RNA 3D Hub

JAR3D Query RF03087-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03087 maps to these 30 chains: 9ISV|1|A, 9J3R|1|A, 9J3R|1|B, 9J3R|1|C, 9J3R|1|D, 9J3T|1|A, 9J3T|1|B, 9J3T|1|C, 9J3T|1|D, 9J3T|1|E, 9J3T|1|F, 9J3T|1|G, 9J3T|1|H, 9MM6|1|A, 9MM6|1|E, 9MM6|1|I, 9MM6|1|M, 9MM6|1|Q, 9MM6|1|U, 9MM6|1|Y, 9MM6|1|c, 9MME|1|U, 9MME|1|Y, 9MME|1|c, 9MME|1|g, 9MME|1|k, 9MME|1|o, 9MME|1|s, 9MME|1|w, 9MMG|1|c See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 25 3-way junction loop

Column numbers: 422-446, 490-506, 625-750 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UUC--AAU---AGAC-G-------U*A-A----A-----UA*AC*GA--------------------------------------------------------------------------------------------------------AUAAUCA---------AA-A   11

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UAA--   10

    
    AAC--AAU---AGAC-G-------G*C-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------A-UCCAA-------UAA-U    7

    
    AAC--AAU---AGAG---GGU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    5

    
    AAG--AAU---AGAG---GGU-U-A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    5

    
    GAC--AAC---AGAC-G-------G*C-A----G-----UA*AC*GC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-C    5

    
    GAC--AAU---UGAU-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    4

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA--    4

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    4

    
    AAG--AAU---AGAG---GGU-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    3

    
    CAC--AAU---AAGU-U-GAU----*--A-AUCA-----GC*UU*AA---------------------------------------------------------------------------------------------------------UGACCAA-------CAA-G    3

    
    CGU--AAU---AGAG-A-G-----U*A-U--GCU-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA------UAA-G    3

    
    CGUAGAAU---AGAC-G-------C*G-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA----G-CAA--    3

    
    UGAU-AAU---AGAU-G-------G*C-A----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA----A-UAA-G    3

    
    UGAUUAAU---AGAC-A-------U*A-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    UGAUUAAU---AGAC-G-------U*A-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AUUCUCAA-------UAA-G    3

    
    AAU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AAGCCAAA------CAA-U    3

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UA--A    3

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA--    3

    
    GAU--AAU---AGAU-G-------G*C-A----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA----A-UAA--    3

    
    AAC--AAU---AGAC-G-------U*A-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------GGCCAA-------CAA-U    3

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------GGCCAA-------CAA-U    3

    
    CGC--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCA--------UAA-G    3

    
    -AC--AAG---AGGC-UC------U*A------U-----CC*CA*U-----------------------------------------------------------------------------------------------------------UCUCAAA----A-GAA--    3

    
    CGU--AAU---UGAA---AGG-U-A*UGC-CCUA-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    2

    
    AAG--AAU---AGAG-G-G-U-U-A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    2

    
    AAG--AAU---AGAG-G-GUU---A*U---GCCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    2

    
    CGC--AAU---AGAU---AUG---A*U---CAUU-----GA*AC*GA---------------------------------------------------------------------------------------------------------GUGCCA--------UAA-G    2

    
    CGUAGAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAA------UAA-G    2

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA-----CCAA--    2

    
    AAU--AAU---AGAC-G-------G*C-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAAA----A-CAA-U    2

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AACUCAU-------UAA-G    2

    
    CAU--AAU---AGAC-G-------A*U-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    2

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    2

    
    UGC--AAU---AAAA-AG-----U-*--U----C-----CU*CU*AA---------------------------------------------------------------------------------------------------------AUACCCAA------CAA-A    2

    
    -AU--AAG---UAUC-U-------A*U-A----G-----GU*CA*UG---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    2

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCAA-------UAA-U    2

    
    AAU--AAU---ACAC-G-------C*G-A----A-----UA*AA*UA---------------------------------------------------------------------------------------------------------AAGCCAU-------CAA-U    2

