RNA 3D Hub

JAR3D Query RF03121-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF03121 Alphacoronavirus 3'UTR

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222333333333333333333333333333333333333333
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
..((((.....................................................................................................................((((((.(((...........)))).))))).))))(((((((((((((....(((((....((((((((((((((((.(((((.....(......((((((((....))))))...............)).....)....)).))))))))))))))))))).....))))).....))......)))))))))))..................
>NC_010437.1_28026-28309
ACUCUGUUGCUUGAGU---------CAAUCUGUUGCGCU-----------------AUUCACCCCAUAUCUGUACUUUUCAGAAUGGACAAGGUGACCUACUUAUACUAAAAUGUAAGCCUGUAUUUAAG-CA-GUAUAAGCAAUACU-UAAAUAUAUUACUGCCCUUAGAUCAAAGCUAUAUGCAUUAGUACCUCUAUGU-UCUGGAGUAA-UCAAAGAUCCGCUUAGACGAGCCU----------------AUAUGGAAGAGCU-AGAACAUAU-G-UGCUACAU-GCUAUAGUUAGUAGUUG-UAGAUGGGUGUGGUUUUGAUAG--GGAUUCAC
>NC_010438.1_28473-28757
GCCGUGAGGAGCUUCC---------UAAUCU-UGAUGCUGAAUAC--------AUAAUCCACCCUAC-UGAG------UCUCAGUAG-UUUGGUGGCAGUCUUAUACACUAUGGUAAGCCUGUAAUUAAA-UA-GUAUAAGCAAUGUU-UAAUUAUAUUACUAGCCUUAGAUGAAAAUUAGUUGCCUACAGUGCUACCCCU-UUCGGAGUAA-UUGAAAGAUCGCUUUGACGAGCCU---------------AAUGUGGAAGAGCC-GUUUGGAGU-G-CCUGUAGU-GUUAUAAUUAGUAAUUG-UAGAUAGGUGUAGUUUUGAUAG--GGAUUCAC
>NC_005831.2_27253-27551
AGGUUUUGC-AUUAAAUUGUUUUGUAAUUCCAGUUGAAUGUUUAUUAUUAUUAGUUGCAACCCCAUG-CGU-----U-UAGCGCAUGAUAAGGGUUUAGUCUUACACACAAUGGUAGGCCAGUGAUAGUA-AA-GUGUAAGUAAUUUG-CUAUCAUAUUAACAUGUCUAGAGGAAAGUCAG-AACUUUUUCUGUUUGUGUU-GUUGGAGUACUU-AAAGAU-CGCAUAGGCGCGCCA---------------ACAAUGGAAGAGCC-AACAACAUA-U-CUAAAAAU-GUUUUGUCUGGUACUUGUUAAUGAUAU-UGUUUUUGAUAU--GGAUAC--
>NC_018871.1_28194-28493
ACGACAUCAGACUUUCGCUGUGACUACUUUUAGGUGGUCUACUCCUUCAAAUUAAUACGCACCCUUU-CUU-----CGGAUUGACAA----GGUGCUACUCUUAUACAGAAUGGUAAGCCUGUUUAUAAG-CUAGUAUAAGUAGAGUU-UAUAGAUAUUGCUGUGCCUAGACCAACGUACA-UAUUACAAGACACUCCAGA-GUCAGAGUAAUUUAAAGAUCCGCAUAGACGAGCCA---------------ACAAUGGAAGAGCU-GUCA-UGGA-A-UCUUGUAU-AUAUGUAUCAGUAGUUGUUAGUGGA-CACGGCUUUGAUAG--GGAUACG-
>NC_009988.1_26865-27149
GCAUUUUUUUAUUAACAUUGGCAAAUUUUGC-AGAUUUGUUUGAC---------AUACAAUCCCUAG-CU----------UUGCUUG---UGGAUUUAGUCUCAUACACAAUGGUAAGCACGUAAUUAUG-CUAGUAUGAGUAGAGUA-UAAUUAUAUUGAGUCCUAUAGACCAACGCAGUUAACUACAUGU--CCGGUGU-GGCGGAGUAA-UCAAAGAUCCGC-UUGACGAGCCU---------------AU-AUGGAAGAGCC-GUCACACCU-C-GUAUGUAU-GUUGCUGCUAGUAGUUGUUAAUUAGUUGAUUCUUUGACAG--UGAUACAC
