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
1 100.00 56.08 3 1

2 100.00 47.45 1 1

Major groove intercalation

3 100.00 39.26 3 1

4 100.00 38.80 3 1

5 100.00 36.20 3 1

Multiple bulged bases

6 100.00 26.72 1 1

Major groove platform; stack outside cWW

7 100.00 26.46 3 1

8 100.00 24.27 3 1

9 100.00 15.32 4 1

Multiple bulged bases

10 100.00 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
1 100.00 98.00 2 0

Single stack bend

2 100.00 96.22 4 0

Multiple bulged bases

3 100.00 94.62 0 0

Single stack bend

4 100.00 91.28 0 0

Single bulged A

5 100.00 89.76 1 0

Major groove intercalation

6 100.00 87.26 3 0

7 100.00 84.29 2 0

Stack and bulge

8 100.00 74.49 2 0

Major groove platform

9 100.00 73.37 0 0

Minor groove platform

10 100.00 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
1 100.00 98.15 4 0

2 100.00 94.69 4 0

3 100.00 93.59 2 0

Decoding loop related

4 100.00 87.30 3 0

5 100.00 87.03 1 0

6 100.00 85.59 3 0

Isolated non-canonical cWW pair

7 100.00 82.22 3 0

Stack and bulge

8 100.00 70.91 3 1

9 100.00 47.04 3 1

10 100.00 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
1 100.00 36.30 6 2

2 100.00 22.36 4 2

3 100.00 22.21 4 2

4 100.00 13.10 5 2

Kink-turn related

5 100.00 7.99 4 2

6 90.91 39.69 4 1

Triple non-canonical cWW pairs

7 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
1 100.00 29.75 4 2

Other HL

2 63.64 5.65 4 2

tRNA anticodon loop with synthetase

3 63.64 3.31 3 2

4 27.27 -15.80 4 3

5 27.27 -28.28 4 4

6 27.27 -40.75 5 4

7 27.27 -46.06 5 5

8 27.27 -58.77 6 4

9 9.09 -14.59 3 3

Pseudoknot geometry

10 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
1 100.00 60.45 3 1

2 100.00 58.22 3 0

Isolated non-canonical cWW pair

3 100.00 55.61 2 0

Multiple bulged bases

4 100.00 52.55 1 1

Isolated tHS basepair with bulges

5 100.00 42.66 3 1

6 100.00 36.16 2 0

Isolated tWW turn

7 100.00 29.42 3 1

8 100.00 26.93 4 1

9 100.00 24.85 3 1

Decoding loop related

10 100.00 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
1 100.00 63.18 1 1

2 100.00 54.80 2 1

Pseudoknot geometry with 3' bulge

3 100.00 40.74 1 1

4 100.00 38.45 3 1

Pseudoknot geometry

5 100.00 33.64 4 2

6 100.00 25.28 2 2

7 100.00 21.45 2 2

8 100.00 21.10 2 2

9 100.00 18.89 2 2

10 100.00 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
1 100.00 99.35 2 0

Intercalated cWS

2 100.00 95.89 4 0

3 100.00 88.62 2 0

Single stack bend

4 100.00 85.02 0 0

Single bulged U

5 100.00 83.91 2 0

Major groove platform

6 100.00 80.80 4 0

7 100.00 75.64 3 0

Single stack bend

8 100.00 67.84 1 1

Multiple bulged bases

9 100.00 66.79 3 0

Major groove platform

10 100.00 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
1 100.00 80.49 2 0

Tandem non-canonical cWW pairs

2 100.00 65.72 5 1

3 100.00 59.56 3 1

4 100.00 46.30 3 1

5 100.00 45.91 2 1

Tandem non-canonical cWW pairs

6 100.00 15.18 4 2

7 100.00 7.69 6 2

Major groove minor groove platform with intercalation; mini C-loop

8 81.82 17.54 6 2

9 81.82 17.37 5 1

Tandem non-canonical cWW pairs

10 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
1 100.00 94.82 4 0

2 100.00 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
1 100.00 59.27 3 1

2 100.00 55.93 5 1

3 100.00 41.86 5 1

Receptor of 11-nt loop-receptor motif

4 100.00 34.67 5 1

Receptor of 11-nt loop-receptor motif

5 100.00 22.28 6 2

6 100.00 22.12 5 2

180 degree turn

7 100.00 17.10 3 2

8 100.00 16.96 4 2

9 100.00 15.64 5 3

10 100.00 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
1 100.00 89.56 2 0

Tandem non-canonical cWW pairs

2 100.00 77.15 4 0

3 100.00 65.54 3 0

Tandem non-canonical cWW pairs

4 100.00 44.81 5 1

5 100.00 43.11 5 1

6 100.00 34.21 4 2

7 100.00 25.89 4 1

Major groove minor groove platform with intercalation; mini C-loop

8 90.91 6.92 6 2

9 90.91 2.39 5 2

Multiple bulged bases

10 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
1 100.00 67.19 3 1

2 100.00 53.05 3 1

Stack and bulge

3 90.91 79.98 0 0

Isolated tWW turn

4 90.91 61.64 2 0

Isolated cWS basepair

5 90.91 57.06 1 0

Isolated non-canonical cWW pair

6 90.91 54.47 3 0

Isolated non-canonical cWW pair

7 90.91 46.81 1 1

Isolated non-canonical cWW pair

8 90.91 38.05 2 1

Multiple bulged bases

9 90.91 37.57 3 1

Isolated non-canonical cWW pair

10 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
1 100.00 13.33 7 3

7x7 Sarcin-Ricin with intercalated A; G-bulge

2 100.00 5.53 8 4

3 100.00 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 Loop

Loop 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
1 100.00 100.00 1 0

Stack and bulge

2 100.00 90.55 2 0

Isolated cWS basepair

3 100.00 86.24 1 0

Isolated non-canonical cWW pair

4 100.00 82.94 1 0

Isolated non-canonical cWW pair

5 100.00 74.38 1 1

6 100.00 69.92 2 1

Isolated non-canonical cWW pair

7 100.00 62.98 2 0

Isolated cWH basepair

8 100.00 50.43 3 1

Isolated tWW turn

9 100.00 41.49 3 1

Multiple bulged bases

10 100.00 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
1 100.00 99.89 1 0

2 100.00 96.34 0 0

Single bulged A

3 100.00 96.18 4 0

Multiple bulged bases

4 100.00 95.75 0 0

Major groove platform

5 100.00 95.70 2 0

Single stack bend

6 100.00 94.24 1 0

Single stack bend

7 100.00 93.12 1 0

Major groove intercalation

8 100.00 87.40 2 0

Stack and bulge

9 100.00 76.43 2 0

Minor groove platform

10 100.00 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
1 100.00 77.28 1 0

2 100.00 76.76 1 0

3 100.00 72.71 0 0

GNRA

4 100.00 67.38 2 0

5 100.00 64.44 2 0

6 100.00 59.81 1 0

7 100.00 58.11 2 1

8 100.00 58.03 2 0

Pseudoknot geometry

9 100.00 49.30 1 0

10 100.00 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
1 100.00 84.62 2 0

Intercalated cWS

2 100.00 81.29 4 0

3 100.00 81.16 2 0

Single stack bend

4 100.00 81.12 2 0

Major groove platform

5 100.00 76.46 3 0

Single stack bend

6 100.00 66.23 4 0

7 100.00 63.60 3 0

Major groove platform

8 100.00 59.15 1 1

Multiple bulged bases

9 100.00 54.00 1 1

10 100.00 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 90.91 8.90 4 1

2 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
1 100.00 82.71 1 0

Isolated non-canonical cWW pair

2 100.00 72.84 1 1

3 100.00 58.03 1 1

4 100.00 53.53 1 1

5 100.00 49.43 3 0

Isolated tWW turn

6 100.00 47.81 3 0

Multiple bulged bases

7 100.00 45.58 3 1

Isolated tHS basepair with bulges

8 100.00 44.89 1 1

9 100.00 42.13 2 1

Isolated non-canonical cWW pair

10 100.00 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
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# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1 100.00 100.00 2 0

2 100.00 100.00 1 0

3 100.00 100.00 0 0

4 100.00 90.13 1 0

Major groove intercalation

5 100.00 85.25 3 0

Multiple bulged bases

6 100.00 83.33 2 0

Multiple bulged bases

7 100.00 77.63 2 0

Major groove platform; stack outside cWW

8 100.00 63.04 1 1

9 100.00 56.38 1 0

Single stack bend

10 100.00 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
1 100.00 57.79 3 1

2 100.00 40.93 1 1

3 100.00 32.52 0 0

GNRA

4 100.00 8.87 2 1

5 100.00 0.63 2 1

Pseudoknot geometry

6 90.00 57.64 2 1

7 90.00 29.96 3 1

8 90.00 24.68 4 2

tRNA anticodon loop with synthetase

9 90.00 22.85 4 2

10 90.00 21.82 3 1

Purine riboswitch

Loop 24 Hairpin loop

Column numbers: 268-277
    Scored sequences and counts
GGAGAGCUGC 10
GGAGUGCUGC 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 90.91 -0.47 3 3

2 9.09 -24.90 4 4

3 9.09 -26.69 6 4

4 9.09 -29.77 6 4

Loop 25 Hairpin loop

Column numbers: 345-350
    Scored sequences and counts
UUCUUA 10
UUCUCA 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
1 100.00 92.70 2 0

2 100.00 59.81 2 0

3 100.00 54.64 1 1

Mini UNCG

4 100.00 33.29 2 2

5 100.00 21.07 3 1

6 100.00 20.10 2 2

7 100.00 15.31 4 2

8 100.00 6.65 3 2

9 90.91 28.22 4 2

10 90.91 25.71 3 1

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