RNA 3D Hub

JAR3D Query RF03064-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03064 maps to one chain: 8IAZ|1|E See more about it at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 7 Hairpin loop

Column numbers: 71-113 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    ----------------AC-------------------------   39

    
    A---------------UAUUUAUA------------------U   32

    
    ----------------GUGAUUA--------------------   30

    
    G---------------AUUUCGG------------------UC   24

    
    ----------------UU-------------------------   24

    
    ----------------UC-------------------------   19

    
    U---------------AUUUAU--------------------A   17

    
    ----------------AU-------------------------   17

    
    U---------------GUUUA--------------------CA   14

    
    A---------------AGUAAACU------------------U   13

    
    G---------------AUUUCGGU------------------C   13

    
    U-----------------------------------------A   13

    
    G---------------AAUUUAUU------------------C   10

    
    ----------------AA-------------------------   10

    
    U---------------CUUAUG--------------------A    9

    
    ----------------UUCU-----------------------    9

    
    ----------------UA-------------------------    9

    
    U---------------GUUUAU--------------------A    8

    
    ----------------UAU------------------------    8

    
    U-----------------G-----------------------A    8

    
    UUA-------------AUUUUAU-----------------UAA    7

    
    AG--------------AGUUAU-------------------CU    7

    
    G---------------AAUUGAUU------------------C    7

    
    U---------------CAUUUGUA------------------A    7

    
    ----------------GUUAGU---------------------    7

    
    A---------------U-------------------------U    7

    
    G---------------GCUUGC--------------------C    6

    
    U---------------AUUCAU--------------------A    6

    
    C---------------AAA-----------------------G    6

    
    C---------------AA------------------------G    6

    
    U---------------A-------------------------A    6

    
    ----------------CC-------------------------    6

    
    ----------------GC-------------------------    6

    
    UGAA------------AUAUU------------------UUCA    5

    
    G---------------AAGAAUUU------------------C    5

    
    C---------------CUUCGG--------------------G    5

    
    U---------------CUUUUG--------------------A    5

    
    G---------------UUUAU---------------------C    5

    
    ----------------GUAAUU---------------------    5

    
    ----------------AAA------------------------    5

    
    A----------------U------------------------U    5

    
    UUAA------------UUUAUU-----------------UUAA    4

    
    G---------------GAUUUAUC------------------C    4

    
    GA--------------UCUCGG-------------------UC    4

    
    U---------------AGUAAU--------------------A    4

    
    UGC-------------UU----------------------GCA    4

    
    U---------------AUUAU---------------------A    4

    
    U---------------GUUUA---------------------U    4

    
    ----------------GUUUUA---------------------    4

    
    U---------------AUAA----------------------A    4

    
    ----------------UUUAU----------------------    4

    
    ----------------UUUUU----------------------    4

    
    ----------------UUUU-----------------------    4

    
    U------------------AU---------------------A    4

    
    ----------------UUU------------------------    4

    
    A-----------------------------------------U    4

    
    UAAUGAUG--------AUUAUU-------------CAUUUUUA    3

    
    C--AUGAG--------CUUUG--------------CUCAU--G    3

    
    UAAAG-----------UCUUUG----------------CUUUA    3

    
    --UAUAU---------UUCAUG--------------AUA---U    3

    
    ACA-------------UUUCAAG----------------GUGU    3

    
    CC--------------ACUCCCCGU----------------GG    3

    
    C---------------UGUUUAAUA-----------------G    3

    
    UU--------------AAUUUAUU------------------A    3

    
    G---------------GAUUUGUU------------------C    3

    
    G------------G--AUGUAU-------C------------C    3

    
    GA--------------AGAAUU-------------------UC    3

    
    U---------------UACUUGUA------------------A    3

    
    G---------------AUUUAUU-------------------C    3

    
    GU--------------UGCUUG--------------------C    3

    
    U-C-------------UUCG--------------------GGA    3

    
    C---------------AGAAAU--------------------G    3

    
    C---------------CUUCUG--------------------G    3

    
    C---------------GCUUAC--------------------G    3

    
    C---------------UUUCAA--------------------G    3

    
    G---------------AGAAAU--------------------C    3

    
    G---------------AGUCAU--------------------C    3

    
    G---------------UUUCGA--------------------C    3

    
    U---------------GCCUGC--------------------A    3

    
    C---------------ACUUG---------------------C    3

    
    C---------------CGAAA---------------------G    3

    
    U---------------CUUAC---------------------A    3

    
    ----------------GCAAGU---------------------    3

    
    ----------------UUUUC----------------------    3

    
    C---------------UAU-----------------------G    3

    
    ----------------UACG-----------------------    3

    
    ----------------UAUU-----------------------    3

    
    ----------------UUUA-----------------------    3

    
    ----------------UGU------------------------    3

    
    ----------------UUA------------------------    3

    
    ----------------CA-------------------------    3

    
    ----------------GU-------------------------    3

    
    CUGAAUUU--------UCAAUGA------------ACUUUCAG    2

    
    UUUAUAUC--------AUGAUGU------------GAUAUAAA    2

    
    UAAGAAU---------AAUUAUUC------------AUUUUUA    2

    
    UAAUGAUG--------AUUAUU-------------CAUUCUUA    2

    
    UUUACAU---------UUCAAG--------------GUGUA--    2

    
    A---GACG--------AAUG---------------CGUCUUU-    2

    
    ----UAUA--------CGUUAUGA-----------UAU-----    2

    
    U---------------UUUUAUUUCUU-------------GCA    2

    
    ACAU------------UUCAAG--------------A---UGU    2

    
    UG-----A--------GGUUUACU-----------U-----CA    2

    
    UCA-------------ACUUUGU-----------------UGA    2

    
    UGAA------------GUAUU------------------UUCA    2

    
    CAU-------------AGUUU-------------------AUG    2

    
    UU--------------AAUUUUAU------------------A    2

    
    UUA-------------UUUGAU-------------------AA    2

    
    A---------------AGUUUACU------------------U    2

    
    A---------------GAUUUAUU------------------U    2

    
    A---------------GGUUUACU------------------U    2

    
    AAC-------------UUCG--------------------GUU    2

    
    AGC-------------UCCG--------------------GCU    2

    
    C---------------UGUUUACA------------------G    2

    
    CC--------------UGCUUC-------------------GG    2

    
    G---------------AUCUCGUU------------------C    2

    
    G---------------AUUUCGAU------------------C    2

    
    G---------------AUUUCGG------------------UU    2

    
    G---------------AUUUUGGU------------------C    2

    
    G---------------GAUGUAUC------------------C    2

    
    G---------------GAUUUAUU------------------C    2

    
    G---------------UAUUUACU------------------C    2

    
    UGA-------------CUUG--------------------UCA    2

    
    UUGC------------CA---------------------GCAA    2

    
    AG--------------AUUAU--------------------CU    2

    
    G---------------ACUUACU-------------------C    2

    
    A---------------AGUUAU--------------------U    2

    
    C---------------CCUUUG--------------------G    2

    
    G---------------ACUUAC--------------------C    2

    
    G---------------GGACAU--------------------C    2

    
    G---------------UUUC-GA-------------------C    2

    
    U---------------CGGUAU--------------------A    2

    
    U---------------GCUUAC--------------------A    2

    
    U---------------GCUUG--------------------CA    2

    
    U---------------GCUUGC--------------------A    2

    
    U---------------GUUUAC--------------------A    2

    
    A------------G--AAAC----------------------U    2

    
    C---------------UUUCG---------------------G    2

    
    G---------------CUAAA---------------------C    2

    
    U---------------AUAAC---------------------C    2

    
    U---------------CUUCG---------------------G    2

    
    U---------------UAUAC---------------------A    2

    
    U---------------UUCAU---------------------G    2

    
    ----------------GGAAGU---------------------    2

    
    ----------------UUUCAU---------------------    2

    
    A---------------AUGA----------------------U    2

    
    A---------------GAAA----------------------U    2

    
    C-----------------UCCG--------------------G    2

    
    C---------------GCAA----------------------G    2

    
    G---------------GAAA----------------------C    2

    
    -----------------AUAC---------------------A    2

    
    ----------------AGUUU----------------------    2

    
    ----------------CUAAU----------------------    2

    
    ----------------GAAGU----------------------    2

    
    ----------------GGUUU----------------------    2

    
    ----------------GUAAU----------------------    2

    
    ----------------GUUUA----------------------    2

    
    ----------------UUAUU----------------------    2

    
    ----------------UUUGA----------------------    2

    
    U---------------AUU-----------------------A    2

    
    -----------------GUAU----------------------    2

    
    ----------------GGAA-----------------------    2

    
    ----------------GUAA-----------------------    2

    
    ----------------UAUG-----------------------    2

    
    ----------------UUAA-----------------------    2

    
    ----------------UUAU-----------------------    2

    
    ----------------UUGU-----------------------    2

    
    G---------------AA------------------------C    2

    
    U----------------UU-----------------------A    2

    
    U---------------CA------------------------A    2

    
    U---------------UU------------------------A    2

    
    ----------------AUA------------------------    2

    
    ----------------CGG------------------------    2

    
    ----------------UAG------------------------    2

    
    A---------------A-------------------------U    2

    
    U---------------G-------------------------A    2

    
    ----------------AG-------------------------    2

    
    C-----------------------------------------G    2

    
    AACGAAGAUAUUUG--AGUCU--------CAAAUAUUAACGUU    1

    
    AACGAAGAUAUUUG--AGUCU--------CAAGUAUUAACGUU    1

    
    AACGAAUAUGUUUG--AGUCU--------CAAAUAUCAACGUU    1

    
    AACGUUAAUAUUUG--AGUCU--------CAAAUAUUAACGUU    1

    
    AAUGAAGAUAUUU---AAAUCCC-------AAAUAUUGACAUU    1

    
    C---UA-GCAUCCUUUGAAAG------AAAGGAUGUAUAAAUG    1

    
    CGAAGAUAUUUG----AGUCU----------CAAAUAUUGACG    1

    
    ACAAUGAACU------UCUACGA----------AGUUCAUUGU    1

    
    ACAAUGAACU------UCUGCGA----------AGUUCAUUGU    1

    
    AUAAUGAACU------UCUACGA----------AGUUCAUUAU    1

    
    GCUGAAUUU-------UCAAC------------GAAUUUUCGG    1

    
    UAUAUUAU--------UUUGAGAU-----------AUAAUAUA    1

    
    UAUAUUAU--------UUUGAGAU-----------AUGAUAUA    1

    
    UAUAUUGU--------UUUGAGAU-----------AUAAUAUA    1

    
    C--UGAAUUU------UCAAC------------GAAUUUUCAG    1

    
    CU--GAAUUU------UCAAC------------GAAUUUUCAG    1

    
    CUGAAUUU--------UCAAUGA------------AUUUUCAG    1

    
    CUUAAUUUUC------AAU--------------GAAUUUUCAG    1

    
    UUGAAUUUU-------CAACG-------------AAUUUUCAA    1

    
    CAAACAAGC-------GUAA--------------GCGAGUAAG    1

    
    CAAACGAGC-------GUAA--------------GCGAGUAAG    1

    
    CGAAUAAGC-------GCAA--------------GCGAGCGAG    1

    
    GCUGAUUU--------UUCAAC-------------GAAUUUUC    1

    
    UAAGAAUG--------AUUAUU-------------CAUUUUUA    1

    
    UAAGAAUG--------AUUAUU-------------CAUUUUUG    1

    
    UAAUAACGG-------GUAA--------------CCAAUGUUA    1

    
    UAAUAAUGA-------GAAA--------------UCUAAGUUA    1

    
    UAAUGAUGA-------GAAA--------------UCAAAGUUA    1

    
    UAGCAAUG--------AGCAAU-------------CAUCGUUA    1

    
    UCAGAAU---------AAUUAUUC-----------A-UUUUUA    1

    
    UCUAUAGA--------UGUAAA-------------UUUAUGGA    1

    
    UGAACGAGC-------GUAA--------------GUGAGUGAA    1

    
    UGAUAUUG--------GGUAUU-------------UGGUGUCA    1

    
    A-CUUAGUU-------GUUAU-------------AACUUAG-U    1

    
    GUAACAAU--------GAGUA--------------AUUGUUGU    1

    
    GUAACAAU--------GAGUG--------------AUUGUUGU    1

    
    G-AAUGAA--------AAUAUA-------------UUCAUU-U    1

    
    G-AUAUU---------CAGUAUUU------------GGUGU-C    1

    
    GAUAUUGA--------GUAU---------------UUGGUAUU    1

    
    UAGCAGAG--------AGAUCAA------------C---GUUA    1

    
    UGAAUUUU--------CAAC---------------GAAUUUUC    1

    
    UUUACAU---------UUCAAA--------------GUGUAAA    1

    
    UUUACAU---------UUCAAA--------------GUGUGAA    1

    
    UUUAUAC---------CUCAGA--------------GUAUAAA    1

    
    UUUAUAUC--------UCAU---------------GAUAUAAA    1

    
    UUUGCAU---------UUUAAA--------------GUGUGAA    1

    
    G-AAUUUU--------CAAC---------------GAAUUUUC    1

    
    UAACAUU---------GAGUA---------------AACGUUA    1

    
    UAAG---A--------UACAUAGA-----------U--ACAAA    1

    
    UGAAUUA---------UAUAA---------------UGAUGAA    1

    
    UUUAUGC---------UACAA---------------GCAUGAA    1

    
    -UUAUAU---------UGGAAG--------------AUAUGA-    1

    
    UAAUA-----------CAAAGUGA-----------UA---UUA    1

    
    UAAUG-----------CAAAGUGA--------------UAUUG    1

    
    UAAUGCAA--------AGUGAUA-----------------UUG    1

    
    UAUAGAU---------UUGU----------------AUCUAUA    1

    
    UUUACAU---------UUCAAG--------------GUGU--A    1

    
    CAUGAG----------CAAAG----------------UCCAUG    1

    
    CAUGAGC---------AAA-----------------GCUCAUG    1

    
    UUUUCUU---------CAA-----------------GAGAUGA    1

    
    ----UAUA--------AUUGAUGA-----------UAUA----    1

    
    ACG--AAA--------ACAU---------------UUUU--GU    1

    
    U--AAAGC--------CUUU---------------GCUUU--A    1

    
    U--ACAC---------UUCACA--------------GUGU--A    1

    
    UAAAGU----------UUUU-----------------ACCUUA    1

    
    UACA--U---------UUCAAA--------------G--UGUA    1

    
    UACAC-----------UUCAAA----------------GUGUA    1

    
    UACAU-----------UUUAAA----------------GUGUG    1

    
    UAUA------------UUUGAGGA---------------UAUA    1

    
    UGCA------------UUUUAAAG---------------UGUA    1

    
    UUUUUU----------CUUC-----------------AAAAAA    1

    
    U--CAAA---------GUAU----------------UUUCA-A    1

    
    U-UAU-----------AUCUCG----------------AUACA    1

    
    UAA----A--------AUUAUACU----------------UUA    1

    
    UAAAG-----------UCUUA-----------------CUUUA    1

    
    UAAAG-----------UUUUA-----------------CUUUA    1

    
    UAUGC-----------UGUGA-----------------GUGUA    1

    
    UG---GAG--------UGAAU--------------CUCC---A    1

    
    UGA-AA----------UAUU-----------------UUCUCA    1

    
    UUA-------------UUUUAAUUU---------------UAA    1

    
    UUAAU-----------UUAAA-----------------AUUAA    1

    
    UUAAU-----------UUUGU-----------------GUUGA    1

    
    UUUUC-----------UUCAA-----------------GAAAU    1

    
    ---AUAU---------UUCAAG--------------GUA---U    1

    
    ---AUAU---------UUUAAG--------------GUG---U    1

    
    -ACGCU----------UCGA-----------------AGUGU-    1

    
    A---------GACG--AAUG---------CGUC---------U    1

    
    A---GACG--------AAUA---------------CGUC---U    1

    
    A---GACG--------AAUA---------------CGUCU---    1

    
    A---GACG--------AAUA---------------UGUC---U    1

    
    A---GAUG--------AAUA---------------CAUC---U    1

    
    A---GGCG--------AAUA---------------CGUCU---    1

    
    A---UAU---------CUUAUA--------------AUA---U    1

    
    AAA-------------UAAAUUCA----------------UUU    1

    
    ACAC------------UUUAAU-----------------GUGU    1

    
    AGAC------------CGAUAC-----------------GUCU    1

    
    AGGCG-----------AAUA------------------CGUUU    1

    
    AUAU------------UUCAUG-----------------AUAU    1

    
    AUAU------------UUUAAG-----------------GUAU    1

    
    AUAU------------UUUAUA-----------------AUAU    1

    
    AUAUC-----------UCAC------------------GGUAU    1

    
    AUAUC-----------UCAC---------------G---GUAU    1

    
    AUAUC-----------UCAG------------------GAUAU    1

    
    AUAUC-----------UUAG------------------GAUAU    1

    
    AUAUU-----------UUAU------------------GAUAU    1

    
    AUUC------------UUCAAA-----------------GAAU    1

    
    GC---AU---------UUUAAA--------------GU---GU    1

    
    GCAU------------UUCAAU-----------------GUGU    1

    
    U-----GA--------GGUUUACU-----------UU-----A    1

    
    UG-----A--------AGUUUGCU----------------UCA    1

    
    UG-----A--------GAUUUACU-----------U-----CA    1

    
    UG-----A--------GGUUUCCU-----------U-----CA    1

    
    UGA-------------GAUUUACC----------------UCA    1

    
    UGA-------------GGUUUGCU----------------UCA    1

    
    UUA-------------AUUUUUAU----------------UAA    1

    
    UUG-------------AGUUAUUU----------------UAA    1

    
    UUGA------------UUUAUU-----------------UUAA    1

    
    UUGG------------CUUAGU-----------------UUAA    1

    
    AUA---U---------AUCAA---------------G---UAU    1

    
    C--CAU----------CCCAG----------------AUG--G    1

    
    CAA-------------UAUUAU-----------------GUUG    1

    
    CUCA------------CGGUA------------------UAAG    1

    
    UAAG------------AUUUU------------------CUUA    1

    
    UCG-------------ACUUUGU-----------------UGA    1

    
    UCGU------------AGUUU------------------ACGA    1

    
    UGA-------------AGUAUUU-----------------UCA    1

    
    UGG-------------AGUAUUU-----------------UCA    1

    
    UGGA------------CUUGG------------------UUCA    1

    
    UUA-------------ACUGUGU-----------------UAA    1

    
    UUAA------------CUUUG------------------UUGA    1

    
    UUAA------------UUCCA------------------UUAA    1

    
    AA--------------UACAUUUA-----------------UU    1

    
    AAU--A----------GAUU-----------------U--AUU    1

    
    AAUA------------AACC-------------------UAUU    1

    
    AC--------------UCUGUAUA-----------------GU    1

    
    ACGG------------GAAU-------------------CCGU    1

    
    ACU-------------AUUUUAU-----------------A-G    1

    
    AUA-------------UUAAGA------------------UAU    1

    
    AUA-------------UUUCAUGA------------------U    1

    
    AUG-------------UUUUAGGA------------------U    1

    
    CU--------------AUUUAAUU-----------------GG    1

    
    GUA-------------UUUUAAAG------------------U    1

    
    UAA-------------UUUGAU------------------UUA    1

    
    UG--------------AGUUUUCU-----------------CA    1

    
    UGUA------------GAAA-------------------UACA    1

    
    UUA-------------AUUGUGUU------------------A    1

    
    UUA-------------AUUUUAU-----------------U-A    1

    
    UUAG------------GAAC-------------------CUAU    1

    
    AGA-------------UUUAUUAU-------------------    1

    
    AGU-------------AAUUU-------------------ACU    1

    
    AU--------------AUUUUGU------------------AU    1

    
    C---------------GAUAAAUU-----------------UG    1

    
    C---------------GGCAAGGCA-----------------G    1

    
    GAG-------------AGUAU-------------------CUC    1

    
    UAAG------------AUA--------------------CAUA    1

    
    UGAG------------AAAC--------------------UCU    1

    
    A---------------AAUUUAUU------------------U    1

    
    A---------------AGUGAACU------------------C    1

    
    A---------------AGUUUAUU------------------U    1

    
    A---------------GAUUCAUU------------------U    1

    
    A---------------GCUCCGGC------------------U    1

    
    A---------------GGCUUGCU------------------U    1

    
    A---------------GGGUUG-------------CU-----U    1

    
    A---------------GUUUUAUC------------------U    1

    
    A---------------UAGUAAUA------------------U    1

    
    A---------------UAUGAUGA------------------U    1

    
    A---------------UAUUCAUA------------------U    1

    
    A---------------UAUUUGUA------------------U    1

    
    AA--------------UUUCGA-------------------UU    1

    
    AAC-------------CUUG--------------------GUU    1

    
    AAC-------------GCAG--------------------GUU    1

    
    AC--------------AGUAAU-------------------GU    1

    
    AG--------------AACCAU-------------------CU    1

    
    AG--------------AGUCAU-------------------CU    1

    
    AG--------------AGUUAU-C------------------U    1

    
    C---------------UGUCUACA------------------G    1

    
    C---------------UGUUUACC------------------G    1

    
    CGC-------------GCGA--------------------GCG    1

    
    G---------------AACUAAUU------------------C    1

    
    G---------------AAGUUAUU------------------U    1

    
    G---------------AAUCAUUU------------------U    1

    
    G---------------AAUGUAAA------------------C    1

    
    G---------------AAUUUAGU------------------C    1

    
    G---------------AAUUUAUU------------------U    1

    
    G---------------AGCUUGCU------------------C    1

    
    G---------------AGUGUAAA------------------C    1

    
    G---------------AUUUUUGU------------------C    1

    
    G---------------CAGAAUUU------------------C    1

    
    G---------------GAGGUAUC------------------C    1

    
    G---------------GAUUAAUU------------------C    1

    
    G---------------GCUUUAGU------------------C    1

    
    G---------------GCUUUAUU------------------C    1

    
    G---------------GGUUUAUU------------------C    1

    
    G---------------UAUUUAUG------------------C    1

    
    G---------------UAUUUAUU------------------C    1

    
    GA--------------AAAAU-------------------UUC    1

    
    GA--------------UCUCAG-------------------UC    1

    
    GA--------------UUUGUG-------------------UC    1

    
    GAC-------------GUUU--------------------GUC    1

    
    GAU-------------UUCG--------------------GUC    1

    
    GG--------------AGACAU-------------------CC    1

    
    GG--------------AGAUAU-------------------CC    1

    
    GG--------------AGUUAU-------------------CC    1

    
    U---------------AAAGUUAU------------------A    1

    
    U---------------AAUAAUUU------------------A    1

    
    U---------------AUAAUGAU------------------A    1

    
    U---------------AUUUUAUA------------------A    1

    
    U---------------GAACUUUC------------------A    1

    
    U---------------GACUUGUC------------------A    1

    
    U---------------GAUUUAUC------------------A    1

    
    U---------------GAUUUGUC------------------A    1

    
    U---------------GUUUCAAU------------------A    1

    
    U---------------UACUUUUA------------------A    1

    
    U---------------UAGUAAUA------------------A    1

    
    U---------------UAUUUAUA------------------A    1

    
    U---------------UGUUUACA------------------A    1

    
    UC--------------ACUUGU-------------------GA    1

    
    UC--------------AGUGAU-------------------GG    1

    
    UG--------------AGUAAU-------------------CA    1

    
    UU--------------UAAUUU-------------------AA    1

    
    UU--------------UGAUUG-------------------AA    1

    
    UUA-------------CUCG--------------------UAA    1

    
    UUC-------------GAAA--------------------GGA    1

    
    ----------------ACUACGGU------------------U    1

    
    A----------------GUGUACA------------------A    1

    
    A---------------AGUAAU-U------------------G    1

    
    A---------------AUUUA-UU------------------U    1

    
    AU--------------AUGAU--------------------AU    1

    
    C---------------ACUUAGU-------------------G    1

    
    C---------------UUAUAA-------------------GA    1

    
    G---------------AAUUACU-------------------U    1

    
    G---------------AAUUAU------------------U-C    1

    
    G---------------AAUUAUU-------------------C    1

    
    G---------------AAUUUAU-------------------U    1

    
    G---------------CUU-CGGC------------------A    1

    
    GC--------------UGCCU--------------------GC    1

    
    GU--------------UGCCUG--------------------C    1

    
    U---------------ACUUGGU-------------------A    1

    
    U---------------ACUUUGU-------------------A    1

    
    U---------------CUUUUAG-------------------A    1

    
    U---------------GUUUUAU-------------------A    1

    
    UC--------------CUUGU--------------------GA    1

    
    UC--------------UUUUA--------------------GA    1

    
    UG--------------UUUUA--------------------CA    1

    
    UU--------------AAUAAU--------------------A    1

    
    UU--------------CUUA--------------------GAA    1

    
    UUC-------------UUA---------------------GAA    1

    
    A---------------UUUUUU--------------------U    1

    
    C---------------ACUUGC--------------------G    1

    
    C---------------AGUAAU--------------------G    1

    
    C---------------CGCAAG--------------------G    1

    
    C---------------CUUCGA--------------------G    1

    
    C---------------CUUUGG--------------------G    1

    
    C---------------UUAACA--------------------G    1

    
    C---------------UUUCGG--------------------G    1

    
    C---------------UUUUUU--------------------G    1

    
    G---------------AAAAUU--------------------C    1

    
    G---------------AGAAGU--------------------C    1

    
    G---------------AGCAAU--------------------C    1

    
    G---------------AGUAAU--------------------C    1

    
    G---------------AUAAAU--------------------C    1

    
    G---------------AUUAUU--------------------C    1

    
    G---------------AUUUAU--------------------C    1

    
    G---------------AUUUCG--------------------G    1

    
    G---------------GCUUGU--------------------C    1

    
    G---------------GGAAUC--------------------C    1

    
    G---------------GGCAAU--------------------C    1

    
    G---------------UAAAAA--------------------C    1

    
    G---------------UGAGAA--------------------C    1

    
    G---------------UGCUUG--------------------C    1

    
    G---------------UUUCAA--------------------U    1

    
    G---------------UUUCGG--------------------C    1

    
    G---------------UUUGGA--------------------C    1

    
    G---------------UUUUGA--------------------C    1

    
    U----------------------------------GUUUAC-A    1

    
    U---------------AAUAUU--------------------A    1

    
    U---------------AGAAA-U-------------------A    1

    
    U---------------AGAAAU--------------------A    1

    
    U---------------AGCAAC--------------------A    1

    
    U---------------AUAUAU--------------------A    1

    
    U---------------CAUUUG--------------------C    1

    
    U---------------CC-UUGC-------------------A    1

    
    U---------------CUUAG--------------------AA    1

    
    U---------------CUUAGG--------------------A    1

    
    U---------------CUUAGG--------------------G    1

    
    U---------------GCUUAC--------------------G    1

    
    U---------------GCUUCC--------------------A    1

    
    U---------------GUUUGC--------------------A    1

    
    U---------------UUUUAU--------------------A    1

    
    UA--------------CUUGU---------------------A    1

    
    UGC-------------CU----------------------GCA    1

    
    -----------------GCAAUAA-------------------    1

    
    -----------------GUAGUAU-------------------    1

    
    ----------------AGCUUGG--------------------    1

    
    ----------------AGGAAU--------------------C    1

    
    ----------------AGGUAGU--------------------    1

    
    ----------------AGUAGUU--------------------    1

    
    ----------------AGUGGUU--------------------    1

    
    ----------------AUUUAU--------------------U    1

    
    ----------------CUUUAU--------------------A    1

    
    ----------------GGAUAGA--------------------    1

    
    ----------------GUUUUUA--------------------    1

    
    ----------------UGAAAA--------------------U    1

    
    A-----------------UUUAU-------------------A    1

    
    A---------------AACAU---------------------U    1

    
    A---------------UAUUA---------------------U    1

    
    A---------------UUUGUA---------------------    1

    
    A---------------UUUUU-U--------------------    1

    
    C---------------AAUAU---------------------G    1

    
    C---------------AUUUG---------------------G    1

    
    C---------------AUUUU---------------------G    1

    
    C---------------CUUCG---------------------G    1

    
    C---------------CUUGU---------------------G    1

    
    C---------------GUUUA---------------------C    1

    
    C---------------UUAGG---------------------A    1

    
    C-C-------------UUUG----------------------G    1

    
    G---------------AGUGA---------------------U    1

    
    G---------------AUUUC---------------------C    1

    
    G---------------CUUGC---------------------C    1

    
    G---------------GCUUG---------------------C    1

    
    U---------------AGAAAU---------------------    1

    
    U---------------AUAAC---------------------A    1

    
    U---------------AUUAC---------------------A    1

    
    U---------------CUUUG---------------------A    1

    
    U---------------G-AAAA--------------------A    1

    
    U---------------GCUAA---------------------A    1

    
    U---------------GUGAA---------------------A    1

    
    U---------------GUUAU---------------------A    1

    
    U---------------GUUUU---------------------U    1

    
    U---------------UAGAU---------------------U    1

    
    U---------------UAUAU---------------------A    1

    
    U---------------UGUAU---------------------A    1

    
    U---------------UUAAA---------------------A    1

    
    U---------------UUUAG---------------------A    1

    
    U---------------UUUAU---------------------G    1

    
    UC--------------CUUG----------------------U    1

    
    ----------------AAAUAA---------------------    1

    
    ----------------AGCAAU---------------------    1

    
    ----------------AGGAAU---------------------    1

    
    ----------------AUAAGU---------------------    1

    
    ----------------CCAAGU---------------------    1

    
    ----------------CCUUGA---------------------    1

    
    ----------------CGAAGU---------------------    1

    
    ----------------CUUUAU---------------------    1

    
    ----------------GAACAC---------------------    1

    
    ----------------GAGAGC---------------------    1

    
    ----------------GAUAGU---------------------    1

    
    ----------------GCAAUG---------------------    1

    
    ----------------GCAAUU---------------------    1

    
    ----------------GUAAGU---------------------    1

    
    ----------------GUUAUU---------------------    1

    
    ----------------GUUUCA---------------------    1

    
    ----------------GUUUCG---------------------    1

    
    ----------------GUUUGC---------------------    1

    
    ----------------UUAUU---------------------U    1

    
    ----------------UUUAUU---------------------    1

    
    ----------------UUUUAA---------------------    1

    
    ----------------UUUUUU---------------------    1

    
    A---------------CUUU----------------------U    1

    
    A---------------GUAA----------------------U    1

    
    C---------------AAUU----------------------G    1

    
    C---------------GCUUA----------------------    1

    
    C---------------GUAA----------------------G    1

    
    C---------------UUUU----------------------A    1

    
    G----------------CAAA---------------------C    1

    
    G----------------CUUUU---------------------    1

    
    G---------------UUGA----------------------C    1

    
    U----------------UUAU---------------------A    1

    
    U---------------AGCAG----------------------    1

    
    U---------------AUCA----------------------A    1

    
    U---------------AUUU----------------------A    1

    
    U---------------CAGU----------------------A    1

    
    U---------------GA-AA---------------------A    1

    
    U---------------UACC----------------------A    1

    
    U---------------UUUU----------------------A    1

    
    ----------------AUUUU----------------------    1

    
    ----------------CAACA----------------------    1

    
    ----------------CGAAA----------------------    1

    
    ----------------CUUGU----------------------    1

    
    ----------------CUUUA----------------------    1

    
    ----------------GAAAU----------------------    1

    
    ----------------GAUCA----------------------    1

    
    ----------------GCAAC----------------------    1

    
    ----------------GCAAU----------------------    1

    
    ----------------UAUAU----------------------    1

    
    ----------------UCAUA----------------------    1

    
    ----------------UUAGA----------------------    1

    
    ----------------UUGUU----------------------    1

    
    ----------------UUUUA----------------------    1

    
    C---------------UUC-----------------------G    1

    
    C---------------UUU-----------------------A    1

    
    C---------------UUU-----------------------G    1

    
    G---------------AAA-----------------------U    1

    
    G---------------GAA-----------------------U    1

    
    U------------------AGU--------------------A    1

    
    U------------------UAA--------------------A    1

    
    U---------------AAU-----------------------A    1

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

    
    U---------------UAA-----------------------A    1

    
    U---------------UU-U----------------------A    1

    
    ----------------AU-UU----------------------    1

    
    ----------------AUCU-----------------------    1

    
    ----------------CAAG-----------------------    1

    
    ----------------CUUG-----------------------    1

    
    ----------------GCAA-----------------------    1

    
    ----------------GUUA-----------------------    1

    
    ----------------UAAC-----------------------    1

    
    ----------------UAAU-----------------------    1

    
    ----------------UCAA-----------------------    1

    
    ----------------UCAU-----------------------    1

    
    A---------------UU------------------------U    1

    
    C---------------UU------------------------G    1

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

    
    U---------------UG------------------------A    1

    
    ------------------UAU----------------------    1

    
    ------------------UUA----------------------    1

    
    ----------------ACU------------------------    1

    
    ----------------AGU------------------------    1

    
    ----------------AUU------------------------    1

    
    ----------------GG------------------------U    1

    
    C---------------A-------------------------G    1

    
    ------------------UA-----------------------    1

    
    -----------------U------------------------U    1

    
    ----------------CU-------------------------    1

    
    ----------------GA-------------------------    1

    
    U-----------------------------------------G    1

    
    Omitted sequenced and counts

    
    -------------------------------------------  151

    
    ----------------C--------------------------   30

    
    ----------------A--------------------------   14

    
    ----------------U--------------------------    8

    
    ----------------G--------------------------    2

    
    G---------------AUUUCKG------------------UC    1
Click on headings to reorder table
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group HL_48778.2

Basepair signature:
cWW-F

18.78 -3360.90 3 3

Mini UNCG

2

Motif group HL_70782.2

Basepair signature:
cWW-F

13.67 -3336.96 4 4

3

Motif group HL_32346.4

Basepair signature:
cWW-F

12.52 -3537.28 3 3

4

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

12.36 -1531.06 6 4

5

Motif group HL_48417.5

Basepair signature:
cWW-F-F

12.19 -626.43 4 2

6

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

11.61 -1346.99 6 5

7

Motif group HL_56334.1

Basepair signature:
cWW-F

11.20 -3527.80 4 3

Mini UNCG

8

Motif group HL_50006.2

Basepair signature:
cWW-F-F

10.79 -2329.77 5 3

9

Motif group HL_20535.2

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

9.14 -2623.89 5 4

10

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

8.90 -2233.88 4 3

11

Motif group HL_69139.1

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

8.73 -2507.44 7 5

12

Motif group HL_56131.2

Basepair signature:
cWW-F-F

8.65 -795.75 4 3

13

Motif group HL_69752.2

Basepair signature:
cWW-F

8.65 -3936.85 5 3

14

Motif group HL_98252.1

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

7.99 -1428.29 7 6

15

Motif group HL_28075.1

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

7.99 -1704.75 5 4

16

Motif group HL_75660.5

Basepair signature:
cWW-F

7.99 -3927.65 3 3

17

Motif group HL_25967.2

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

7.91 -2176.62 5 4

18

Motif group HL_78677.1

Basepair signature:
cWW-F-F

7.91 -5559.19 5 4

19

Motif group HL_13189.1

Basepair signature:
cWW-F-F

7.41 -1524.07 4 4

20

Motif group HL_57875.1

Basepair signature:
cWW-F-F

7.17 -2901.89 4 3

21

Motif group HL_87553.1

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

5.68 -1729.27 5 4

22

Motif group HL_38168.1

Basepair signature:
cWW-F

5.60 -3927.52 5 3

23

Motif group HL_94980.1

Basepair signature:
cWW-F-F

5.60 -5057.86 5 4

24

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

5.44 -825.02 6 5

tRNA D-loop

25

Motif group HL_37344.1

Basepair signature:
cWW-F-F

5.35 -1271.18 6 4

26

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

5.35 -2136.39 4 3

27

Motif group HL_99867.1

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

5.35 -3927.15 6 5

28

Motif group HL_58224.1

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

4.94 -1821.05 7 6

29

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

4.94 -3831.06 6 5

30

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

4.61 -2912.26 4 3

31

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

4.61 -3207.31 4 3

tRNA D-loop

32

Motif group HL_04642.1

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

4.53 -1363.74 7 6

tRNA D-loop

33

Motif group HL_42046.2

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

4.53 -1768.47 5 4

34

Motif group HL_77436.5

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

4.37 -1629.15 4 3

T-loop related

35

Motif group HL_27483.1

Basepair signature:
cWW-F

4.12 -1136.60 5 4

36

Motif group HL_46501.1

Basepair signature:
cWW-cWS

3.95 -1815.76 5 3

37

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

3.87 -2339.20 5 3

38

Motif group HL_78197.1

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

3.79 -3709.87 5 4

39

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

3.71 -2955.88 5 4

40

Motif group HL_93324.4

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

3.71 -3866.07 4 3

Pseudoknot geometry

41

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

3.62 -2195.53 5 4

42

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

3.54 -2201.00 4 3

43

Motif group HL_25847.2

Basepair signature:
cWW-F-cSH-tHW-F-F-F

3.46 -1376.29 7 6

44

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

3.46 -3935.18 4 3

Pseudoknot geometry with 3' bulge

45

Motif group HL_97917.2

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

3.38 -2747.38 5 4

46

Motif group HL_13963.3

Basepair signature:
cWW-F-F

2.97 -2216.98 5 4

47

Motif group HL_93438.2

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

2.88 -188.74 6 5

48

Motif group HL_04259.3

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

2.80 -648.35 5 4

GNRA with extra cWW

49

Motif group HL_32392.1

Basepair signature:
cWW-F-F

2.72 -1838.16 5 4

50

Motif group HL_31585.4

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

2.72 -3369.05 4 3

Purine riboswitch

51

Motif group HL_78347.4

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

2.64 -566.85 5 3

52

Motif group HL_93535.1

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

2.64 -2813.79 5 4

53

Motif group HL_73255.1

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

2.47 -1748.03 7 5

54

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

2.47 -2189.81 4 3

55

Motif group HL_10453.3

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

2.47 -2839.10 5 3

tRNA anticodon loop

56

Motif group HL_57863.1

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

2.39 -1374.70 7 6

G-quadruplex fragment

57

Motif group HL_64690.6

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

2.39 -1868.71 5 4

58

Motif group HL_35677.3

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

2.39 -2639.65 5 4

59

Motif group HL_77082.1

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

2.31 -2012.49 5 4

Pseudoknot geometry

60

Motif group HL_39243.1

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

2.31 -4039.13 5 4

61

Motif group HL_85993.1

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

2.22 -3830.95 6 5

62

Motif group HL_56676.1

Basepair signature:
cWW-F-F

2.14 -1769.65 5 3

63

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

2.06 -2221.37 5 4

tRNA anticodon loop with synthetase

64

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

2.06 -4138.53 4 3

65

Motif group HL_35941.1

Basepair signature:
cWW-F

2.06 -5581.86 6 5

66

Motif group HL_81100.2

Basepair signature:
cWW

2.06 -6955.55 5 4

67

Motif group HL_52953.3

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

1.89 -4672.54 4 3

68

Motif group HL_37824.7

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

1.81 -775.95 4 3

GNRA

69

Motif group HL_01609.3

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

1.73 -1571.03 5 4

T-loop with 2 bulged bases not stacked

70

Motif group HL_25061.1

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

1.73 -2221.55 6 5

71

Motif group HL_66103.1

Basepair signature:
cWW-F-F

1.73 -2914.93 5 3

72

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

1.73 -4119.00 5 4

73

Motif group HL_22135.1

Basepair signature:
cWW-F-F

1.73 -4761.97 5 5

74

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

1.65 -2433.09 5 4

75

Motif group HL_23509.1

Basepair signature:
cSH-F-F-F-F-F-F-F-F-F

1.57 -1117.32 8 7

76

Motif group HL_75293.5

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

1.57 -1504.69 6 5

77

Motif group HL_33983.1

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

1.57 -2296.99 7 5

78

Motif group HL_38808.1

Basepair signature:
cWW-cWW

1.57 -2867.44 6 4

79

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

1.57 -4119.44 5 4

80

Motif group HL_59735.5

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

1.57 -5145.17 5 4

81

Motif group HL_18978.1

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

1.48 -1244.23 7 6

82

Motif group HL_50779.4

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

1.48 -3183.91 7 6

83

Motif group HL_65794.5

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

1.48 -4328.91 4 3

Pseudoknot geometry

84

Motif group HL_18565.1

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

1.40 -881.58 6 5

85

Motif group HL_15802.1

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

1.40 -1675.05 6 5

86

Motif group HL_99769.3

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

1.40 -1739.25 7 5

87

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

1.40 -2436.64 5 4

88

Motif group HL_04725.1

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

1.40 -3075.27 8 6

89

Motif group HL_04171.7

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

1.32 -273.98 7 5

90

Motif group HL_26934.1

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

1.32 -382.78 6 5

91

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

1.32 -5939.85 5 5

92

Motif group HL_59843.1

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

1.24 -1599.57 5 4

93

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

1.24 -2297.15 6 4

Other HL

94

Motif group HL_55195.3

Basepair signature:
cWW-F

1.24 -4155.15 4 3

95

Motif group HL_49941.1

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

1.15 -1008.65 7 6

tRNA D-loop

96

Motif group HL_34964.1

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

1.15 -1741.35 7 6

97

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

1.15 -2361.48 4 3

UNCG

98

Motif group HL_91503.7

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

1.15 -2368.46 7 6

99

Motif group HL_29762.1

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

1.15 -2454.03 7 5

100

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

1.15 -2664.09 5 4

T-loop with unstacked turn

101

Motif group HL_20167.2

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

1.07 -231.87 5 4

102

Motif group HL_71391.1

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

1.07 -2614.34 5 4

103

Motif group HL_38046.1

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

1.07 -2617.54 7 5

104

Motif group HL_47787.2

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

1.07 -2899.09 4 3

105

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

1.07 -6162.78 6 5

106

Motif group HL_41464.2

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

0.99 -290.42 6 5

107

Motif group HL_98864.1

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

0.99 -1158.72 6 5

T-loop with unstacked turn

108

Motif group HL_30068.2

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

0.99 -1463.08 5 4

109

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

0.99 -2297.33 4 3

110

Motif group HL_36335.1

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

0.91 -254.42 8 6

111

Motif group HL_13529.1

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

0.91 -592.69 5 4

112

Motif group HL_59330.1

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

0.91 -2997.42 6 5

113

Motif group HL_67079.1

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

0.82 -190.42 7 5

114

Motif group HL_68257.1

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

0.82 -446.19 7 6

115

Motif group HL_83808.4

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

0.82 -1078.47 7 6

Pseudoknot

116

Motif group HL_10540.1

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

0.82 -1933.32 6 5

117

Motif group HL_60914.1

Basepair signature:
cWW-F

0.82 -6178.90 6 5

118

Motif group HL_80411.1

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

0.74 -2447.39 9 7

tRNA D-loop

119

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.74 -4146.74 5 4

120

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.66 -3309.02 6 4

121

Motif group HL_20743.5

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

0.58 -385.73 5 4

122

Motif group HL_89893.1

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

0.58 -2705.61 6 5

123

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

0.49 -268.86 5 4

124

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

0.49 -2067.24 5 4

Fab BL3-6 binding hairpin with tSW

125

Motif group HL_81538.2

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

0.49 -2314.90 5 4

GNRA with tandem sheared

126

Motif group HL_80008.1

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

0.49 -2318.94 7 5

127

Motif group HL_83632.1

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

0.49 -2754.52 6 5

tRNA anticodon loop

128

Motif group HL_00914.1

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

0.49 -3131.28 6 5

129

Motif group HL_81545.2

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

0.41 -209.13 6 5

130

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.41 -1055.57 7 6

131

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.41 -1749.88 6 5

132

Motif group HL_84299.4

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

0.41 -1756.23 5 4

133

Motif group HL_97733.1

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

0.41 -2276.77 8 6

134

Motif group HL_93135.1

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

0.41 -2580.88 7 6

Pseudoknot

135

Motif group HL_55436.1

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

0.41 -2850.70 7 6

136

Motif group HL_30680.3

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

0.41 -4319.74 5 4

Pseudoknot geometry

137

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.33 -1044.24 7 6

138

Motif group HL_80599.2

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

0.33 -2160.76 6 5

139

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.33 -3655.65 5 4

Mini UNCG

140

Motif group HL_22622.1

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

0.33 -3811.59 6 4

141

Motif group HL_99040.1

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

0.33 -3923.35 5 5

142

Motif group HL_42998.2

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

0.33 -4434.36 6 4

143

Motif group HL_80241.1

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

0.33 -4879.30 6 4

144

Motif group HL_09260.2

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

0.33 -9999.00 8 7

tRNA D-loop

145

Motif group HL_50860.2

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

0.25 -246.91 6 5

146

Motif group HL_02887.3

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

0.25 -874.95 7 6

T-loop with 3 stacked bulged bases

147

Motif group HL_93616.2

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

0.25 -1542.59 8 6

tRNA D-loop

148

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.25 -1988.69 5 3

tRNA D-loop

149

Motif group HL_06059.6

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

0.25 -2322.18 5 4

tRNA anticodon loop

150

Motif group HL_21372.1

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

0.25 -2373.99 6 5

151

Motif group HL_85367.2

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

0.25 -2591.88 6 4

152

Motif group HL_24792.1

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

0.25 -2633.31 7 6

153

Motif group HL_28791.1

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

0.25 -4693.78 6 4

154

Motif group HL_70751.1

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

0.25 -4791.55 8 6

155

Motif group HL_88205.2

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

0.16 -647.73 6 5

156

Motif group HL_70658.1

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

0.16 -896.96 8 7

157

Motif group HL_90620.1

Basepair signature:
cWW-F-F-F-F-cSW-cSH-F

0.16 -983.16 8 7

158

Motif group HL_73266.9

Basepair signature:
cWW-F-F-cSW-cSH-F

0.16 -1311.40 6 5

159

Motif group HL_37369.2

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

0.16 -2207.19 5 4

160

Motif group HL_88558.1

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

0.16 -2242.56 8 7

161

Motif group HL_32735.2

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

0.16 -2311.45 5 4

162

Motif group HL_47854.1

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

0.16 -2455.03 6 5

163

Motif group HL_67407.5

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

0.16 -2685.65 7 6

164

Motif group HL_02817.2

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

0.16 -2969.73 5 4

165

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.16 -3209.87 7 6

166

Motif group HL_15574.1

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

0.16 -3713.58 6 5

167

Motif group HL_51447.1

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

0.16 -3968.63 6 4

168

Motif group HL_88364.2

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

0.16 -4157.25 10 9

169

Motif group HL_36684.4

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

0.16 -4920.90 6 5

170

Motif group HL_77600.2

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

0.16 -4957.62 5 4

171

Motif group HL_50418.1

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

0.16 -5038.54 7 6

172

Motif group HL_07583.1

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

0.08 -191.25 9 7

173

Motif group HL_41902.1

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

0.08 -207.86 9 8

174

Motif group HL_86012.1

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

0.08 -321.81 6 5

T-loop with unstacked turn

175

Motif group HL_60266.1

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

0.08 -1062.60 8 6

176

Motif group HL_28252.8

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

0.08 -1198.08 5 4

T-loop with 2 stacked bulged bases

177

Motif group HL_05304.3

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

0.08 -1435.15 8 7

178

Motif group HL_04641.1

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

0.08 -1914.52 8 6

179

Motif group HL_16398.2

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

0.08 -2837.08 9 8

180

Motif group HL_01255.1

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

0.08 -2871.15 8 7

181

Motif group HL_08510.1

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

0.08 -3100.44 6 5

182

Motif group HL_12870.1

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

0.08 -6153.15 9 8

183

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.08 -9999.00 7 5

tRNA D-loop

184

Motif group HL_41543.1

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

0.00 -193.89 8 7

185

Motif group HL_74055.2

Basepair signature:
cWW-tWH-cWH-tSH-tHW-tHW-tSW

0.00 -228.14 10 9

186

Motif group HL_08602.1

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

0.00 -235.13 9 8

187

Motif group HL_68767.1

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

0.00 -265.63 9 7

tRNA D-loop

188

Motif group HL_53504.3

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

0.00 -281.19 7 6

189

Motif group HL_14757.1

Basepair signature:
cWW-cWW-F-F-tSW-tWW-cWW-tHW-tSW-F-cWH-F

0.00 -292.04 12 11

190

Motif group HL_61996.2

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

0.00 -296.88 6 5

191

Motif group HL_13971.1

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

0.00 -370.92 10 8

192

Motif group HL_92488.1

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

0.00 -427.86 11 10

193

Motif group HL_97756.2

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

0.00 -601.62 10 9

194

Motif group HL_81205.3

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

0.00 -840.13 10 9

195

Motif group HL_73247.1

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

0.00 -862.24 10 9

Pseudoknot geometry

196

Motif group HL_86109.1

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

0.00 -872.47 9 8

197

Motif group HL_84847.1

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

0.00 -873.66 10 9

198

Motif group HL_74379.3

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

0.00 -881.14 8 7

199

Motif group HL_91641.1

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

0.00 -902.04 12 10

200

Motif group HL_98870.1

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

0.00 -902.66 11 10

201

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -1060.44 8 6

202

Motif group HL_51921.1

Basepair signature:
cWW-tSH-tSS-tHS-F-F-F-F-F-F-F-F-F-F-F

0.00 -1064.90 14 13

203

Motif group HL_02581.1

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

0.00 -1164.21 10 9

tRNA D-loop

204

Motif group HL_16991.1

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

0.00 -1178.47 8 8

G-quadruplex fragment

205

Motif group HL_91939.2

Basepair signature:
cWW-tSH-tHH-tWW-F-F-F

0.00 -1189.87 8 7

206

Motif group HL_06226.4

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

0.00 -1208.53 7 6

207

Motif group HL_02483.1

Basepair signature:
cWW-tWH-F-cSH-F-F-F

0.00 -1405.00 8 7

208

Motif group HL_07480.2

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

0.00 -1436.15 8 7

209

Motif group HL_45785.1

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

0.00 -1446.32 8 7

210

Motif group HL_85434.1

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

0.00 -1494.60 7 6

211

Motif group HL_89881.5

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

0.00 -1515.84 7 6

212

Motif group HL_87463.1

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

0.00 -1663.57 7 5

213

Motif group HL_10456.1

Basepair signature:
cWW-F-cWW-tWW-F-tHW-F-F-F-F-F-F-F

0.00 -1679.60 14 12

214

Motif group HL_66482.1

Basepair signature:
cWW-cWW-tWW-F-F-tWH-F-F-F-F-F-F-F-F

0.00 -1723.28 12 11

215

Motif group HL_23010.1

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

0.00 -1784.82 8 7

216

Motif group HL_29129.3

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

0.00 -1837.43 7 6

217

Motif group HL_11542.1

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

0.00 -1853.67 10 9

218

Motif group HL_53454.2

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

0.00 -1869.12 7 5

219

Motif group HL_89346.1

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

0.00 -1960.18 13 12

220

Motif group HL_20751.2

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

0.00 -1991.06 10 8

221

Motif group HL_33074.4

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

0.00 -2049.52 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

222

Motif group HL_23115.1

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

0.00 -2332.28 8 7

tRNA D-loop

223

Motif group HL_72628.1

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

0.00 -2333.58 7 5

224

Motif group HL_73183.1

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

0.00 -2454.66 11 10

Pseudoknot geometry with G-bulge

225

Motif group HL_38649.1

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

0.00 -2679.51 8 6

226

Motif group HL_81312.1

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

0.00 -2698.60 8 7

227

Motif group HL_19210.3

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

0.00 -2827.91 7 5

228

Motif group HL_55305.1

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

0.00 -2861.92 8 7

229

Motif group HL_50851.1

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

0.00 -2882.01 9 8

G-quadruplex fragment

230

Motif group HL_64292.1

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

0.00 -2996.91 11 10

231

Motif group HL_07903.1

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

0.00 -3028.92 10 8

232

Motif group HL_63355.1

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

0.00 -3090.22 10 9

233

Motif group HL_47732.1

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

0.00 -3105.07 9 8

234

Motif group HL_31581.6

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

0.00 -3162.36 8 7

235

Motif group HL_29958.1

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

0.00 -3295.08 9 8

236

Motif group HL_93383.1

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

0.00 -3331.35 7 5.5

237

Motif group HL_59564.1

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

0.00 -3431.28 15 14

238

Motif group HL_15118.1

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

0.00 -3455.33 8 7

239

Motif group HL_00317.1

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

0.00 -3460.62 15 14

240

Motif group HL_94376.1

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

0.00 -3505.52 7 6

Pseudoknot geometry

241

Motif group HL_74292.1

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

0.00 -3551.28 8 7

242

Motif group HL_99324.1

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

0.00 -3584.84 11 10

243

Motif group HL_85461.1

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

0.00 -3697.39 13 13

244

Motif group HL_60293.1

Basepair signature:
cWW-cWH-F-cWH-cHW-cHW-cWH-cHW-cWH-F-cWH-cWH-cWH-F

0.00 -3710.38 17 15

G-quadruplex

245

Motif group HL_78284.1

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

0.00 -3720.02 8 7

246

Motif group HL_21400.1

Basepair signature:
cWW-tWH-tSW-cWW-cWH-cHW-cWH-cWH-cHW-cWH-cHW-cWH-cWH-cWH-cWH-cWH

0.00 -3772.16 17 16

G-quadruplex

247

Motif group HL_12758.3

Basepair signature:
cWW-tSH-F-cHW-F-F-cWH-cHW-cWH-cHW-cWH-cWH-F-tSH-F-cHW-F-cWH-cWH

0.00 -3820.23 20 19

G-quadruplex

248

Motif group HL_20781.1

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

0.00 -3849.31 8 7

249

Motif group HL_35354.1

Basepair signature:
cWW-cWH-cHW-F-cWH-cHW-F-F-tHH-cWH-tWW-cWH-F-tWW-cWH-F-cWH

0.00 -3896.53 18 17

250

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -3943.55 7 5

251

Motif group HL_73916.1

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

0.00 -4125.63 32 32

252

Motif group HL_58539.1

Basepair signature:
cWW-tWS-F-tHW-F-F-F-F-F-F-F-F

0.00 -4686.97 11 10

253

Motif group HL_68572.1

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

0.00 -5087.54 9 8

Coloring options: