JAR3D
Query RF03125-3.98 completed
Run on Motif Atlas Version 3.98
using the Rfam secondary structure. Run with the CaCoFold secondary structure.
RF03125 Sarbecovirus 3'UTR
Input Summary
000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222223333333333333333333333333333333333333333333333333333333333333
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
.....................................((((((..((.(((((((((((..(((...((......))...))).)))))))))))))))))))...............(((((((((.((....))..))))))))).((((((..((((((((((..((..(((.(((.....(((((((((.((.(((....))))).)..(((((((((....(((.((((.....))..))..)))...))))).)))).((((........))))...........)))))))).....))).)))..))...)))))......)))))..)))).))((....)).........
>DQ071615.1/29386-29716
-----------------------------GAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGCGUAGAAUGAGUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>DQ022305.2/29378-29704
---------------------------------ACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KJ473812.1/29093-29436
----------------CAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUUAAUAAAUGUGUAAUGUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>AY772062.1/29111-29460
----------CUCAGGCAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KF367457.1/29959-30293
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUCUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUCAGGAGAAUGAC
>DQ412043.1/29399-29733
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAGAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGUGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KP886809.1/29373-29707
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUCAAUCAAUGUGUAACAUUAGGGAGGACUUAAAAGAGCCACCACACUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>NC_014470.1/28926-29254
----------U--------------------UGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCUAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUGGAAAGAGCCACCACAUAGUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGACUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUU-AUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT276597.1/29501-29850
----------AACUCAGGCCUAAACUCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGUGUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT007544.1/29543-29860
--------------------------------GACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUA----------UACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT344952.1/29511-29849
GUGCUGACUCAACUCAGGCCUAAACUCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAG---------------------UGUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
There are no chains in PDB that we map to Rfam family RF03125.
Rfam family RF03125
is part of clan CL00117, which includes Rfam families
RF03121,
RF03123,
RF03125,
RF03122,
RF00164,
RF03124,
RF00165
.
There is 1 chain in PDB that we map to these Rfam families:
1XJR|1|A
.
See it at RNA 3D Hub
by filtering on Rfam family, clan, or chain.
Jump to results for:
- Loop 1IL Column numbers: 43-46, 97-98
- Loop 2IL Column numbers: 47-49, 95-96
- Loop 3IL Column numbers: 59-62, 83-85
- Loop 4IL Column numbers: 64-68, 77-81
- Loop 5HL Column numbers: 69-76
- Loop 6IL Column numbers: 127-129, 136-139
- Loop 7HL Column numbers: 130-135
- Loop 8IL Column numbers: 150-151, 340-342
- Loop 9IL Column numbers: 154-157, 334-337