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAA-------CAA-U    2

    
    CAC--AAU---AGAC-G-------G*C-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAACCAA-------UAA-G    2

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------A-GCCAA-------GAA-U    2

    
    GAC--AAC---AGAC-G-------U*A-A----G-----UA*AC*GC---------------------------------------------------------------------------------------------------------A-UUCA--------GGA-C    2

    
    CGC--AAU---AGAG-A-------C*G-C----C-----GA*AU*AA--------CUUGAAUUGUCGGAGUGAGUCGCAGUUGCUGCGUCAGAAAACUCCCAGAGGUUAAUCUCUGCUGACAGUUC--------------------------UUCCCAA-------UAA-G    1

    
    UGAAGAAU---AGAC-G-------A*U-A----A-----UA*AG*CAGAUUGUUGACAUUGUUGCCGCAAGGUGCAAUCUU--------------------------------------------------------------CAGUAAUC-GUGUUAG-------UAA-G    1

    
    AAU--AAU---UGAA-GAAGUGUAC*GGAUACUAAC---AC*GG*UA---------------------------------------------------------------------------------------------------------AUAUCCAAA---A-CAA--    1

    
    GAC--AAU---UGAACAGGUA-UAC*GGA-UACUGAC--AC*GG*UA--------------------------------------------------------------------------------------------------------AUAUCCA-----AAACAA--    1

    
    GAC--AAUU-GAGCA-G-GUA-UAC*GGA-UACUGAC--AC*GA*UA--------------------------------------------------------------------------------------------------------AUAUCCAAA----A-CAA--    1

    
    GAC--AAUU-GAGCA-G-GUA-UAC*GGA-UACUGAC--AC*GG*UA--------------------------------------------------------------------------------------------------------AUAUCCAAA----A-CAA--    1

    
    GAU--AAU---UGAG-GAGAU-U-C*G-A-AUCAAU---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    CGC--AAU---AGAA-A-GCU-AGG*U-A-AGCC-----GA*AU*AA--------------------------------------------------------------------------------------------------------AAGACCAA-------UAA-G    1

    
    AAC--AAG---UGUC-A-GUG-AAC*U-AUAGCU-----GG*CC*G-----------------------------------------------------------------------------------------------------------UGUCGAA------CAA-U    1

    
    CAU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---A*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------GUUCGAA-----U-CAA-G    1

    
    CGU--AAU---UGAA-A-GGU---G*U-A-CCCU-A---GA*AU*AA---------------------------------------------------------------------------------------------------------AUUCGAAU------CAA-G    1

    
    AAU--AAU---AGAA---GAC-AAG*U-A-GUCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-U    1

    
    AGC--AAU---AGAA---GGU-GGG*U-G-ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AGACCAA-------CAA-U    1

    
    CAC--AAU---AGAA---GCU-AAG*U-A-AGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------GUGCCAC-------UAA-G    1

    
    CAC--AAU---AGAA-A-GGA-U-A*G-A-UCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------ACUCGAA-------CAA-G    1

    
    CAU--AAU---AGAA---GUC-AAG*U-A-GACU-----GA*AU*AA---------------------------------------------------------------------------------------------------------AGACCAA-------UAA-G    1

    
    CGC--AAU---ACGA-A-GGG---G*C-C-CCCG-----AA*AC*GA---------------------------------------------------------------------------------------------------------ACCUCACC------CAC-G    1

    
    CGC--AAU---AGAA---GGC-AAG*U-A-GCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-G    1

    
    CGC--AAU---AGAA---GGC-AAG*U-A-GCCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------UAA-G    1

    
    CGC--AAU---AGAA---GUU-GAG*U-G-AACU-----GA*AG*UA---------------------------------------------------------------------------------------------------------AAGCCAA-------UAA-G    1

    
    GGU--AAU---AGAA-A-GCA-U-U*A-A-UGCC-----GA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    UGU--AAU---AGAG-A-GUU-AC-*----UGCU-----UA*AC*GA---------------------------------------------------------------------------------------------------------GUACCAAA----A-UAA-G    1

    
    CAUA-AAG---AGAA---GCA---C*G---UGCU-U---AC*UC*AA---------------------------------------------------------------------------------------------------------AAUCCAA-------UAA-G    1

    
    CGC--AAU---AGGA-A-GCC-A-G*C-A-GGCC-----AA*AU*AA---------------------------------------------------------------------------------------------------------AAACCA--------CAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAU-ACCAAUAA-C    1

    
    UGUAUAAU---AGAC-GA------C*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AUAUGCAG-------GCG-G    1

    
    UGUAUAAU---AGAC-GA------C*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AUAUGCAG-------GUG-G    1

    
    AAG--AAU---AGAG---GGU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG---GGU-UA-*--C-ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G--GU-U-G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-G-U-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-GUU---A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    AAG--AAU---AGAG-G-GUU---G*C---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    CGC--AAU---AGCA-G-GAG----*----CUCU-G---AA*AG*CA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    1

    
    GAC--AAU---AGAA-A-GCC---U*A---GGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------ACACCAA-------CAA-C    1

    
    GGC--AAU---AGAC-A-GCC---U*A---GGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAC-------CAA-C    1

    
    U----AAUC--ACAA---AGC-AAC*G-A-GAUA-----AA*AG*GA----------------------------------------------------------------------------------------------------------UACCAA-------UAA-A    1

    
    UGC--AAU---AGAC-A-GCU---U*A---AGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-A    1

    
    UGUAAAAU---AGAC-G------AC*GGA----A-----UA*AC*GA------------------------------------------------------------------------------------------------------A-AAAUGCAG-----G-C---A    1

    
    -AU--AAU---AGAA---GCG-G-U*U-C-CGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA--    1

    
    AAC--AAU---AGAA-A-GUU---A*U---AGCC-----U-*CU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-U    1

    
    AAU--AAU---AGAG-A-G-----C*G-U--GCU-----GA*AG*UA---------------------------------------------------------------------------------------------------------AUACCAAC----A-UAA--    1

    
    AG---AAU---AGAG---GGU-U-A*U---ACCU-----GA*AU*AA---------------------------------------------------------------------------------------------------------UAGCCAA-------UAA-U    1

    
    CAC--AAU---AGAG-A---G-CUG*C------U-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA----A-UAA-G    1

    
    CGC--AAU---AGAU-A-GCA---G*U---UGCC-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUACCA--------UAA-G    1

    
    UGAUUAAU---AGAC-A-------U*A-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCUCAA----A-UAA-G    1

    
    CAU--AAU---UGAA-A-------C*GGA----G-----UA*GU*AA--------------------------------------------------------------------------------------------------------AUCUUCAA-----C-CAA-G    1

    
    CCUACAAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUGCAG-------GAAGG    1

    
    CCUACAAU---AGAC-G-------C*G-A----A-----UA*AC*GA--------------------------------------------------------------------------------------------------------AUUGCAG--------AAAGG    1

    
    CG---AAUA--AUAA-AC-----GC*G-A-A--U-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA--------------------------------------------------------------------------------------------------------AAUCUCAA-------UAA-G    1

    
    CGUAGAAA---AGAC-G-------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------CUCUAAA----A-GAA-G    1

    
    GAAU-AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCUCAA----ACUAA--    1

    
    GAC--AAU---AGAC-GC------U*AGA----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------ACUCCGAA------CCA-A    1

    
    GAC--AAU---UGAG-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    GAU--AAU---AGAU-G---G---U*A---C--A-U---GA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAAAA-----UAA--    1

    
    GAU--AAU---UGAG-GA------G*C-A----A-U---GC*GG*UA---------------------------------------------------------------------------------------------------------AUUCCAAA----A-CAA--    1

    
    GAU--AAU---UGAG-GA------G*CGA----U-----GC*GG*UA----------------------------------------------------------------------------------------------------------AUUCCAAA---A-CAA--    1

    
    GAU--AAU---UGAG-U------AA*UAA----U-----GC*GG*UA---------------------------------------------------------------------------------------------------------AAUCCAAA----A-CAA--    1

    
    UGC--AAU---AAAA-A-----GUC*G-U----C-----CU*CU*AA--------------------------------------------------------------------------------------------------------AUACCCAA-------CAA-A    1

    
    UGU--AAU---AGAC-G-------G*C-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUACCAA----AACAA-G    1

    
    ---A-AAU---CGGG-A-G----AC*GG----CA-U---AC*CC*GA--------------------------------------------------------------------------------------------------------AUAUCGC--------UAA-A    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------A-UGCAAA----AGCAA-U    1

    
    AAU--AAU---AGAC-G-------G*C-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUGUCAAA----A-CAA-U    1

    
    AUA--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA------------------------------------------------------------------------------------------------------C-UAAACCAA-------GUA-U    1

    
    CAC--AAU---AGAG-A-------G*CGC----U-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCUAAU------UAA-G    1

    
    CAU--AAU---AGAC-CG------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------GUUCUAAA------UAA-G    1

    
    CAU--AAU---AGAC-G-------A*U-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AAGCUAUA----A-UAA-G    1

    
    CG---AAUA--AUAA-AC-----GC*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGA--AUA---AUAA-AC-----GC*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGAAUAAU---AAAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUUUCAU-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCUAA----A-UAA-G    1

    
    CGC--AAU---AGAC-GC------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------ACGCACAA-----UAA-G    1

    
    CGU--AAU---AGAC-G-------U*A-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------AUCCCAAA----A-CAA-G    1

    
    GAC--AAG---AAGC-UC-----UA*U-A----U-----CU*CA*UA---------------------------------------------------------------------------------------------------------A-CUCAC-----AGGAA--    1

    
    UGUAUAAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUCUCAU-------UAA-G    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AAGCCAAA------CAA-U    1

    
    AAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-U    1

    
    AAU--AAU---AGAC-G-------G*C-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAA------CAA-U    1

    
    AAU--AAU---AUAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUUCCAAA------UAA-U    1

    
    AAUA-AAU---AGAC-G-------C*G-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-U    1

    
    AGU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------UUCCAAA----A-UAA-U    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAAC------CAA-G    1

    
    CAU--AAU---AGAC-GC------C*G-A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-G    1

    
    CGC--AAU---AGAC-G-------U*A-A----A-----GA*AA*UA---------------------------------------------------------------------------------------------------------AUACCA------AAUAA-G    1

    
    GAC--AAG---AAGC-UC------U*A-A----C-----UC*AC*G----------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*AA---------------------------------------------------------------------------------------------------------ACGCUAUA----A-UAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AACUCAAA----C-CAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------ACGCUAAA----A-UAA--    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAAA----U-UAA--    1

    
    GAG--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUGCUAAA----G-CAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCUAAA----U-UAA--    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------UAGCUAAA----A-UAA--    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------A-UCCAAA----U-UAA-C    1

    
    GGU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA---------------------------------------------------------------------------------------------------------A-UCCAAA----C-UAA-C    1

    
    U----AAU---CAAAAC--CG---C*G-A-CG-A-----UA*AC*GA----------------------------------------------------------------------------------------------------------UACCA--------UAA-A    1

    
    UAU--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-G    1

    
    UGC--AAU---AAAA-AG-----U-*--U----C-----CU*CU*AA---------------------------------------------------------------------------------------------------------AUACCCAG------CAA-A    1

    
    UGU--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAAA------UAA-A    1

    
    A----AAUC--GGGAGAC------C*G-C----G-----UA*CC*AA----------------------------------------------------------------------------------------------------------UGUCAA-------GAA-A    1

    
    AAC--AAU---AGAC-G-------C*A-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCUC-------UAA-U    1

    
    AAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------UUGCCUC-------UAA-U    1

    
    AGU--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------AGCCAAA------UAA-U    1

    
    CA---AAC---AGAC-GC------C*GGA----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AGACCCU--------GC-G    1

    
    CAA--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------CAA-G    1

    
    CAC--AAU---AGAC-G-------G*C-A----A-----AA*AU*AA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-G    1

    
    CAC--AAU---AGAC-G-------G*C-A----G-----GA*AU*AA---------------------------------------------------------------------------------------------------------AAACCAA-------UAA-G    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AAUCCAC-------UAA-G    1

    
    CAU--AAU---AGAC-GC------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------UGCCAA-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AGCCAAA-------CAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    GAU--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------AUCCAAA------CAA-C    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAA-------UAA-C    1

    
    UAC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCAA-------UAA-G    1

    
    UGC--AAU---AGAG-G-------U*G-C----U-----GA*AU*AA---------------------------------------------------------------------------------------------------------CGGUUCA-------UAA-G    1

    
    -AC--AAG---AAGC-UC------U*A------U-----CU*CA*G----------------------------------------------------------------------------------------------------------UUCUCAA-----AGUAA--    1

    
    AAG--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-CUCAA-------UAA-U    1

    
    AGC--AAU---AGAC-G--------*--A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAC------CAA-U    1

    
    AGC--AAU---AGAC-G-------C*G-A----A-----UA*AC*GA----------------------------------------------------------------------------------------------------------UGCCAA-------UAA-U    1

    
    AGU--AAU---AGAC-G--------*--A----A-----GA*AC*GA---------------------------------------------------------------------------------------------------------AUACCAAC------CAA-U    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------CAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----CA*AU*AA---------------------------------------------------------------------------------------------------------A-UGCAC-------CAA-G    1

    
    CAG--AAU---AUGG-G-------G*C-A----C-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-CGCAC-------UAA-G    1

    
    CAU--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA----------------------------------------------------------------------------------------------------------UACCAA-------UAA-G    1

    
    CGC--AAU---AGAC-G-------C*G-A----A-----GA*AU*AA---------------------------------------------------------------------------------------------------------AUGCCA--------UAA-G    1

    
    CGC--AAU---AGAU-A-------U*A-U----U-----GA*AC*GA---------------------------------------------------------------------------------------------------------GUGCCA--------UAA-G    1

    
    GAC--AAU---AGAC-G-------C*G-A----A-----UA*AG*UA----------------------------------------------------------------------------------------------------------CAUCAA-------UAA-C    1

    
    GGC--AAU---AGAC-G-------C*G-A----A-----UA*AU*AA---------------------------------------------------------------------------------------------------------A-GCCAC-------UAA-C    1

    
    UUC--AAU---AGAC-G-------U*A-A----A-----UA*AC*GA---------------------------------------------------------------------------------------------------------AUAAUC--------AAA-A    1

    
    -AC--AAG---AAGC-UC------U*A------U-----CU*CG*C-----------------------------------------------------------------------------------------------------------UCUCA-----AAGGAA--    1

    
    -AC--AAG---AGGC-UC------U*A------U-----CC*CA*U-----------------------------------------------------------------------------------------------------------CCUCAA-----AGGAA--    1

    
    -AC--AAG---UAU--U-------U*A-A----A-----U-*CA*UA---------------------------------------------------------------------------------------------------------UUCUCAA-----AGGAA--    1

    
    -AU--AAG---AGGC-UC------U*A------U-----CC*CG*U-----------------------------------------------------------------------------------------------------------UCCUAAA-----GGAA--    1

    
    CAC--AAG---AA-----------G*C------U-------*CG*UA----------------------------------------------------------------------------------------------------------UGCCAAA----A-AAA-G    1

    
    CGC--AAG---AA-----------G*C------U-------*CG*UA----------------------------------------------------------------------------------------------------------UGCCAAA------UAA-G    1

    
    Omitted sequenced and counts

    
    AUUACAAU-----------------*---------------*--*----------UGCCGGCGGAGAUUUAGGCGCUCCGUGUAAAGCAGUCUCACGCUAAUCUGGCAGACAUGUCAGGGAACCACGAGAUAAAUGUAAGUUA-----------------------AAA-U    2

    
    CGC--AAU---AUGC----------*-------C-------*AU*AA----------------------------------------------------------------------------------------------------------UAUCAAC------UAA-G    2

    
    GAC--AAUCGCAUAA-G-------U*A-A------------*--*----------GCGGGGACUGACGCGGCUCUUUCGCGCCACAUAGGGAUAUGUGGGGAACGCUAAGAGAAUUCCAAAA--------------------------------------------CAA--    1

    
    -AU--AAG-----------------*---------------*--*-----------UAUCUAAUGCGUGUCAUUAGGUCACCUCGGUAUGACUAGGGUGAGAGCUAGGAACCGUAGAGGUGUUCUCAAGG------------------------------------GAA--    1

    
    -------------------------*---------------*--*----------AAAUCGGGAGACCAACAUGGGCGUACCCACAUAUCCCACUACUGGAGACAGUGGUAAGGGCAAUGAGUGAAGAUCGCU---------------------------------AAA--    1

    
    AUAG-AAGU--AAGC-A-----CAU*G-A----U-GACUUU*A-*-A--------C------------------------U-----------------------------------------------------------------------AAAUCAAA------CAA-U    1

    
    CGAAUAAU---AGAC-G-------C*G-A----A-----UA*A-*AA---------------------------------------------------------------------------------------------------------AUCUCAU-------AAA-G    1

    
    -AC--AAG---------UACC-UA-*-UA-GGUC-------*-G*UA----------------------------------------------------------------------------------------------------------UCUCAAA----AACAA--    1

    
    GAC--AAU---AGAC-GC------U*A-A----U-----G-*A-*-A---------------------------------------------------------------------------------------------------------AUGCUAAA----A-UAA--    1

    
    CGC--AAU---AUAC----------*-------C-------*AU*AA----------------------------------------------------------------------------------------------------------UAUCAAU------UAA-G    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 J4_12209.1

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

0.00 -498.50 23 18

RNase P junction

2

Motif group J4_70672.1

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

0.00 -519.51 24 19

3

Motif group J4_57327.1

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

0.00 -631.30 26 23

4

Motif group J4_19572.1

Basepair signature:
cWW-F-cSW-F-F-tWH-cWW-F-cHW-F-cWW-F-tWS-F-cWW-F-F-F-cSH-tWH-cWW-F-F-F

0.00 -697.10 25 20

RNase P junction

5

Motif group J4_45801.6

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

0.00 -722.36 20 15

6

Motif group J4_01665.1

Basepair signature:
cWW-tWH-F-tWH-cWW-tSS-F-tHW-tSS-cWW-cWW

0.00 -782.10 24 19

7

Motif group J4_16596.1

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

0.00 -836.53 22 19

Cobalamin riboswitch junction

8

Motif group J4_59845.1

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

0.00 -841.55 21 18

9

Motif group J4_11418.1

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

0.00 -870.52 24 21

10

Motif group J4_80682.1

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

0.00 -889.85 25 21

tRNA junction

11

Motif group J4_47701.1

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

0.00 -902.03 25.5 22

12

Motif group J4_36540.1

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

0.00 -913.32 25 20

13

Motif group J4_61885.6

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

0.00 -948.86 23 19

14

Motif group J4_07509.2

Basepair signature:
cWW-tSW-F-F-tHS-F-cWW-F-cWW-F-F-tHS-F-cWW

0.00 -958.08 26 24

15

Motif group J4_69051.6

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

0.00 -959.66 23 19

16

Motif group J4_12410.1

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

0.00 -978.42 26 22

17

Motif group J4_54165.1

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

0.00 -986.58 25 23

18

Motif group J4_44058.1

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

0.00 -1012.37 25 21

19

Motif group J4_91813.1

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

0.00 -1017.02 24 20

20

Motif group J4_88771.1

Basepair signature:
cWW-tSS-cWW-tSS-cWW-cWW-tWH-tWH-cSH-cWW

0.00 -1025.85 25 21

21

Motif group J4_13620.1

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

0.00 -1027.53 27 25

22

Motif group J4_61477.5

Basepair signature:
cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

0.00 -1044.63 25 23

23

Motif group J4_98739.1

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

0.00 -1045.21 27 24

24

Motif group J4_15241.1

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

0.00 -1082.88 24 19

25

Motif group J4_63658.1

Basepair signature:
cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tSW-F-cSH-F-F

0.00 -1173.23 22 17

26

Motif group J4_95838.1

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

0.00 -1239.39 24 22

27

Motif group J4_77044.4

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

0.00 -1241.60 27 24

28

Motif group J4_71729.5

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

0.00 -1256.90 25 24

29

Motif group J4_97085.2

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

0.00 -1328.88 25 22

30

Motif group J4_04930.6

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

0.00 -1329.24 23 20

31

Motif group J4_60168.1

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

0.00 -1356.86 27 24

32

Motif group J4_94519.1

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

0.00 -1388.34 24 22

tRNA junction

33

Motif group J4_26776.1

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

0.00 -1490.76 29 25

34

Motif group J4_47842.1

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

0.00 -1500.15 24 19

35

Motif group J4_59634.1

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

0.00 -1502.21 28 26

36

Motif group J4_65285.1

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

0.00 -1550.17 25 23

tRNA junction

37

Motif group J4_93343.1

Basepair signature:
cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

0.00 -1561.34 22 17

38

Motif group J4_10571.1

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

0.00 -1573.35 26 24

39

Motif group J4_40477.1

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

0.00 -1636.71 25 23

tRNA junction

40

Motif group J4_24220.1

Basepair signature:
cWW-F-F-tWS-F-F-cWW-tHS-cWW-cWW

0.00 -1658.53 26 23

41

Motif group J4_99897.1

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

0.00 -1683.09 28 25

42

Motif group J4_36296.3

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

0.00 -1708.32 24 23

tRNA junction

43

Motif group J4_70449.28

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

0.00 -1737.37 24 23

tRNA junction

44

Motif group J4_64571.5

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

0.00 -1954.45 24 21

45

Motif group J4_04237.1

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

0.00 -2118.72 45 44

46

Motif group J4_89787.1

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

0.00 -2777.55 25 20

47

Motif group J4_35578.3

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

0.00 -2944.57 24 20

48

Motif group J4_07491.2

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

0.00 -2986.79 27 25

Purine riboswitch junction

49

Motif group J4_10313.5

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

0.00 -2990.62 26 23

50

Motif group J4_63076.1

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

0.00 -3109.72 26 24

class I ligase product junction

51

Motif group J4_87855.1

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

0.00 -3111.66 23 20

52

Motif group J4_28426.1

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

0.00 -3130.94 27 22

SAM-I/IV riboswitch junction

53

Motif group J4_65356.1

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

0.00 -3331.08 28 25

54

Motif group J4_40439.2

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

0.00 -3363.73 23 20

SAM-I riboswitch junction

55

Motif group J4_48692.1

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

0.00 -3878.28 27 25

56

Motif group J4_75852.1

Basepair signature:
cWW-tSW-cSS-cWW-F-cSH-cWW-cWW-F-F

0.00 -4407.28 25.5 24

57

Motif group J4_65052.1

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

0.00 -4580.55 28.5 26

58

Motif group J4_28473.1

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

0.00 -4810.69 27 24

59

Motif group J4_80390.1

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

0.00 -5385.76 27 23

tRNA junction

60

Motif group J4_47478.1

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

0.00 -6888.30 27 23

61

Motif group J4_69073.1

Basepair signature:
cWW-cHS-cWW-cWS-cHW-cWW-cWW

0.00 -6888.30 27 23

62

Motif group J4_72305.5

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

0.00 -7413.61 27 25

tRNA junction

63

Motif group J4_57344.1

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

0.00 -7959.97 28 25

64

Motif group J4_46448.1

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

0.00 -8219.07 28 26

65

Motif group J4_45582.1

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

0.00 -8668.07 29 25

66

Motif group J4_43687.2

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

0.00 -9971.61 27 26

67

Motif group J4_00691.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -9999.00 27 25

68

Motif group J4_24280.2

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -9999.00 27 25

69

Motif group J4_76096.5

Basepair signature:
cWW-cWW-cWW-cWW

0.00 -9999.00 27 26

Coloring options: