	Multiple bulged bases
2	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	19.39	2	1	Major groove intercalation
3	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	90.91	15.41	2	1
4	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	90.91	14.23	4	1	Intercalated cWS
5	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	90.91	11.19	1	1	Single stack bend
6	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	63.64	5.67	2	1	Major groove platform
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	63.64	-2.32	3	1
8	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	54.55	2.90	1	1	Single stack bend
9	Motif group IL_61258.15 View motif instance in 3D Basepair signature: cWW-L-cWW	54.55	-3.07	1	1	Single bulged C
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	54.55	-10.22	2	1	Multiple bulged bases

Loop 7 Internal loop

Column numbers: 91-95, 102-106

    Scored sequences and counts

    
    GAACC*GCACC    8

    
    GAACC*GCAAC    1

    
    GAACC*GCCAC    1

    
    GACCC*GCACC    1

    
    Omitted sequenced and counts

    
    -----*AUAAG    3

    
    -----*-CAU-    3

    
    -----*-CGCA    2

    
    -----*ACAUG    1

    
    -----*CCAUG    1

    
    -----*GAUGA    1

    
    -----*CCAA-    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_17948.2 View motif instance in 3D Basepair signature: cWW-L-R-tSH-tHS-cWW	100.00	63.52	2	1	Double sheared with non-canonical cWW
2	Motif group IL_58103.11 View motif instance in 3D Basepair signature: cWW-cSH-cWS-L-tSW-R-R-cWW	100.00	48.95	3	1	Symmetric double minor groove platform
3	Motif group IL_63519.1 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-cWW	100.00	17.08	3	3
4	Motif group IL_97631.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tHS-cWW	90.91	8.95	7	3	Triple sheared related
5	Motif group IL_80231.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-tHS-cWW	81.82	18.59	6	2	Other IL
6	Motif group IL_62654.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-tHS-cWW	81.82	-0.36	5	4	tSH-tHH-tHS
7	Motif group IL_67780.1 View motif instance in 3D Basepair signature: cWW-cSH-L-R-L-L-R-L	81.82	-2.45	6	4
8	Motif group IL_49751.4 View motif instance in 3D Basepair signature: cWW-cWW-cWW-cWW-cWW	72.73	-9.51	3	3	Triple non-canonical cWW pairs
9	Motif group IL_50730.2 View motif instance in 3D Basepair signature: cWW-tSH-tHS-tHS-cWW	72.73	-9.78	4	2	Triple sheared
10	Motif group IL_25186.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-cWW	27.27	-1.32	3	3

Loop 8 Hairpin loop

Column numbers: 95-102

    Scored sequences and counts

    
    CCAUCCAG    9

    
    ------CA    4

    
    ------CC    2

    
    CACGCCAG    1

    
    CCCUCCAG    1

    
    ----CAAG    1

    
    Omitted sequenced and counts

    
    --------    5

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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_26934.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	55.56	-71.22	5	3
2	Motif group HL_64690.6 View motif instance in 3D Basepair signature: cWW-cSW-F-F-F-F	55.56	-2635.67	3	2
3	Motif group HL_80362.1 View motif instance in 3D Basepair signature: cWW-F-F-F	55.56	-2838.48	3	3
4	Motif group HL_77082.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	55.56	-3131.72	3.5	2	Pseudoknot geometry
5	Motif group HL_87553.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	55.56	-3569.82	2	2
6	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	55.56	-4119.09	3	1	Purine riboswitch
7	Motif group HL_93324.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	55.56	-4127.82	4	2	Pseudoknot geometry
8	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	50.00	-83.74	2.5	2.5
9	Motif group HL_99748.1 View motif instance in 3D Basepair signature: cWW-F-F-cSH	50.00	-2652.95	3.5	3	Other HL
10	Motif group HL_78197.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	50.00	-3913.28	4.5	2.5