- Loop 10IL Column numbers: 161-162, 323-330
- Loop 11IL Column numbers: 166-169, 315-319
- Loop 12IL Column numbers: 170-173, 311-314
- Loop 13IL Column numbers: 175-177, 307-309
- Loop 14IL Column numbers: 179-185, 299-305
- Loop 15J4 Column numbers: 192-193, 211-214, 263-265, 280-292
- Loop 16IL Column numbers: 193-195, 209-211
- Loop 17IL Column numbers: 196-198, 207-208
- Loop 18HL Column numbers: 200-205
- Loop 19IL Column numbers: 217-218, 258-260
- Loop 20IL Column numbers: 222-227, 250-254
- Loop 21IL Column numbers: 229-231, 245-248
- Loop 22IL Column numbers: 232-233, 241-244
- Loop 23HL Column numbers: 234-240
- Loop 24HL Column numbers: 268-277
- Loop 25HL Column numbers: 345-350
Loop 1 Internal loop
Column numbers: 43-46, 97-98
Scored sequences and counts
GGCA*UC 11
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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_79895.1
Basepair signature:
|
100.00 | 56.08 | 3 | 1 |
|
| 2 |
Motif group IL_66635.5
Basepair signature:
|
100.00 | 47.45 | 1 | 1 |
Major groove intercalation |
| 3 |
Motif group IL_20031.1
Basepair signature:
|
100.00 | 39.26 | 3 | 1 |
|
| 4 |
Motif group IL_76709.2
Basepair signature:
|
100.00 | 38.80 | 3 | 1 |
|
| 5 |
Motif group IL_82107.4
Basepair signature:
|
100.00 | 36.20 | 3 | 1 |
Multiple bulged bases |
| 6 |
Motif group IL_50694.7
Basepair signature:
|
100.00 | 26.72 | 1 | 1 |
Major groove platform; stack outside cWW |
| 7 |
Motif group IL_42626.2
Basepair signature:
|
100.00 | 26.46 | 3 | 1 |
|
| 8 |
Motif group IL_33761.2
Basepair signature:
|
100.00 | 24.27 | 3 | 1 |
|
| 9 |
Motif group IL_84476.1
Basepair signature:
|
100.00 | 15.32 | 4 | 1 |
Multiple bulged bases |
| 10 |
Motif group IL_73452.2
Basepair signature:
|
100.00 | 7.61 | 3 | 2 |
|
Loop 2 Internal loop
Column numbers: 47-49, 95-96
Scored sequences and counts
GAU*AC 11
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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
Basepair signature:
|
100.00 | 98.00 | 2 | 0 |
Single stack bend |
| 2 |
Motif group IL_42771.1
Basepair signature:
|
100.00 | 96.22 | 4 | 0 |
Multiple bulged bases |
| 3 |
Motif group IL_90729.1
Basepair signature:
|
100.00 | 94.62 | 0 | 0 |
Single stack bend |
| 4 |
Motif group IL_31462.6
Basepair signature:
|
100.00 | 91.28 | 0 | 0 |
Single bulged A |
| 5 |
Motif group IL_66635.5
Basepair signature:
|
100.00 | 89.76 | 1 | 0 |
Major groove intercalation |
| 6 |
Motif group IL_33761.2
Basepair signature:
|
100.00 | 87.26 | 3 | 0 |
|
| 7 |
Motif group IL_31737.3
Basepair signature:
|
100.00 | 84.29 | 2 | 0 |
Stack and bulge |
| 8 |
Motif group IL_07039.3
Basepair signature:
|
100.00 | 74.49 | 2 | 0 |
Major groove platform |
| 9 |
Motif group IL_51454.3
Basepair signature:
|
100.00 | 73.37 | 0 | 0 |
Minor groove platform |
| 10 |
Motif group IL_48076.6
Basepair signature:
|
100.00 | 72.18 | 2 | 0 |
Major groove platform |
Loop 3 Internal loop
Column numbers: 59-62, 83-85
Scored sequences and counts
AAAC*GAU 11
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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_41344.1
Basepair signature:
|
100.00 | 98.15 | 4 | 0 |
|
| 2 |
Motif group IL_08770.1
Basepair signature:
|
100.00 | 94.69 | 4 | 0 |
|
| 3 |
Motif group IL_31531.3
Basepair signature:
|
100.00 | 93.59 | 2 | 0 |
Decoding loop related |
| 4 |
Motif group IL_55516.2
Basepair signature:
|
100.00 | 87.30 | 3 | 0 |
|
| 5 |
Motif group IL_90351.1
Basepair signature:
|
100.00 | 87.03 | 1 | 0 |
|
| 6 |
Motif group IL_57744.1
Basepair signature:
|
100.00 | 85.59 | 3 | 0 |
Isolated non-canonical cWW pair |
| 7 |
Motif group IL_31737.3
Basepair signature:
|
100.00 | 82.22 | 3 | 0 |
Stack and bulge |
| 8 |
Motif group IL_83389.2
Basepair signature:
|
100.00 | 70.91 | 3 | 1 |
|
| 9 |
Motif group IL_15698.3
Basepair signature:
|
100.00 | 47.04 | 3 | 1 |
|
| 10 |
Motif group IL_14688.1
Basepair signature:
|
100.00 | 44.61 | 2 | 1 |
Isolated non-canonical cWW pair |
Loop 4 Internal loop
Column numbers: 64-68, 77-81
Scored sequences and counts
UUUUC*GUUUA 10
UCUUC*GUUUA 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_61242.1
Basepair signature:
|
100.00 | 36.30 | 6 | 2 |
|
| 2 |
Motif group IL_29223.1
Basepair signature:
|
100.00 | 22.36 | 4 | 2 |
|
| 3 |
Motif group IL_74367.1
Basepair signature:
|
100.00 | 22.21 | 4 | 2 |
|
| 4 |
Motif group IL_70096.1
Basepair signature:
|
100.00 | 13.10 | 5 | 2 |
Kink-turn related |
| 5 |
Motif group IL_96236.1
Basepair signature:
|
100.00 | 7.99 | 4 | 2 |
|
| 6 |
Motif group IL_49751.4
Basepair signature:
|
90.91 | 39.69 | 4 | 1 |
Triple non-canonical cWW pairs |
| 7 |
Motif group IL_99498.1
Basepair signature:
|
9.09 | -9.31 | 8 | 4 |
|
Loop 5 Hairpin loop
Column numbers: 69-76
Scored sequences and counts
GCAAUUCC 7
GCUUUUCC 3
GCUAUUCC 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_99748.1
Basepair signature:
|
100.00 | 29.75 | 4 | 2 |
Other HL |
| 2 |
Motif group HL_50537.6
Basepair signature:
|
63.64 | 5.65 | 4 | 2 |
tRNA anticodon loop with synthetase |
| 3 |
Motif group HL_02817.2
Basepair signature:
|
63.64 | 3.31 | 3 | 2 |
|
| 4 |
Motif group HL_28075.1
Basepair signature:
|
27.27 | -15.80 | 4 | 3 |
|
| 5 |
Motif group HL_64690.6
Basepair signature:
|
27.27 | -28.28 | 4 | 4 |
|
| 6 |
Motif group HL_50006.2
Basepair signature:
|
27.27 | -40.75 | 5 | 4 |
|
| 7 |
Motif group HL_09452.1
Basepair signature:
|
27.27 | -46.06 | 5 | 5 |
|
| 8 |
Motif group HL_42046.2
Basepair signature:
|
27.27 | -58.77 | 6 | 4 |
|
| 9 |
Motif group HL_77082.1
Basepair signature:
|
9.09 | -14.59 | 3 | 3 |
Pseudoknot geometry |
| 10 |
Motif group HL_33983.1
Basepair signature:
|
9.09 | -19.58 | 6 | 4 |
|
Loop 6 Internal loop
Column numbers: 127-129, 136-139
Scored sequences and counts
CAG*UAGG 8
UAG*UAGA 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 IL_41344.1
Basepair signature:
|
100.00 | 60.45 | 3 | 1 |
|
| 2 |
Motif group IL_57744.1
Basepair signature:
|
100.00 | 58.22 | 3 | 0 |
Isolated non-canonical cWW pair |
| 3 |
Motif group IL_82107.4
Basepair signature:
|
100.00 | 55.61 | 2 | 0 |
Multiple bulged bases |
| 4 |
Motif group IL_85599.2
Basepair signature:
|
100.00 | 52.55 | 1 | 1 |
Isolated tHS basepair with bulges |
| 5 |
Motif group IL_90351.1
Basepair signature:
|
100.00 | 42.66 | 3 | 1 |
|
| 6 |
Motif group IL_67095.2
Basepair signature:
|
100.00 | 36.16 | 2 | 0 |
Isolated tWW turn |
| 7 |
Motif group IL_55516.2
Basepair signature:
|
100.00 | 29.42 | 3 | 1 |
|
| 8 |
Motif group IL_83389.2
Basepair signature:
|
100.00 | 26.93 | 4 | 1 |
|
| 9 |
Motif group IL_31531.3
Basepair signature:
|
100.00 | 24.85 | 3 | 1 |
Decoding loop related |
| 10 |
Motif group IL_08770.1
Basepair signature:
|
100.00 | 24.42 | 3 | 1 |
|
Loop 7 Hairpin loop
Column numbers: 130-135
Scored sequences and counts
CACAAG 11
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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_53890.2
Basepair signature:
|
100.00 | 63.18 | 1 | 1 |
|
| 2 |
Motif group HL_57176.2
Basepair signature:
|
100.00 | 54.80 | 2 | 1 |
Pseudoknot geometry with 3' bulge |
| 3 |
Motif group HL_75660.5
Basepair signature:
|
100.00 | 40.74 | 1 | 1 |
|
| 4 |
Motif group HL_65794.5
Basepair signature:
|
100.00 | 38.45 | 3 | 1 |
Pseudoknot geometry |
| 5 |
Motif group HL_56131.2
Basepair signature:
|
100.00 | 33.64 | 4 | 2 |
|
| 6 |
Motif group HL_93535.1
Basepair signature:
|
100.00 | 25.28 | 2 | 2 |
|
| 7 |
Motif group HL_04783.2
Basepair signature:
|
100.00 | 21.45 | 2 | 2 |
|
| 8 |
Motif group HL_50006.2
Basepair signature:
|
100.00 | 21.10 | 2 | 2 |
|
| 9 |
Motif group HL_48417.5
Basepair signature:
|
100.00 | 18.89 | 2 | 2 |
|
| 10 |
Motif group HL_13963.3
Basepair signature:
|
100.00 | 11.60 | 4 | 2 |
|
Loop 8 Internal loop
Column numbers: 150-151, 340-342
Scored sequences and counts
UU*AUA 11
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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_81831.1
Basepair signature:
|
100.00 | 99.35 | 2 | 0 |
Intercalated cWS |
| 2 |
Motif group IL_73452.2
Basepair signature:
|
100.00 | 95.89 | 4 | 0 |
|
| 3 |
Motif group IL_90729.1
Basepair signature:
|
100.00 | 88.62 | 2 | 0 |
Single stack bend |
| 4 |
Motif group IL_89505.4
Basepair signature:
|
100.00 | 85.02 | 0 | 0 |
Single bulged U |
| 5 |
Motif group IL_48076.6
Basepair signature:
|
100.00 | 83.91 | 2 | 0 |
Major groove platform |
| 6 |
Motif group IL_33761.2
Basepair signature:
|
100.00 | 80.80 | 4 | 0 |
|
| 7 |
Motif group IL_26793.1
Basepair signature:
|
100.00 | 75.64 | 3 | 0 |
Single stack bend |
| 8 |
Motif group IL_42771.1
Basepair signature:
|
100.00 | 67.84 | 1 | 1 |
Multiple bulged bases |
| 9 |
Motif group IL_07039.3
Basepair signature:
|
100.00 | 66.79 | 3 | 0 |
Major groove platform |
| 10 |
Motif group IL_10569.1
Basepair signature:
|
100.00 | 63.34 | 1 | 1 |
|
Loop 9 Internal loop
Column numbers: 154-157, 334-337
Scored sequences and counts
AUCU*AUUU 9
AUUU*AUUU 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_77658.1
Basepair signature:
|
100.00 | 80.49 | 2 | 0 |
Tandem non-canonical cWW pairs |
| 2 |
Motif group IL_51479.1
Basepair signature:
|
100.00 | 65.72 | 5 | 1 |
|
| 3 |
Motif group IL_78800.1
Basepair signature:
|
100.00 | 59.56 | 3 | 1 |
|
| 4 |
Motif group IL_02203.1
Basepair signature:
|
100.00 | 46.30 | 3 | 1 |
|
| 5 |
Motif group IL_85033.2
Basepair signature:
|
100.00 | 45.91 | 2 | 1 |
Tandem non-canonical cWW pairs |
| 6 |
Motif group IL_92446.2
Basepair signature:
|
100.00 | 15.18 | 4 | 2 |
|
| 7 |
Motif group IL_81522.2
Basepair signature:
|
100.00 | 7.69 | 6 | 2 |
Major groove minor groove platform with intercalation; mini C-loop |
| 8 |
Motif group IL_41344.1
Basepair signature:
|
81.82 | 17.54 | 6 | 2 |
|
| 9 |
Motif group IL_13404.2
Basepair signature:
|
81.82 | 17.37 | 5 | 1 |
Tandem non-canonical cWW pairs |
| 10 |
Motif group IL_07785.1
Basepair signature:
|
81.82 | -0.07 | 2 | 1 |
Isolated non-canonical cWW pair |
Loop 10 Internal loop
Column numbers: 161-162, 323-330
Scored sequences and counts
AU*AUCCCCAU 11
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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
Basepair signature:
|
100.00 | 94.82 | 4 | 0 |
|
| 2 |
Motif group IL_41203.4
Basepair signature:
|
100.00 | 32.44 | 5 | 2 |
SSU/LSU pseudoknot |
Loop 11 Internal loop
Column numbers: 166-169, 315-319
Scored sequences and counts
AAUC*GUAGU 11
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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_91920.1
Basepair signature:
|
100.00 | 59.27 | 3 | 1 |
|
| 2 |
Motif group IL_64231.5
Basepair signature:
|
100.00 | 55.93 | 5 | 1 |
|
| 3 |
Motif group IL_53448.1
Basepair signature:
|
100.00 | 41.86 | 5 | 1 |
Receptor of 11-nt loop-receptor motif |
| 4 |
Motif group IL_67767.4
Basepair signature:
|
100.00 | 34.67 | 5 | 1 |
Receptor of 11-nt loop-receptor motif |
| 5 |
Motif group IL_90346.1
Basepair signature:
|
100.00 | 22.28 | 6 | 2 |
|
| 6 |
Motif group IL_11344.2
Basepair signature:
|
100.00 | 22.12 | 5 | 2 |
180 degree turn |
| 7 |
Motif group IL_16218.2
Basepair signature:
|
100.00 | 17.10 | 3 | 2 |
|
| 8 |
Motif group IL_68909.1
Basepair signature:
|
100.00 | 16.96 | 4 | 2 |
|
| 9 |
Motif group IL_65718.4
Basepair signature:
|
100.00 | 15.64 | 5 | 3 |
|
| 10 |
Motif group IL_70096.1
Basepair signature:
|
100.00 | 6.96 | 7 | 3 |
Kink-turn related |
Loop 12 Internal loop
Column numbers: 170-173, 311-314
Scored sequences and counts
UUUA*UUUA 10
UUCA*UUUA 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_77658.1
Basepair signature:
|
100.00 | 89.56 | 2 | 0 |
Tandem non-canonical cWW pairs |
| 2 |
Motif group IL_51479.1
Basepair signature:
|
100.00 | 77.15 | 4 | 0 |
|
| 3 |
Motif group IL_85033.2
Basepair signature:
|
100.00 | 65.54 | 3 | 0 |
Tandem non-canonical cWW pairs |
| 4 |
Motif group IL_02203.1
Basepair signature:
|
100.00 | 44.81 | 5 | 1 |
|
| 5 |
Motif group IL_92446.2
Basepair signature:
|
100.00 | 43.11 | 5 | 1 |
|
| 6 |
Motif group IL_78800.1
Basepair signature:
|
100.00 | 34.21 | 4 | 2 |
|
| 7 |
Motif group IL_81522.2
Basepair signature:
|
100.00 | 25.89 | 4 | 1 |
Major groove minor groove platform with intercalation; mini C-loop |
| 8 |
Motif group IL_61242.1
Basepair signature:
|
90.91 | 6.92 | 6 | 2 |
|
| 9 |
Motif group IL_84476.1
Basepair signature:
|
90.91 | 2.39 | 5 | 2 |
Multiple bulged bases |
| 10 |
Motif group IL_68909.1
Basepair signature:
|
90.91 | -0.81 | 5 | 1 |
|
Loop 13 Internal loop
Column numbers: 175-177, 307-309
Scored sequences and counts
UCA*UAA 9
UAA*UAA 1
UCA*U-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_08770.1
Basepair signature:
|
100.00 | 67.19 | 3 | 1 |
|
| 2 |
Motif group IL_31737.3
Basepair signature:
|
100.00 | 53.05 | 3 | 1 |
Stack and bulge |
| 3 |
Motif group IL_67095.2
Basepair signature:
|
90.91 | 79.98 | 0 | 0 |
Isolated tWW turn |
| 4 |
Motif group IL_42997.3
Basepair signature:
|
90.91 | 61.64 | 2 | 0 |
Isolated cWS basepair |
| 5 |
Motif group IL_87907.2
Basepair signature:
|
90.91 | 57.06 | 1 | 0 |
Isolated non-canonical cWW pair |
| 6 |
Motif group IL_57744.1
Basepair signature:
|
90.91 | 54.47 | 3 | 0 |
Isolated non-canonical cWW pair |
| 7 |
Motif group IL_07785.1
Basepair signature:
|
90.91 | 46.81 | 1 | 1 |
Isolated non-canonical cWW pair |
| 8 |
Motif group IL_42771.1
Basepair signature:
|
90.91 | 38.05 | 2 | 1 |
Multiple bulged bases |
| 9 |
Motif group IL_14688.1
Basepair signature:
|
90.91 | 37.57 | 3 | 1 |
Isolated non-canonical cWW pair |
| 10 |
Motif group IL_44465.1
Basepair signature:
|
90.91 | 22.02 | 2 | 1 |
Isolated non-canonical cWW contact |
Loop 14 Internal loop
Column numbers: 179-185, 299-305
Scored sequences and counts
UGUGUAA*UGUAAAA 11
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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_29198.2
Basepair signature:
|
100.00 | 13.33 | 7 | 3 |
7x7 Sarcin-Ricin with intercalated A; G-bulge |
| 2 |
Motif group IL_04736.1
Basepair signature:
|
100.00 | 5.53 | 8 | 4 |
|
| 3 |
Motif group IL_26307.2
Basepair signature:
|
100.00 | 0.34 | 5 | 2 |
7x6 Sarcin-Ricin; G-bulge |
Loop 15 4-way junction loop
Column numbers: 192-193, 211-214, 263-265, 280-292
Scored sequences and counts
GG*CCAC*GCU*AUAUGGAAGAGCC 11
No Matches Found
View All Results for this LoopLoop 16 Internal loop
Column numbers: 193-195, 209-211
Scored sequences and counts
GAG*CAC 11
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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_31737.3
Basepair signature:
|
100.00 | 100.00 | 1 | 0 |
Stack and bulge |
| 2 |
Motif group IL_42997.3
Basepair signature:
|
100.00 | 90.55 | 2 | 0 |
Isolated cWS basepair |
| 3 |
Motif group IL_57744.1
Basepair signature:
|
100.00 | 86.24 | 1 | 0 |
Isolated non-canonical cWW pair |
| 4 |
Motif group IL_87907.2
Basepair signature:
|
100.00 | 82.94 | 1 | 0 |
Isolated non-canonical cWW pair |
| 5 |
Motif group IL_08770.1
Basepair signature:
|
100.00 | 74.38 | 1 | 1 |
|
| 6 |
Motif group IL_14688.1
Basepair signature:
|
100.00 | 69.92 | 2 | 1 |
Isolated non-canonical cWW pair |
| 7 |
Motif group IL_10167.6
Basepair signature:
|
100.00 | 62.98 | 2 | 0 |
Isolated cWH basepair |
| 8 |
Motif group IL_67095.2
Basepair signature:
|
100.00 | 50.43 | 3 | 1 |
Isolated tWW turn |
| 9 |
Motif group IL_42771.1
Basepair signature:
|
100.00 | 41.49 | 3 | 1 |
Multiple bulged bases |
| 10 |
Motif group IL_07785.1
Basepair signature:
|
100.00 | 34.72 | 1 | 1 |
Isolated non-canonical cWW pair |
Loop 17 Internal loop
Column numbers: 196-198, 207-208
Scored sequences and counts
GAC*GC 11
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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_33761.2
Basepair signature:
|
100.00 | 99.89 | 1 | 0 |
|
| 2 |
Motif group IL_31462.6
Basepair signature:
|
100.00 | 96.34 | 0 | 0 |
Single bulged A |
| 3 |
Motif group IL_42771.1
Basepair signature:
|
100.00 | 96.18 | 4 | 0 |
Multiple bulged bases |
| 4 |
Motif group IL_48076.6
Basepair signature:
|
100.00 | 95.75 | 0 | 0 |
Major groove platform |
| 5 |
Motif group IL_26793.1
Basepair signature:
|
100.00 | 95.70 | 2 | 0 |
Single stack bend |
| 6 |
Motif group IL_90729.1
Basepair signature:
|
100.00 | 94.24 | 1 | 0 |
Single stack bend |
| 7 |
Motif group IL_66635.5
Basepair signature:
|
100.00 | 93.12 | 1 | 0 |
Major groove intercalation |
| 8 |
Motif group IL_31737.3
Basepair signature:
|
100.00 | 87.40 | 2 | 0 |
Stack and bulge |
| 9 |
Motif group IL_51454.3
Basepair signature:
|
100.00 | 76.43 | 2 | 0 |
Minor groove platform |
| 10 |
Motif group IL_07039.3
Basepair signature:
|
100.00 | 72.38 | 4 | 0 |
Major groove platform |
Loop 18 Hairpin loop
Column numbers: 200-205
Scored sequences and counts
UGAAAG 8
GGAAAG 1
UAAAAG 1
UGAGAG 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_53890.2
Basepair signature:
|
100.00 | 77.28 | 1 | 0 |
|
| 2 |
Motif group HL_04783.2
Basepair signature:
|
100.00 | 76.76 | 1 | 0 |
|
| 3 |
Motif group HL_37824.7
Basepair signature:
|
100.00 | 72.71 | 0 | 0 |
GNRA |
| 4 |
Motif group HL_52953.3
Basepair signature:
|
100.00 | 67.38 | 2 | 0 |
|
| 5 |
Motif group HL_82710.2
Basepair signature:
|
100.00 | 64.44 | 2 | 0 |
|
| 6 |
Motif group HL_50006.2
Basepair signature:
|
100.00 | 59.81 | 1 | 0 |
|
| 7 |
Motif group HL_93535.1
Basepair signature:
|
100.00 | 58.11 | 2 | 1 |
|
| 8 |
Motif group HL_65794.5
Basepair signature:
|
100.00 | 58.03 | 2 | 0 |
Pseudoknot geometry |
| 9 |
Motif group HL_75660.5
Basepair signature:
|
100.00 | 49.30 | 1 | 0 |
|
| 10 |
Motif group HL_59843.1
Basepair signature:
|
100.00 | 47.75 | 2 | 1 |
|
Loop 19 Internal loop
Column numbers: 217-218, 258-260
Scored sequences and counts
UU*AUA 7
UU*ACA 3
AG*CUA 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_81831.1
Basepair signature:
|
100.00 | 84.62 | 2 | 0 |
Intercalated cWS |
| 2 |
Motif group IL_73452.2
Basepair signature:
|
100.00 | 81.29 | 4 | 0 |
|
| 3 |
Motif group IL_90729.1
Basepair signature:
|
100.00 | 81.16 | 2 | 0 |
Single stack bend |
| 4 |
Motif group IL_48076.6
Basepair signature:
|
100.00 | 81.12 | 2 | 0 |
Major groove platform |
| 5 |
Motif group IL_26793.1
Basepair signature:
|
100.00 | 76.46 | 3 | 0 |
Single stack bend |
| 6 |
Motif group IL_33761.2
Basepair signature:
|
100.00 | 66.23 | 4 | 0 |
|
| 7 |
Motif group IL_07039.3
Basepair signature:
|
100.00 | 63.60 | 3 | 0 |
Major groove platform |
| 8 |
Motif group IL_42771.1
Basepair signature:
|
100.00 | 59.15 | 1 | 1 |
Multiple bulged bases |
| 9 |
Motif group IL_10569.1
Basepair signature:
|
100.00 | 54.00 | 1 | 1 |
|
| 10 |
Motif group IL_66635.5
Basepair signature:
|
100.00 | 48.82 | 3 | 1 |
Major groove intercalation |
Loop 20 Internal loop
Column numbers: 222-227, 250-254
Scored sequences and counts
CCGAGG*UACAG 9
UCGAGG*UACAG 1
CCGAG-*UACAG 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_75294.1
Basepair signature:
|
90.91 | 8.90 | 4 | 1 |
|
| 2 |
Motif group IL_45444.1
Basepair signature:
|
81.82 | 3.38 | 4 | 2 |
|
Loop 21 Internal loop
Column numbers: 229-231, 245-248
Scored sequences and counts
CAC*GAGG 8
CAC*GAGU 1
Omitted sequenced and counts
CAC*---- 1
---*---U 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_57744.1
Basepair signature:
|
100.00 | 82.71 | 1 | 0 |
Isolated non-canonical cWW pair |
| 2 |
Motif group IL_90351.1
Basepair signature:
|
100.00 | 72.84 | 1 | 1 |
|
| 3 |
Motif group IL_55516.2
Basepair signature:
|
100.00 | 58.03 | 1 | 1 |
|
| 4 |
Motif group IL_41344.1
Basepair signature:
|
100.00 | 53.53 | 1 | 1 |
|
| 5 |
Motif group IL_67095.2
Basepair signature:
|
100.00 | 49.43 | 3 | 0 |
Isolated tWW turn |
| 6 |
Motif group IL_82107.4
Basepair signature:
|
100.00 | 47.81 | 3 | 0 |
Multiple bulged bases |
| 7 |
Motif group IL_85599.2
Basepair signature:
|
100.00 | 45.58 | 3 | 1 |
Isolated tHS basepair with bulges |
| 8 |
Motif group IL_08770.1
Basepair signature:
|
100.00 | 44.89 | 1 | 1 |
|
| 9 |
Motif group IL_14688.1
Basepair signature:
|
100.00 | 42.13 | 2 | 1 |
Isolated non-canonical cWW pair |
| 10 |
Motif group IL_83389.2
Basepair signature:
|
100.00 | 41.26 | 5 | 1 |
|
Loop 22 Internal loop
Column numbers: 232-233, 241-244
Scored sequences and counts
GC*GAUC 9
Omitted sequenced and counts
GC*---- 1
--*---- 1
Click on headings to reorder table
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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_79895.1
Basepair signature:
|
100.00 | 100.00 | 2 | 0 |
|
| 2 |
Motif group IL_76709.2
Basepair signature:
|
100.00 | 100.00 | 1 | 0 |
|
| 3 |
Motif group IL_59877.1
Basepair signature:
|
100.00 | 100.00 | 0 | 0 |
|
| 4 |
Motif group IL_66635.5
Basepair signature:
|
100.00 | 90.13 | 1 | 0 |
Major groove intercalation |
| 5 |
Motif group IL_82107.4
Basepair signature:
|
100.00 | 85.25 | 3 | 0 |
Multiple bulged bases |
| 6 |
Motif group IL_84476.1
Basepair signature:
|
100.00 | 83.33 | 2 | 0 |
Multiple bulged bases |
| 7 |
Motif group IL_50694.7
Basepair signature:
|
100.00 | 77.63 | 2 | 0 |
Major groove platform; stack outside cWW |
| 8 |
Motif group IL_73452.2
Basepair signature:
|
100.00 | 63.04 | 1 | 1 |
|
| 9 |
Motif group IL_90729.1
Basepair signature:
|
100.00 | 56.38 | 1 | 0 |
Single stack bend |
| 10 |
Motif group IL_42626.2
Basepair signature:
|
100.00 | 51.68 | 3 | 1 |
|
Loop 23 Hairpin loop
Column numbers: 234-240
Scored sequences and counts
GGAGUAC 9
GGAGUA- 1
Omitted sequenced and counts
------- 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
Basepair signature:
|
100.00 | 57.79 | 3 | 1 |
|
| 2 |
Motif group HL_97917.2
Basepair signature:
|
100.00 | 40.93 | 1 | 1 |
|
| 3 |
Motif group HL_37824.7
Basepair signature:
|
100.00 | 32.52 | 0 | 0 |
GNRA |
| 4 |
Motif group HL_75660.5
Basepair signature:
|
100.00 | 8.87 | 2 | 1 |
|
| 5 |
Motif group HL_65794.5
Basepair signature:
|
100.00 | 0.63 | 2 | 1 |
Pseudoknot geometry |
| 6 |
Motif group HL_80922.2
Basepair signature:
|
90.00 | 57.64 | 2 | 1 |
|
| 7 |
Motif group HL_49922.4
Basepair signature:
|
90.00 | 29.96 | 3 | 1 |
|
| 8 |
Motif group HL_50537.6
Basepair signature:
|
90.00 | 24.68 | 4 | 2 |
tRNA anticodon loop with synthetase |
| 9 |
Motif group HL_86769.4
Basepair signature:
|
90.00 | 22.85 | 4 | 2 |
|
| 10 |
Motif group HL_31585.4
Basepair signature:
|
90.00 | 21.82 | 3 | 1 |
Purine riboswitch |
Loop 24 Hairpin loop
Column numbers: 268-277
Scored sequences and counts
GGAGAGCUGC 10
GGAGUGCUGC 1
Click on headings to reorder table
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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_61996.2
Basepair signature:
|
90.91 | -0.47 | 3 | 3 |
|
| 2 |
Motif group HL_99867.1
Basepair signature:
|
9.09 | -24.90 | 4 | 4 |
|
| 3 |
Motif group HL_66853.7
Basepair signature:
|
9.09 | -26.69 | 6 | 4 |
|
| 4 |
Motif group HL_40252.4
Basepair signature:
|
9.09 | -29.77 | 6 | 4 |
|
Loop 25 Hairpin loop
Column numbers: 345-350
Scored sequences and counts
UUCUUA 10
UUCUCA 1
Click on headings to reorder table
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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_86870.2
Basepair signature:
|
100.00 | 92.70 | 2 | 0 |
|
| 2 |
Motif group HL_80709.3
Basepair signature:
|
100.00 | 59.81 | 2 | 0 |
|
| 3 |
Motif group HL_56334.1
Basepair signature:
|
100.00 | 54.64 | 1 | 1 |
Mini UNCG |
| 4 |
Motif group HL_70782.2
Basepair signature:
|
100.00 | 33.29 | 2 | 2 |
|
| 5 |
Motif group HL_75660.5
Basepair signature:
|
100.00 | 21.07 | 3 | 1 |
|
| 6 |
Motif group HL_56131.2
Basepair signature:
|
100.00 | 20.10 | 2 | 2 |
|
| 7 |
Motif group HL_53890.2
Basepair signature:
|
100.00 | 15.31 | 4 | 2 |
|
| 8 |
Motif group HL_46501.1
Basepair signature:
|
100.00 | 6.65 | 3 | 2 |
|
| 9 |
Motif group HL_81100.2
Basepair signature:
|
90.91 | 28.22 | 4 | 2 |
|
| 10 |
Motif group HL_86883.1
Basepair signature:
|
90.91 | 25.71 | 3 | 1 |
|