RNA 3D Hub

JAR3D Query RF03121-3.98 completed
Run on Motif Atlas Version 3.98 using the Rfam secondary structure. Run with the CaCoFold 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 1HL Column numbers: 105-114
  • Loop 2IL Column numbers: 128-129, 148-150
  • Loop 3IL Column numbers: 130-132, 146-147
  • Loop 4HL Column numbers: 133-145
  • Loop 5IL Column numbers: 165-170, 304-315
  • Loop 6IL Column numbers: 172-177, 296-302
  • Loop 7IL Column numbers: 181-188, 284-292
  • Loop 8IL Column numbers: 192-196, 276-280
  • Loop 9IL Column numbers: 200-203, 270-272
  • Loop 10IL Column numbers: 205-206, 266-268
  • Loop 11J3 Column numbers: 207-225, 234-235, 259-265
  • Loop 12HL Column numbers: 226-233
  • Loop 13HL Column numbers: 236-258

Loop 1 Hairpin loop

Column numbers: 105-114 
    Scored sequences and counts

    
    UACAGAAUGG    4

    
    UACACAAUGG    3

    
    CACACAACGG    2

    
    CACAGAAUGG    2

    
    AGCUUUAGAU    1

    
    CACACAAUGG    1

    
    UACACAACGG    1

    
    UACACUAUGG    1

    
    UACAGAAUCA    1

    
    UACUAAAAUG    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_50779.4

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

52.94 12.88 5 3

2

Motif group HL_06226.4

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

41.18 -9.01 4 2

3

Motif group HL_93438.2

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

23.53 -22.99 5 4

4

Motif group HL_36335.1

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

11.76 -17.31 4 4

5

Motif group HL_75293.5

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

5.88 -39.13 5 4

6

Motif group HL_69139.1

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

5.88 -42.33 6 6

7

Motif group HL_88205.2

Basepair signature:
cWW-cWS-tSW-F-F

5.88 -49.33 5 4

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: 130-132, 146-147 
    Scored sequences and counts

    
    GGA*CC    3

    
    GCA*UC    2

    
    A-A*UU    2

    
    G-C*GU    2

    
    A-G*UU    1

    
    A-U*GU    1

    
    G-A*UU    1

    
    G-C*AC    1

    
    G-U*AU    1

    
    U-A*UA    1

    
    U-U*AA    1

    
    Omitted sequenced and counts

    
    C--*UG    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

93.75 27.57 3 1

Major groove platform

2

Motif group IL_42771.1

Basepair signature:
cWW-cWW

93.75 17.52 3 1

Multiple bulged bases

3

Motif group IL_00225.13

Basepair signature:
cWW-L-cWW

81.25 16.45 1 1

Single bulged G

4

Motif group IL_81831.1

Basepair signature:
cWW-L-cWW

68.75 18.86 3 1

Intercalated cWS

5

Motif group IL_73452.2

Basepair signature:
cWW-L-cWW

68.75 17.32 3 1

6

Motif group IL_84476.1

Basepair signature:
cWW-cWW

68.75 3.89 3 2

Multiple bulged bases

7

Motif group IL_66635.5

Basepair signature:
cWW-L-cWW

56.25 19.22 2 1

Major groove intercalation

8

Motif group IL_16386.4

Basepair signature:
cWW-L-cWW

56.25 16.27 4 1

9

Motif group IL_90729.1

Basepair signature:
cWW-L-cWW

56.25 15.32 2 1

Single stack bend

10

Motif group IL_26793.1

Basepair signature:
cWW-L-cWW

56.25 13.19 2 1

Single stack bend

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: 165-170, 304-315 
    Scored sequences and counts

    
    GUUUAG*UGUUUGAAAAUU    3

    
    GUUUAG*UG-AUGAUAAUU    2

    
    ACCUAG*UGCUAAU--GGA    2

    
    CUAUAG*UGUUAAUUAGUU    1

    
    GCCUAG*UUAAUCUAAAUA    1

    
    GUCUAG*UGUUAAUGAUAU    1

    
    CCUUAG*UG-UAGAUAGGU    1

    
    CCUUAG*UG-UAGAUGGGU    1

    
    GCCUAG*UGUUAGUGGA-C    1

    
    --CUAG*UCAAAAUUUUUC    1

    
    CACGAG*UG--AAGACCUG    1

    
    UACGAG*UG--AAGACCUA    1

    
    UCCGAG*UU--AAGACAGU    1
No Matches Found View All Results for this Loop

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: 181-188, 284-292 
    Scored sequences and counts

    
    G---CAAU*GAUUGUUUA    3

    
    GUA--UAA*AGACCUAUC    2

    
    GGACGAAA*GGAAGUCCC    1

    
    GUACCUUU*CUUAAGGAC    1

    
    GU-CUUUU*AUAUUUGAC    1

    
    GUUGCCUA*UAGU-GUUA    1

    
    UAUGCAUU*ACAU-GCUA    1

    
    UUAACUAC*GUAU-GUUG    1

    
    A-UAUUAC*GUAU-AUAU    1

    
    G-AACUUU*AAAU-GUUU    1

    
    UGUUUUAA*C--UACGCA    1

    
    G----UGC*AUUAACAAG    1

    
    U---CAAU*CACUUGUU-    1

    
    U---CAAU*UAAUUGCU-    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_16665.1

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

29.41 -90.72 9 6

2

Motif group IL_31915.1

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

5.88 -107.58 9 8

3

Motif group IL_80604.6

Basepair signature:
cWW-cWW-tWH-tWH-tHW-tHW-cWW

5.88 -173.37 9 7

Loop 8 Internal loop

Column numbers: 192-196, 276-280 
    Scored sequences and counts

    
    AGAUU*GAUCU    5

    
    UCUAA*-AU-U    2

    
    UAACG*ACUAU    1

    
    UAGUG*CCCUU    1

    
    AUUAC*UGU-A    1

    
    AUUAC*UGU-C    1

    
    AUUAU*AAA-U    1

    
    ACACU*A-A-U    1

    
    ACCUC*U-G-U    1

    
    UGCUA*U-G-C    1

    
    UGUUU*A-U-C    1

    
    U--CC*U-C-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_57881.1

Basepair signature:
cWW-L-cWW

17.65 -111.04 7 4

Multiple bulged bases

2

Motif group IL_44325.1

Basepair signature:
cWW-cWH-cWW-L

17.65 -119.23 7 3

3

Motif group IL_70096.1

Basepair signature:
cWW-L-cWW-cWW

11.76 -53.50 7 4

Kink-turn related

4

Motif group IL_11415.1

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

11.76 -96.41 7 5

5

Motif group IL_10389.1

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

11.76 -101.25 6 4

6

Motif group IL_42314.1

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

11.76 -108.76 6 4

7

Motif group IL_36516.3

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

11.76 -130.50 5 2

8

Motif group IL_01994.1

Basepair signature:
cWW-cWH-tHS-cWW-cSH-cWW

11.76 -136.23 7 4

9

Motif group IL_82741.2

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

11.76 -137.43 6 4

10

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

11.76 -138.92 4 3

Isolated non-canonical cWW pair

Loop 9 Internal loop

Column numbers: 200-203, 270-272 
    Scored sequences and counts

    
    UAAU*CGU    3

    
    UGUG*U-C    2

    
    AAAU*CUU    1

    
    AAUU*CUU    1

    
    AUAG*CAU    1

    
    GAUU*UAG    1

    
    GGAG*CAC    1

    
    UUUG*CCA    1

    
    CU-U*UUG    1

    
    GU-G*CAC    1

    
    GU-U*AAC    1

    
    UU-G*CAA    1

    
    UU-G*UAG    1

    
    GA-G*CA-    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_57744.1

Basepair signature:
cWW-cWW-cWW

64.71 -4.79 2 1

Isolated non-canonical cWW pair

2

Motif group IL_31737.3

Basepair signature:
cWW-L-cWW

58.82 0.11 3 1

Stack and bulge

3

Motif group IL_08770.1

Basepair signature:
cWW-L-R-cWW

47.06 15.00 3 1

4

Motif group IL_99358.1

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

47.06 5.74 3 1

5

Motif group IL_14688.1

Basepair signature:
cWW-cWW-cWW

47.06 -10.12 4 1

Isolated non-canonical cWW pair

6

Motif group IL_90351.1

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

47.06 -59.95 3 1

7

Motif group IL_42997.3

Basepair signature:
cWW-L-R-cWW

41.18 -25.80 3 1

Isolated cWS basepair

8

Motif group IL_07785.1

Basepair signature:
cWW-cWW-cWW

41.18 -32.18 3 1

Isolated non-canonical cWW pair

9

Motif group IL_82107.4

Basepair signature:
cWW-cWW

35.29 -12.88 3 1

Multiple bulged bases

10

Motif group IL_83389.2

Basepair signature:
cWW-cWW

35.29 -14.23 4 1

Loop 10 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 11 3-way junction loop

Column numbers: 207-225, 234-235, 259-265 
    Scored sequences and counts

    
    GAGAAGUUUAAAGAUCCGC*GC*GAAGAGC    3

    
    GAGUAAUUUAAAGAUCCGC*GC*GAAGGGC    2

    
    GAGUAA-UCAAAGAUCCGC*GC*GAAGAGC    2

    
    GAGUAAUUUAAAGAUCCGC*GC*GAAGAGC    1

    
    GAGUGAUUUAAAGAUCGCU*GC*GAAGAGC    1

    
    GAGUAA-UUGAAAGAUCGC*GC*GAAGAGC    1

    
    GAGUAAUC-AAAGAUCCGC*GC*GAAGAGC    1

    
    GAGUAAUU-AAAGAUCCGC*GC*GAAGAGC    1

    
    GUUUAGUCUUACACACAAU*AG*AGAGUG-    1

    
    GAGUAA-UCAAAGAU-CGC*GC*GAAGAGC    1

    
    GAGUAA-UUAAAGAU-CGC*GC*GAAGAGC    1

    
    GAGUACUU-AAAGAU-CGC*GC*GAAGAGC    1

    
    GAGUA-UCUAAAGAUCG--*GC*GAAGAGC    1
No Matches Found View All Results for this Loop

Loop 12 Hairpin loop

Column numbers: 226-233 
    Scored sequences and counts

    
    UUAGACGA    3

    
    UU-GACGA    3

    
    UAUGACGA    2

    
    UUUGACGA    2

    
    AUAGACGA    1

    
    AUAGGCGC    1

    
    AUUGACGA    1

    
    CAAGACGA    1

    
    GGUAGGCC    1

    
    UACGACGA    1

    
    -UUGACGA    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_59330.1

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

52.94 1.56 4 3

2

Motif group HL_20535.2

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

41.18 -10.50 4 3

3

Motif group HL_13529.1

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

41.18 -20.80 4 3

4

Motif group HL_85367.2

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

35.29 -30.91 5 3

5

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

23.53 -21.39 5 3

6

Motif group HL_84299.4

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

23.53 -21.68 3 2

7

Motif group HL_50006.2

Basepair signature:
cWW-F-F

23.53 -33.51 4 3

8

Motif group HL_93324.4

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

23.53 -57.13 3 3

Pseudoknot geometry

9

Motif group HL_87553.1

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

17.65 -35.87 3 3

10

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

17.65 -36.19 5 3

tRNA anticodon loop with synthetase

Loop 13 Hairpin loop

Column numbers: 236-258 
    Scored sequences and counts

    
    CA---------------ACAAUG   10

    
    CU---------------AU-AUG    3

    
    CAUGUCUGCCAGUGAGUAGAAUG    1

    
    CU---------------AAUGUG    1

    
    UG---------------GUAGUG    1

    
    CU----------------AUAUG    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_39243.1

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

82.35 -613.36 3 1

2

Motif group HL_85993.1

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

64.71 -488.56 4 2

3

Motif group HL_04259.3

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

58.82 -674.39 3 2

GNRA with extra cWW

4

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

29.41 -666.23 3 3

5

Motif group HL_77436.5

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

23.53 -101.98 3 3

T-loop related

6

Motif group HL_25967.2

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

23.53 -508.48 3 3

7

Motif group HL_10453.3

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

23.53 -581.37 5 3

tRNA anticodon loop

8

Motif group HL_20535.2

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

23.53 -644.60 5 3

9

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

23.53 -648.47 2 2

10

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

23.53 -673.80 1 1

Coloring options: