RNA 3D Hub

JAR3D Query RF01703-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF01703 Dictyoglomi-1 RNA

Input Summary

      000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222222222222222222222222222222222222
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456
((((((((((.((((.((((((....((..((((((...((((((....((((((((......(((((((((..(((((((....(((.((((((.....))))))))).....)))))))((((((.....(((((((((((((......)))))))))))))....))))))....)))))))))....))))))))....))))))))))))...)).....)))))).))))))))))))))
>CP001146.1_1770511-1770277
UGCUACAGGCGUCAAGGGGUCCGAAAGGUACUCC-UGA-UGUACCUUGGC----ACUGAGUAAAGUCUUGGGUACC-UAGGGAAAGGUGAAGGAGCUAGACUCCUUACCAAGUACUUAGGGGGUGGAGAGUAGUAGGAGUGUUGGAGAAGCCCGGUGCUCCUAUGAAAUCUGGAAAAUCCUGAGGCUGAAAGGU----GAGAAGGUACAAGGAGGCUUCCAAGUAGGGUCUGUUGAGCCUGUGGCA
>CP001146.1_383960-384195
UGCCACAGGCAUCAAGGGGUCCGAAAGG--CUCCCUGA-UGUGCCU-GACUGGGACUGAGUAAGUCUCAGGG--GC-CAAGGAAAGGU-AAGGAGUAAAA-UCCUUACUAAGUACUUGGAGGCCAGAAGGUAACAGGGGUAUUGGAAAAGCCCGGUACCUCUGUGAAAUCUGGUAAAACCCUGGGAUGAGAGGUCUCGGGA-GGGUGCAAGGGAGAAGCUGAGUAGGGUCCGUUGAGCCUGUGGCA
>CP001251.1_100291-100057
UGCCACAGGCGUCAAGGGGUCCAAAAGGUACUCC-UGA-UGUACCUUGGC----ACUGAGUAAAGUCUUGGGUAGC-UGGGGAAAAGUGGAGGAGCAAGACUCCUUACUGAGUACUUAGGGUUUAGAGAGUAGUAGGGGUGUUGGAGAAACCUGGUACUCCUACGAAAUCUGAAAAAUCCUGAGGCUGAAAGGU----GAGAGGGUACAGGGGAGUUUCCAAGUAGGAUCUGUUGAGCCUGUGGCA
>CP001251.1_520396-520631
UGCCACAGGCAUCAAGGGGUCCGAAAGG--CUCC-UGAGUGCACUU-GGCUGGGACUAAGUAAGUCCCGGAG--GCUCAAGGAAAGGU-AAGGGGUAAAAACCCUUACUAAGUACUUGAGAUCUAGAAAGUAACAGGGGUAUUGAUAAAGCUCGGUACCUCUGUGAAAUCUGGAAGAA-UCUGGGAUGAAAGGUCUCAGAG--GGUGCAAGGGAGAGGCUGAGUAGGGUCCGUUGAGCCUGUGGCA

There are no chains in PDB that we map to Rfam family RF01703.

Jump to results for:

  • Loop 1IL Column numbers: 10-12, 236-237
  • Loop 2IL Column numbers: 15-17, 231-233
  • Loop 3IL Column numbers: 22-27, 220-226
  • Loop 4IL Column numbers: 28-31, 215-219
  • Loop 5IL Column numbers: 36-40, 209-210
  • Loop 6IL Column numbers: 45-50, 199-204
  • Loop 7IL Column numbers: 57-64, 187-192
  • Loop 8J3 Column numbers: 72-75, 121-122, 174-179
  • Loop 9IL Column numbers: 81-86, 109-115
  • Loop 10IL Column numbers: 88-90, 106-107
  • Loop 11HL Column numbers: 95-101
  • Loop 12IL Column numbers: 127-133, 164-169
  • Loop 13HL Column numbers: 145-152

Loop 1 Internal loop

Column numbers: 10-12, 236-237 
    Scored sequences and counts

    
    CAU*AG    2

    
    CGU*AG    2
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_66635.5

Basepair signature:
cWW-L-cWW

100.00 88.68 2 0

Major groove intercalation

2

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 80.18 2 0

Major groove platform

3

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 79.31 2.5 0

Single stack bend

4

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 77.36 1.5 0

Major groove platform

5

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 71.32 2.5 0.5

Multiple bulged bases

6

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

100.00 70.31 2.5 0.5

7

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 66.61 1 0.5

Single stack bend

8

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 63.11 2.5 0.5

9

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 61.90 3.5 1

10

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 61.27 4.5 1

Intercalated cWS

Loop 2 Internal loop

Column numbers: 15-17, 231-233 
    Scored sequences and counts

    
    AGG*CGU    2

    
    AGG*UGU    2
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_44465.1

Basepair signature:
cWW-L-R-cWW

100.00 93.75 2 0

Isolated non-canonical cWW contact

2

Motif group IL_10167.6

Basepair signature:
cWW-cHW-cWW

100.00 87.15 2 0

Isolated cWH basepair

3

Motif group IL_87907.2

Basepair signature:
cWW-cWW-cWW

100.00 50.01 1.5 0

Isolated non-canonical cWW pair

4

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

100.00 28.02 1.5 1

Isolated cWS basepair

5

Motif group IL_99358.1

Basepair signature:
cWW-L-R-L-cWW

100.00 15.71 3.5 1

6

Motif group IL_67095.2

Basepair signature:
cWW-tWW-cWW

100.00 9.63 3.5 2

Isolated tWW turn

7

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

50.00 6.18 2.5 2

8

Motif group IL_85599.2

Basepair signature:
cWW-tHS-cWW

50.00 3.48 1.5 1

Isolated tHS basepair with bulges

9

Motif group IL_57744.1

Basepair signature:
cWW-cWW-cWW

50.00 2.20 2.5 1

Isolated non-canonical cWW pair

10

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

50.00 2.13 2.5 1

Major groove platform

Loop 3 Internal loop

Column numbers: 22-27, 220-226 
    Scored sequences and counts

    
    CGAAAG*UGAGUAG    2

    
    CAAAAG*CAAGUAG    1

    
    CGAAAG*CAAGUAG    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

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 88.25 1 0.5

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

100.00 32.88 5.5 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

3

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

100.00 27.14 4.5 1.5

8x6 Sarcin-Ricin with inserted Y; G-bulge

4

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

100.00 21.18 4 2

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

5

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

100.00 18.26 5.5 3

8x6 Sarcin-Ricin with inserted A; G-bulge

6

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

100.00 17.15 4.5 2.5

8x6 Sarcin-Ricin with bulged A; G-bulge

7

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

75.00 16.31 4 2

tSH-tSH-tHH-tHS

8

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

75.00 7.89 3 2

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_16458.4

Basepair signature:
cWW-L-R-L-R-cSH-tWH-tHS-cWW

75.00 -4.41 5 3

Sarcin-Ricin target in LSU H95; G-bulge

10

Motif group IL_87284.1

Basepair signature:
cWW-tSH-tHW-tWH-tHS-cWW

50.00 -12.27 3 2.5

tSH-tHW-tWH-tHS

Loop 4 Internal loop

Column numbers: 28-31, 215-219 
    Scored sequences and counts

    
    GUAC*GCUUC    1

    
    GUAC*GUUUC    1

    
    G--C*GAAGC    1

    
    G--C*GAGGC    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_70096.1

Basepair signature:
cWW-L-cWW-cWW

50.00 -40.35 8 4

Kink-turn related

2

Motif group IL_76758.2

Basepair signature:
cWW-L-R-L-cWW-L-L

50.00 -45.40 6.5 3

Intercalated tWH

3

Motif group IL_26728.3

Basepair signature:
cWW-cSH-R-cSH-cWW-cWW

50.00 -60.94 7 4

4

Motif group IL_06300.1

Basepair signature:
cWW-L-R-L-R-L-cWW

50.00 -71.20 6.5 3

5

Motif group IL_99646.2

Basepair signature:
cWW-tWH-tHS-cWW

50.00 -126.62 6 2.5

tSH-tHW

6

Motif group IL_96236.1

Basepair signature:
cWW-tWW-cWW-L-cWW

50.00 -3108.44 5.5 3.5

7

Motif group IL_81522.2

Basepair signature:
cWW-L-L-cWW

25.00 -17.13 2.5 1.5

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

8

Motif group IL_70335.1

Basepair signature:
cWW-L-R-L-cWW

25.00 -49.21 8 4.5

9

Motif group IL_82741.2

Basepair signature:
cWW-L-cWW-L-L

25.00 -64.82 6.5 3

10

Motif group IL_20031.1

Basepair signature:
cWW-L-cWW-L

25.00 -85.13 5 3

Loop 5 Internal loop

Column numbers: 36-40, 209-210 
    Scored sequences and counts

    
    UGA-U*AA    2

    
    UGAGU*AA    1

    
    UGA-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_66635.5

Basepair signature:
cWW-L-cWW

75.00 57.84 1 0

Major groove intercalation

2

Motif group IL_82107.4

Basepair signature:
cWW-cWW

75.00 55.67 2 0

Multiple bulged bases

3

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

75.00 47.66 3 0

4

Motif group IL_50694.7

Basepair signature:
cWW-tSH-cWW-L

75.00 45.87 2 0

Major groove platform; stack outside cWW

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

75.00 34.87 5 1

6

Motif group IL_00881.1

Basepair signature:
cWW-L-cWW-L

75.00 22.36 5 1

7

Motif group IL_84476.1

Basepair signature:
cWW-cWW

75.00 22.08 4 0

Multiple bulged bases

8

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

75.00 22.03 3 1

Intercalated cWS

9

Motif group IL_73355.1

Basepair signature:
cWW-L-cWW-L

75.00 19.27 5 1

10

Motif group IL_26685.1

Basepair signature:
cWW-L-cWW-L

75.00 18.17 3 1

Multiple bulged bases

Loop 6 Internal loop

Column numbers: 45-50, 199-204 
    Scored sequences and counts

    
    CUUGGC*GAGAAG    1

    
    CUUGGC*GAGAGG    1

    
    CU-GAC*GGA-GG    1

    
    UU-GGC*GAG--G    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_16218.2

Basepair signature:
cWW-L-R-L-R-L-cWW

50.00 -18.76 5 3

2

Motif group IL_21001.1

Basepair signature:
cWW-L-R-tHW-L-cWW

25.00 -29.22 6 3.5

3

Motif group IL_80926.1

Basepair signature:
cWW-cWW-tSH-tHS-L-cWW

25.00 -38.53 4 4

4

Motif group IL_89099.1

Basepair signature:
cWW-L-R-L-R-L-R-L-R-cWW

25.00 -50.89 6 4

Other IL

5

Motif group IL_25186.4

Basepair signature:
cWW-L-R-L-R-L-R-cWW

25.00 -56.08 5.5 4.5

6

Motif group IL_76308.6

Basepair signature:
cWW-tSH-tHW-tHS-cWW-cWW

25.00 -59.05 5.5 4

tSH-tWH-tHS-cWW

7

Motif group IL_38634.5

Basepair signature:
cWW-cWH-L-R-cWW

25.00 -73.84 7.5 4

cWH basepair and non-canonical AC

8

Motif group IL_05192.4

Basepair signature:
cWW-L-R-L-R-L-cWW-L

25.00 -74.36 6 4

9

Motif group IL_00981.1

Basepair signature:
cWW-tWH-tHH-tHS-cWW

25.00 -83.56 5 4.5

UAA/GAN with tHH

10

Motif group IL_63519.1

Basepair signature:
cWW-cWW-L-R-cSH-cWW

25.00 -85.63 6.5 4.5

Loop 7 Internal loop

Column numbers: 57-64, 187-192 
    Scored sequences and counts

    
    UGAGUAAA*UGAAAG    2

    
    UAAGUAAG*UGAAAG    1

    
    UGAGUAAG*UGAGAG    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_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

100.00 40.36 4 1.5

8x6 Sarcin-Ricin with inserted Y; G-bulge

2

Motif group IL_26307.2

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 24.87 3 1.5

7x6 Sarcin-Ricin; G-bulge

3

Motif group IL_78349.3

Basepair signature:
cWW-L-R-L-R-L-R-L-cWW-L-L

25.00 -9.19 7 5

Loop 8 3-way junction loop

Column numbers: 72-75, 121-122, 174-179 
    Scored sequences and counts

    
    GUAC*GG*AAAAUC    1

    
    GUAG*GU*AAAAUC    1

    
    G--G*GG*UAAAAC    1

    
    G--G*AU*AAGAA-    1
No Matches Found View All Results for this Loop

Loop 9 Internal loop

Column numbers: 81-86, 109-115 
    Scored sequences and counts

    
    GGAAAG*UAAGUAC    2

    
    GGAAAA*UGAGUAC    1

    
    GGAAAG*CAAGUAC    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

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 85.19 3 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

100.00 49.55 3 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

3

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

100.00 29.90 3 2

8x6 Sarcin-Ricin with inserted A; G-bulge

4

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

100.00 22.89 5 2

8x6 Sarcin-Ricin with inserted Y; G-bulge

5

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

100.00 20.99 6 2

tSH-tSH-tHH-tHS

6

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 14.05 3 2

8x7 Sarcin-Ricin; G-bulge

7

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

100.00 13.39 6 3

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

8

Motif group IL_16458.4

Basepair signature:
cWW-L-R-L-R-cSH-tWH-tHS-cWW

100.00 9.94 3 3

Sarcin-Ricin target in LSU H95; G-bulge

9

Motif group IL_88269.4

Basepair signature:
cWW-tWW-cSH-tWH-tHS-cWW

75.00 4.57 4 2

6x5 Sarcin-Ricin; G-bulge

10

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

50.00 10.13 7 3

8x6 Sarcin-Ricin with bulged A; G-bulge

Loop 10 Internal loop

Column numbers: 88-90, 106-107 
    Scored sequences and counts

    
    U-A*UA    2

    
    UGA*UA    1

    
    UGG*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

Basepair signature:
cWW-L-cWW

100.00 51.70 2 0.5

Major groove platform

2

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

100.00 48.97 1 0.5

Single bulged G

3

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

100.00 48.15 4.5 0.5

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 46.72 2.5 0.5

Major groove intercalation

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 35.54 2.5 1

Intercalated cWS

6

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 33.53 2 1

Multiple bulged bases

7

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 31.68 2 0.5

Single stack bend

8

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

100.00 31.55 4 1

9

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

100.00 17.68 2 1

Single stack bend

10

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 17.41 4 1

Loop 11 Hairpin loop

Column numbers: 95-101 
    Scored sequences and counts

    
    GCAAGAC    1

    
    GCUAGAC    1

    
    GUAAAAA    1

    
    GUAAAA-    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_53890.2

Basepair signature:
cWW-F-F-F

100.00 21.52 3 1

2

Motif group HL_31585.4

Basepair signature:
cWW-F-F-F-F-F

75.00 -18.90 2 1.5

Purine riboswitch

3

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

50.00 16.02 2.5 2

Pseudoknot geometry with 3' bulge

4

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

50.00 8.74 4 2

5

Motif group HL_97917.2

Basepair signature:
cWW-F-F-F-F

50.00 -10.55 3.5 3

6

Motif group HL_37344.1

Basepair signature:
cWW-F-F

50.00 -18.45 4.5 3

7

Motif group HL_15574.1

Basepair signature:
cWW-F-F-F-F-F

50.00 -19.68 2 1.5

8

Motif group HL_87553.1

Basepair signature:
cWW-F-F-F-F-F

50.00 -25.76 3.5 3

9

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

25.00 -4.04 2.5 2

10

Motif group HL_59843.1

Basepair signature:
cWW-F-F-F-F

25.00 -15.63 3.5 2.5

Loop 12 Internal loop

Column numbers: 127-133, 164-169 
    Scored sequences and counts

    
    AAAGUAA*UGAAAU    1

    
    AAGGUAA*UGAAAU    1

    
    AGAGUAG*CGAAAU    1

    
    AGAGUAG*UGAAAU    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

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW

100.00 78.51 2.5 0.5

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_24254.1

Basepair signature:
cWW-cWW-tHH-cSH-tWH-tHS-cWW

100.00 29.86 6 2

7x6 Sarcin-Ricin with UU cWW pair; G-bulge

3

Motif group IL_29198.2

Basepair signature:
cWW-cWW-L-R-cSH-R-tWH-tHS-cWW

100.00 21.08 4 2

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

4

Motif group IL_61286.1

Basepair signature:
cWW-L-R-L-R-L-tWH-L-tHS-cWW

100.00 16.79 6 3

8x6 Sarcin-Ricin with inserted A; G-bulge

5

Motif group IL_41756.4

Basepair signature:
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

75.00 27.67 4.5 1.5

8x6 Sarcin-Ricin with inserted Y; G-bulge

6

Motif group IL_02349.4

Basepair signature:
cWW-tSH-tWH-cSH-tWH-tHS-cWW

75.00 15.16 6 2.5

8x6 Sarcin-Ricin with bulged A; G-bulge

7

Motif group IL_47346.2

Basepair signature:
cWW-tSH-L-R-tHH-tHS-cWW

75.00 14.36 5.5 2

tSH-tSH-tHH-tHS

8

Motif group IL_04346.10

Basepair signature:
cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

75.00 10.63 3 2

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_32016.1

Basepair signature:
cWW-tSH-tSH-tSS-tHS-L-R-cWW

50.00 6.12 5.5 3.5

Kink-turn

10

Motif group IL_88269.4

Basepair signature:
cWW-tWW-cSH-tWH-tHS-cWW

50.00 -1.64 4 2.5

6x5 Sarcin-Ricin; G-bulge

Loop 13 Hairpin loop

Column numbers: 145-152 
    Scored sequences and counts

    
    AUAAAGCU    1

    
    GAAAAGCC    1

    
    GAGAAACC    1

    
    GAGAAGCC    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_27670.2

Basepair signature:
cWW-tWH-F-F

100.00 24.66 2 2

T-loop with unstacked turn

2

Motif group HL_47854.1

Basepair signature:
cWW-F-F-F-F

75.00 16.23 2 2

3

Motif group HL_89893.1

Basepair signature:
cWW-F-F-F-F

75.00 15.29 4 2

4

Motif group HL_93324.4

Basepair signature:
cWW-F-F-F-F-F-F

50.00 -8.35 4 2

Pseudoknot geometry

5

Motif group HL_39243.1

Basepair signature:
cWW-F-F-F-F

50.00 -13.33 2.5 2.5

6

Motif group HL_38046.1

Basepair signature:
cWW-F-F-F-F-F-F

50.00 -13.81 4.5 3.5

7

Motif group HL_04641.1

Basepair signature:
cWW-F-F-F-F-F

25.00 -11.80 5 3

8

Motif group HL_10540.1

Basepair signature:
cWW-F-F-F-F-F

25.00 -15.87 5 3

9

Motif group HL_04259.3

Basepair signature:
cWW-F-F-F-F-F-F

25.00 -18.25 3.5 2.5

GNRA with extra cWW

10

Motif group HL_15574.1

Basepair signature:
cWW-F-F-F-F-F

25.00 -20.26 3 2.5

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