>NC_028811.1_27635-27924
-------AUAACAUCUUGCACUGGCUACUUAGUG--------AUAUGCGGCCCCUAGGCUUCC------UCCUUUGGAUCCUAGUUAUUUUGGGCCUGGUCUUAUACACAACGGUAGUCCAGUGGUAAUU-UCAGUAUAAGAAGGAAA-UCACCAUAUUGCAGAUCCGAGGUGAACGCUAUGUUUUAACUAUCUAACACGGAGUUGGAGUGAUUUAAAGAUCGCUUU-GACGAGCCA---------------ACAAUGGAAGAGCC-AACACGUG-AU-UUAGC--UACGCAUAGUUACUAACUU--AAGACAGUUCUGCUUUGCUAU--GGAUACAC
>NC_009657.1_27903-28179
----------------AUCUUUCUUGUUCAUGAUCUU-------AACAUGGCUGCUGGGCAUUGGAAUCUUCC--AAUACUAGC-------GGUCUUGGUCUUGCACACAACGGUAAGCCUGUAAUAAUG-ACAGUGCAAGCAGGUUA-UUAUUAUAUUGCAGCUACGAGGCGAAC-GUAGU-CUUUUACAAUUAUUUCAUAGCAUGAGUAAUC-AAAGAUCCGCUU-GACGAGCCU---------------AU-AUGGAAGAGCA-UGCAUGAAAAA-UUGUAUAUUUGACUAUCUAGUAACUG--AAGACCUAGCUGCUUUGAUAG--GGAUACG-
>NC_003436.1_27733-28031
CAGGGUAGUGCCAUUACACUGUUAUUACUGAGUGUUUUUCUAGCGACUUGGCUGCUGGGCUAUGGC-UUUGCCCUCUAACCAGC-------GGUCUUGGUCUUGCACACAACGGUAAGCCAGUGGUAAUG-UCAGUGCAAGAAGGAUA-UUACCAUAGCACUGUCACGAGGGGAAC-GCAGUACCUUUUCAUCUAAACCUUUGCACGAGUAAUU-AAAGAUCCGCUU-GACGAGCCU---------------AU-AUGGAAGAGCG-UGCCAGGU-AU-UUGACUUAAGGACUGU-UAGUAACUG--AAGACCUGACGGUGUUGAUAU--GGAUAC--
>NC_002645.1_27017-27277
---------------------------------------AGCUGCUUUUAAUUAACAUGAUCCCUUGCUU----------UGGCUUGACAAGGAUCUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUA-AAGGUAUAAGAAAUUUG-CUACUAUGUUACUGAACCUAGGUGAACGCUAGUA--UAACUCAUUACAAAUGUGCUGGAGUAA-UCAAAGAU-CGCAUUGACGAGCCA---------------ACAAUGGAAGAGCC-AGU-CAUUUGU-CUUGAGACCUAUCUAGUUAGUAACUGCUAAU--GGAACGGUUUCGAUAU--GGAUACAC
>NC_028752.1_27095-27383
UCCGGUCUAUGCA-----------UGAUGGCAUGAUCAGAGCUGCUUUUAACUAACAUGAUCCCUUGCUU----------CGGCUUGAUAAGGAUCUAGUCUUAUACACAAUGGUAAGCCAGUAGUAGUA-GAGGUAUAAGAAAUUUG-CUACUAUGUUACUGAACCUAGGUGAACACUAGUA--UAACUCAUUACAAAUGUGCUGGAGUAA-UUAAAGAU-CGCUUUGACGAGCCA---------------ACAAUGGAAGAGCC-AGU-CAUUUGU-AUUGAGACCUAUCUAGUUAGUAACUGCUAAU--GGAACGGUUUCGAUAU--GGAUACAC
>NC_038861.1_28286-28580
-----AUUGUUAGUCACAUUA-AUGUAAGGCAACCCGAUGUCUAAA-------ACUGGUUUUUCCGAGGAAUU-----ACUGGUCAUCGCGCUGUCUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGA-GGUACAAGCAACCCU-AUUGCAUAUUAGGAAGUUUAGAUUUGAUUUGG---CAAUGCUAGAUUUAGUAAUUUAGAGAAGUUUAAAGAUCCGCUACGACGAGCCA---------------ACAAUGGAAGAGCU-AACGUCUGGAUCUAGUGAUUGUUUAAAAUGUAAAAUUGUUUGAAAAUUUUCCUUUUGAUAG--UGAU--AC
>NC_028806.1_27811-28110
UAUAGAUUGUUAGUUAUAUUA-AUGUAAGGCAACCCGAUGUUUAAA-------ACUGGUUUUUCUGAGGAACU-----ACUGGUCAUCGCGCUGUCUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGA-GGUACAAGCAACCCU-AUUGCAUAUUAGGAGGUUUAGAUUUGAUUUGG---CAAUGCUAGAUUUAGUAAUUUAGAGAAGUUUAAAGAUCCGCUAUGACGAGCCA---------------ACAAUGGAAGAGCU-AACGUCUGGAUCUAGUGAUUGUUUAAAAUGUAAAAUUGUUUGAAAAUUUUCCUUUUGAUAG--UGAU--AC
>NC_002306.3_29055-29354
CAACCAACAUCAUAAAACUGAGUUAUAAGGCAACCCGAUGUCUAAA-------ACUGGUCUUUCCGAGGAAUU-----ACGGGUCAUCGCGCUGCCUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGA-GGUACAAGCAACCCU-AUUGCAUAUUAGGAAGUUUAGAUUUGAUUUGG---CAAUGCUAGAUUUAGUAAUUUAGAGAAGUUUAAAGAUCCGCUAUGACGAGCCA---------------ACAAUGGAAGAGCU-AACGUCUGGAUCUAGUGAUUGUUUAAAAUGUAAAAUUGUUUGAAAAUUUUCCUUUUGAUAG--UGAU--A-
>NC_030292.1_28134-28416
-------CCUGUAUCUAAUAAAAUUGAACAUGAUGAUUUAUAAGAA-------GAUCUUCGGGCGAGUACCGC-----UAGAUC------------UACUCUUACACAGAAUGGUAAGCACGUAUCUAUGCAGGGUGUAAGUAACUCA-UAGAUAUAUUAGGAAGUUUAGAUUGAACUAUU---CAAUACUAGAUUGAAAAAUUGAGAGUAAUUUAAAGAUCCGCUUAGACGAGCCA---------------ACAAUGGAAGGGCUCAACUUUUGGAUCUAGUCACUUGUU--UAUAGUAAAUUG-AUGAUAAUUCUCCUUUUGAUAG--UGAUACAC
>NC_023760.1_28641-28894
------------------------------------AUUAUAACAA-------GAUCUUCAGGCGUGUACUGC-----GAGAUC------------UACUCUUACACAGAAUGGUAAGCACGUAUCUAUGCAGGGUGUAAGUAACUCA-UAGAUAUAUUAGGAAGUUUAGAUUGAAUUAAU---CAAUACUAGAUUGAAAAUUUGAGAGUAAUUUAAAGAUCCGCUUAGACGAGCCA---------------ACAAUGGAAGGGCUCAACUUUUGGAUCUAGUUAAUUGCU--AAUUUUAAAUUG-AUGAUAAUUUUCCUUUUGAUAG--UGAUACAC
>NC_032107.1_28063-28362
UUUUCACAUGGAAUUUUCUAAUAUGCUAUGCCUUUCUUUACUUCAUUCUUGUUCCUUUAGUUCAAGAACUUUU----------UCUUCCUGGUGCAUUAGAUUUAGCUUUAGAUCAAUUACGUGGUUUUC---AUGAUUUUAUUGUGA-GAGCCAUGUUUUG----CUAGUUGCAACCCCG----UGCGCUUAACGCACGAUUAGGGUUUAGUCUUACACACAAUGGUAGGCCAGUG---------------GUAGUGAGAGUG-UAAGUAGCUUACUAUCAUAUUAACAAGUCUAGGGGAAUUCAAAAUUUUUCUGCACUAUGUUAGCUGGAGUAAU
>NC_032730.1_28463-28732
UGAGUGAGA----------------------------------------------UGCUCUUAUGUUAGCA------------UGCUAAUAUAAGACACUAGUGUACAGAAUCAUUACCACGUCUAUAGU-AGGGUACACAUAACUAUCUAUAGAUA-UAGAAAGCCUAGAUGAAC---AGGACGAAAGACUAGUGACAUU-GCAGGAGUA-UCUAAAGAUCG--CAAGACGAGCCAUGUCUGCCAGUGAGUAGAAUGGAAGAGCC-UGUAGUGCCCCUUUUCGGAAGUCCCUAGUAGUUAUGUUAAUCUAAAUAGGGGAUCUUUGAGGGUGGGAUGC

There are no chains in PDB that we map to Rfam family RF03121.

Rfam family RF03121 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: 6-124, 154-156
  • Loop 2IL Column numbers: 128-129, 148-150
  • Loop 3IL Column numbers: 129-131, 147-148
  • Loop 4HL Column numbers: 133-145
  • Loop 5IL Column numbers: 170-171, 303-310
  • Loop 6IL Column numbers: 172-177, 296-302
  • Loop 7IL Column numbers: 181-186, 286-292
  • Loop 8IL Column numbers: 201-203, 270-271
  • Loop 9IL Column numbers: 205-206, 266-268
  • Loop 10IL Column numbers: 207-213, 260-265
  • Loop 11IL Column numbers: 213-220, 254-260
  • Loop 12IL Column numbers: 221-222, 237-253
  • Loop 13HL Column numbers: 227-232

Loop 1 Internal loop

Column numbers: 6-124, 154-156 
    Scored sequences and counts

    
    UAGUGCCAUUACACUGUUAUUACUGAGUGUUUUUCUAGCGACUUGGCUGCUGGGCUAUGGC-UUUGCCCUCUAACCAGC-------GGUCUUGGUCUUGCACACAACGGUAAGCCAGUG*CAU    1

    
    UUGC-AUUAAAUUGUUUUGUAAUUCCAGUUGAAUGUUUAUUAUUAUUAGUUGCAACCCCAUG-CGU-----U-UAGCGCAUGAUAAGGGUUUAGUCUUACACACAAUGGUAGGCCAGUG*CAU    1

    
    ACAUGGAAUUUUCUAAUAUGCUAUGCCUUUCUUUACUUCAUUCUUGUUCCUUUAGUUCAAGAACUUUU----------UCUUCCUGGUGCAUUAGAUUUAGCUUUAGAUCAAUUACGUG*CAU    1

    
    AUCAGACUUUCGCUGUGACUACUUUUAGGUGGUCUACUCCUUCAAAUUAAUACGCACCCUUU-CUU-----CGGAUUGACAA----GGUGCUACUCUUAUACAGAAUGGUAAGCCUGUU*GAU    1

    
    AACAUCAUAAAACUGAGUUAUAAGGCAACCCGAUGUCUAAA-------ACUGGUCUUUCCGAGGAAUU-----ACGGGUCAUCGCGCUGCCUACUCUUGUACAGAAUGGUAAGCACGUG*CAU    1

    
    AUUGUUAGUCACAUUA-AUGUAAGGCAACCCGAUGUCUAAA-------ACUGGUUUUUCCGAGGAAUU-----ACUGGUCAUCGCGCUGUCUACUCUUGUACAGAAUGGUAAGCACGUG*CAU    1

    
    AUUGUUAGUUAUAUUA-AUGUAAGGCAACCCGAUGUUUAAA-------ACUGGUUUUUCUGAGGAACU-----ACUGGUCAUCGCGCUGUCUACUCUUGUACAGAAUGGUAAGCACGUG*CAU    1

    
    --AUAACAUCUUGCACUGGCUACUUAGUG--------AUAUGCGGCCCCUAGGCUUCC------UCCUUUGGAUCCUAGUUAUUUUGGGCCUGGUCUUAUACACAACGGUAGUCCAGUG*CAU    1

    
    UCUAUGCA-----------UGAUGGCAUGAUCAGAGCUGCUUUUAACUAACAUGAUCCCUUGCUU----------CGGCUUGAUAAGGAUCUAGUCUUAUACACAAUGGUAAGCCAGUA*UAU    1

    
    UUUUUAUUAACAUUGGCAAAUUUUGC-AGAUUUGUUUGAC---------AUACAAUCCCUAG-CU----------UUGCUUG---UGGAUUUAGUCUCAUACACAAUGGUAAGCACGUA*UAU    1

    
    --CCUGUAUCUAAUAAAAUUGAACAUGAUGAUUUAUAAGAA-------GAUCUUCGGGCGAGUACCGC-----UAGAUC------------UACUCUUACACAGAAUGGUAAGCACGUA*UAU    1

    
    GAGGAGCUUCC---------UAAUCU-UGAUGCUGAAUAC--------AUAAUCCACCCUAC-UGAG------UCUCAGUAG-UUUGGUGGCAGUCUUAUACACUAUGGUAAGCCUGUA*UAU    1

    
    GUUGCUUGAGU---------CAAUCUGUUGCGCU-----------------AUUCACCCCAUAUCUGUACUUUUCAGAAUGGACAAGGUGACCUACUUAUACUAAAAUGUAAGCCUGUA*UAU    1

    
    -----------AUCUUUCUUGUUCAUGAUCUU-------AACAUGGCUGCUGGGCAUUGGAAUCUUCC--AAUACUAGC-------GGUCUUGGUCUUGCACACAACGGUAAGCCUGUA*UAU    1

    
    ----------------------------------AGCUGCUUUUAAUUAACAUGAUCCCUUGCUU----------UGGCUUGACAAGGAUCUAGUCUUAUACACAAUGGUAAGCCAGUG*UAU    1

    
    -------------------------------AUUAUAACAA-------GAUCUUCAGGCGUGUACUGC-----GAGAUC------------UACUCUUACACAGAAUGGUAAGCACGUA*UAU    1

    
    GAGA----------------------------------------------UGCUCUUAUGUUAGCA------------UGCUAAUAUAAGACACUAGUGUACAGAAUCAUUACCACGUC*GAU    1
No Matches Found View All Results for this Loop

Loop 2 Internal loop

Column numbers: 128-129, 148-150 
    Scored sequences and counts

    
    AU*A-U    6

    
    AA*U-U    3

    
    GU*G-C    3

    
    UA*U-A    3

    
    AG*UCU    1

    
    UU*A-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_07039.3

Basepair signature:
cWW-L-cWW

100.00 20.36 2 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 19.99 3 1

Multiple bulged bases

3

Motif group IL_84476.1

Basepair signature:
cWW-cWW

94.12 23.08 3 2

Multiple bulged bases

4

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

94.12 16.82 4 1

5

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

94.12 6.81 1 1

Single bulged G

6

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

82.35 18.10 4 1

Intercalated cWS

7

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

76.47 13.42 2 1

Single stack bend

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

76.47 10.44 3 1

Major groove intercalation

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

76.47 7.12 2 1

Single stack bend

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

76.47 6.46 5 1

Loop 3 Internal loop

Column numbers: 129-131, 147-148 
    Scored sequences and counts

    
    AGG*CU    3

    
    UA-*UG    3

    
    UG-*UA    3

    
    UGC*CA    2

    
    AA-*UU    1

    
    AG-*CU    1

    
    AG-*UU    1

    
    GU-*AU    1

    
    UC-*GA    1

    
    UU-*AA    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 53.39 2 0

Major groove platform

2

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

100.00 36.26 2 0

Single stack bend

3

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

100.00 34.73 1 0

Single bulged G

4

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 26.87 3 1

Multiple bulged bases

5

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 23.85 3 1

Intercalated cWS

6

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

100.00 -90.60 2 0

Major groove platform

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

94.12 44.13 2 0

Major groove intercalation

8

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

76.47 32.01 4 0

9

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

76.47 18.88 4 1

10

Motif group IL_84476.1

Basepair signature:
cWW-cWW

70.59 26.19 3 1

Multiple bulged bases

Loop 4 Hairpin loop

Column numbers: 133-145 
    Scored sequences and counts

    
    -GGUACAAGCAAC    3

    
    AGGUAUAAGAAAU    2

    
    GGGUGUAAGUAAC    2

    
    A-GUAUAAGCAAU    2

    
    CAGUAUAAGAAGG    1

    
    CAGUGCAAGAAGG    1

    
    CAGUGCAAGCAGG    1

    
    GGGUACACAUAAC    1

    
    UAGUAUAAGUAGA    1

    
    UAGUAUGAGUAGA    1

    
    -AUGAUUUUAUUG    1

    
    A-GUGUAAGUAAU    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_05304.3

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

5.88 -31.41 6 5

2

Motif group HL_67079.1

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

5.88 -65.11 6 6

Loop 5 Internal loop

Column numbers: 170-171, 303-310 
    Scored sequences and counts

    
    GA*UUGUUUGA    3

    
    GA*UUGUUAAU    2

    
    GG*CUGCUAAU    2

    
    GA*UUG-AUGA    2

    
    GA*UUG-UAGA    2

    
    GG*CUG--AAG    2

    
    GA*GUUAAUCU    1

    
    GA*UUGUUAGU    1

    
    GU*UUCAAAAU    1

    
    GG*CUU--AAG    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_38394.1

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

23.53 -1331.02 6 3

2

Motif group IL_41203.4

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

11.76 -61.80 5 3

SSU/LSU pseudoknot

3

Motif group IL_33711.1

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

5.88 -48.29 7 4

Minor groove platform

4

Motif group IL_38186.6

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

5.88 -66.55 6 3

Loop 6 Internal loop

Column numbers: 172-177, 296-302 
    Scored sequences and counts

    
    UUUGAU*UGUAAAA    3

    
    CCAACG*CUAGUAG    1

    
    CCAACG*UCAGUAG    1

    
    GGAAAG*CUGGUAC    1

    
    UCAAAG*UUAGUAG    1

    
    UGAAAA*UUAGUAA    1

    
    UGAACA*UUAGUAA    1

    
    UGAACG*UUACUAA    1

    
    UGAACG*UUAGUAA    1

    
    UGCAAC*AGGGGAA    1

    
    UUGAAC*UAGUAAA    1

    
    UUGAAU*UUUUAAA    1

    
    CGAAC-*CUAGUAA    1

    
    UGAAC-*UAGUUAU    1

    
    GGAAC-*-UAGUAA    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

58.82 13.08 3 1

7x6 Sarcin-Ricin; G-bulge

2

Motif group IL_16458.4

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

52.94 -28.72 5 3

Sarcin-Ricin target in LSU H95; G-bulge

3

Motif group IL_24254.1

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

47.06 -22.35 6 2

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

4

Motif group IL_61286.1

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

41.18 -30.56 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

23.53 -44.71 6 4

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

6

Motif group IL_04346.10

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

23.53 -55.51 5 3

8x7 Sarcin-Ricin; G-bulge

7

Motif group IL_88269.4

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

17.65 -42.87 5 4

6x5 Sarcin-Ricin; G-bulge

8

Motif group IL_65594.1

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

17.65 -51.80 5 4

8x7 Sarcin-Ricin; G-bulge

9

Motif group IL_47346.2

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

11.76 -36.72 7 4

tSH-tSH-tHH-tHS

10

Motif group IL_32016.1

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

11.76 -52.71 6 5

Kink-turn

Loop 7 Internal loop

Column numbers: 181-186, 286-292 
    Scored sequences and counts

    
    G---CA*UUGUUUA    3

    
    GUA--U*ACCUAUC    2

    
    GGACGA*AAGUCCC    1

    
    GUACCU*UAAGGAC    1

    
    GU-CUU*AUUUGAC    1

    
    GUUGCC*GU-GUUA    1

    
    UAUGCA*AU-GCUA    1

    
    UGUUUU*-UACGCA    1

    
    UUAACU*AU-GUUG    1

    
    A-UAUU*AU-AUAU    1

    
    G-AACU*AU-GUUU    1

    
    G----U*UAACAAG    1

    
    U---CA*AUUGCU-    1

    
    U---CA*CUUGUU-    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

11.76 -79.71 7 4

Kink-turn related

2

Motif group IL_33141.1

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

11.76 -87.72 9 5

3

Motif group IL_22829.2

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

11.76 -94.43 7 5

4

Motif group IL_29223.1

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

11.76 -101.24 6 4

5

Motif group IL_99498.1

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

5.88 -96.61 7 5

6

Motif group IL_25186.4

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

5.88 -111.30 8 6

7

Motif group IL_07173.1

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

5.88 -112.35 6 5

8

Motif group IL_80231.1

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

5.88 -135.65 8 5

Other IL

9

Motif group IL_62654.1

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

5.88 -175.60 8 6

tSH-tHH-tHS

10

Motif group IL_49751.4

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

5.88 -263.62 6 4

Triple non-canonical cWW pairs

Loop 8 Internal loop

Column numbers: 201-203, 270-271 
    Scored sequences and counts

    
    AAU*CG    3

    
    U-G*CA    2

    
    AAU*CU    1

    
    AUU*CU    1

    
    AUU*UA    1

    
    GAG*CA    1

    
    UAG*CA    1

    
    UUG*CC    1

    
    A-G*CA    1

    
    U-G*UA    1

    
    U-U*AA    1

    
    U-U*UU    1

    
    Omitted sequenced and counts

    
    GUG*U-    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_07039.3

Basepair signature:
cWW-L-cWW

93.33 37.05 2 0

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

86.67 29.86 2 1

Multiple bulged bases

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

86.67 24.19 3 1

Intercalated cWS

4

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

80.00 27.75 2 0

Single stack bend

5

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

80.00 25.81 2 0

Single stack bend

6

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

80.00 24.64 3 1

7

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

80.00 24.24 4 0

8

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

73.33 20.90 2 1

Major groove intercalation

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

66.67 11.90 2 1

Stack and bulge

10

Motif group IL_48076.6

Basepair signature:
cWW-cSH-cWW

60.00 -59.82 2 0

Major groove platform

Loop 9 Internal loop

Column numbers: 205-206, 266-268 
    Scored sequences and counts

    
    UG*C-A    4

    
    UA*U-A    3

    
    GA*UCA    2

    
    CG*C-G    2

    
    GG*UAA    1

    
    AC*G-U    1

    
    AG*C-U    1

    
    AU*A-U    1

    
    CA*U-G    1

    
    UG*U-A    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

100.00 25.78 2 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

100.00 24.69 2 1

Multiple bulged bases

3

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

100.00 21.56 3 1

Intercalated cWS

4

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

100.00 16.04 3 1

Major groove intercalation

5

Motif group IL_33761.2

Basepair signature:
cWW-L-cWW

100.00 10.07 3 1

6

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

94.12 21.03 3 1

Single stack bend

7

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

94.12 20.41 3 1

8

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

94.12 16.06 1 1

Single stack bend

9

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

94.12 3.47 4 1

Stack and bulge

10

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

88.24 9.93 4 1

Loop 10 Internal loop

Column numbers: 207-213, 260-265 
    Scored sequences and counts

    
    GAGUAA-*AAGAGC    5

    
    GAGAAGU*AAGAGC    3

    
    GAGUAAU*AAGAGC    3

    
    GAGUAAU*AAGGGC    2

    
    GAGUACU*AAGAGC    1

    
    GAGUGAU*AAGAGC    1

    
    GAGUA-U*AAGAGC    1

    
    GUUUAGU*GAGUG-    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_70801.1

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

35.29 -21.24 7 4

2

Motif group IL_32016.1

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

17.65 -23.70 7 4

Kink-turn

3

Motif group IL_89099.1

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

17.65 -25.33 6 4

Other IL

4

Motif group IL_18487.1

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

17.65 -52.38 7 6

5

Motif group IL_80926.1

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

5.88 -18.10 5 3

6

Motif group IL_42778.1

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

5.88 -19.43 6 4

7

Motif group IL_82292.1

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

5.88 -28.68 7 4

8

Motif group IL_85536.2

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

5.88 -37.22 7 4

9

Motif group IL_31561.1

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

5.88 -40.44 6 4

10

Motif group IL_71294.3

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

5.88 -40.59 6 4

Double sheared; A in syn; two near cWW pairs

Loop 11 Internal loop

Column numbers: 213-220, 254-260 
    Scored sequences and counts

    
    UUUAAAGA*CAAUGGA    7

    
    UCUAAAGA*GAAUGGA    1

    
    UCUUACAC*UAGUGAG    1

    
    -UCAAAGA*AUAUGGA    1

    
    -UCAAAGA*CAAUGGA    1

    
    -UUAAAGA*CAAUGGA    1

    
    -UUGAAAG*AUGUGGA    1

    
    UU-AAAGA*CAAUGGA    1

    
    -UCAAAGA*U-AUGGA    1

    
    UC-AAAGA*U-AUGGA    1

    
    UU-AAAGA*U-AUGGA    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_68405.1

Basepair signature:
cWW-cSS-L-tWH-tHW-cWW-cWW

11.76 -66.88 9 6

Kink-turn related

Loop 12 Internal loop

Column numbers: 221-222, 237-253 
    Scored sequences and counts

    
    UC*A---------------A    7

    
    UC*U---------------A    3

    
    UC*AUGUCUGCCAGUGAGUA    1

    
    AC*G---------------G    1

    
    AU*U---------------A    1

    
    Omitted sequenced and counts

    
    U-*A---------------A    3

    
    UC*U----------------    1
Click on headings to reorder table - View All Results for this Loop
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group IL_84476.1

Basepair signature:
cWW-cWW

84.62 -834.90 4 2

Multiple bulged bases

2

Motif group IL_07039.3

Basepair signature:
cWW-L-cWW

76.92 -650.75 3 1

Major groove platform

3

Motif group IL_42771.1

Basepair signature:
cWW-cWW

53.85 -843.88 2 1

Multiple bulged bases

Loop 13 Hairpin loop

Column numbers: 227-232 
    Scored sequences and counts

    
    UAGACG    4

    
    UUGACG    4

    
    U-GACG    3

    
    AUGACG    2

    
    AAGACG    1

    
    ACGACG    1

    
    GUAGGC    1

    
    UAGGCG    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_56334.1

Basepair signature:
cWW-F

76.47 3.27 3 2

Mini UNCG

2

Motif group HL_93535.1

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

64.71 2.99 3 2

3

Motif group HL_56131.2

Basepair signature:
cWW-F-F

58.82 9.49 2 2

4

Motif group HL_70782.2

Basepair signature:
cWW-F

52.94 3.44 3 2

5

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

52.94 -2.63 3 2

6

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

52.94 -6.26 3 2

tRNA D-loop

7

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

52.94 -16.53 2 2

tRNA D-loop

8

Motif group HL_89893.1

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

35.29 -8.15 3 2

9

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

35.29 -13.28 2 2

Mini UNCG

10

Motif group HL_55195.3

Basepair signature:
cWW-F

35.29 -15.84 2 2

Coloring options: