RNA 3D Hub

JAR3D Query RF03072-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03072 maps to these 6 chains: 9CXF|1|A, 9E73|1|A, 9E74|1|A, 9E75|1|A, 9ELY|1|A, 9G7C|1|A See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 9 Hairpin loop

Column numbers: 364-495 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    -------------------------------GAAAA------------------------------------------------------------------------------------------------   41

    
    -------------------------------AAA--------------------------------------------------------------------------------------------------   25

    
    UGUUAUAUCAAA--------------GAGACAAAGG-----------------------------------------------------------------GUCUC-----------------------GCA   14

    
    G------------------------------AAA-------------------------------------------------------------------------------------------------C   14

    
    -------------------------------GAAA-------------------------------------------------------------------------------------------------   14

    
    -------------------------------UAAAA------------------------------------------------------------------------------------------------   13

    
    -------------------------------AAAAA------------------------------------------------------------------------------------------------   11

    
    CGUUCUACUUUCU--UUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    9

    
    -------------------------------GGAAA------------------------------------------------------------------------------------------------    8

    
    AU-G--C------------------------GGAA------------------------------------------------------------------------------------------G---CGU    7

    
    CA-----------------------------AUAA-----------------------------------------------------------------------------------------------AG    7

    
    -------------------------------UUAAAU-----------------------------------------------------------------------------------------------    7

    
    -------------------------------UUAAA------------------------------------------------------------------------------------------------    7

    
    -------------------------------AUUAAA-----------------------------------------------------------------------------------------------    6

    
    -------------------------------AAAAU------------------------------------------------------------------------------------------------    6

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

    
    -------------------------------AAAA-------------------------------------------------------------------------------------------------    6

    
    -------------------------------AAUAAA-----------------------------------------------------------------------------------------------    5

    
    -------------------------------GUAA-------------------------------------------------------------------------------------------------    5

    
    -------------------------------AAU--------------------------------------------------------------------------------------------------    5

    
    UGAGUA--UCGCGAC----------------AUCCG---------------------------------------------------------------------------------GUUGCG------ACG    4

    
    -------------------------------AAAAAAAUUAUGG----------------------------------------------------------------------------------------    4

    
    G------------------------------CGAUU-----------------------------------------------------------------------------------------------C    4

    
    -------------------------------UAAA-------------------------------------------------------------------------------------------------    4

    
    CG-UUCUACUUU-CUUUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    3

    
    CGUUUUAUUCUUAU-----------GGGGCAAUAGG-----------------------------------------------------------------UGCCUC----------------------GCG    3

    
    UGUUAUAUCAAU--------------GAGACAAAGG-----------------------------------------------------------------GUCUC-----------------------GCA    3

    
    UGCGGGAUAUGCAGC----------------AUAGG---------------------------------------------------------------------------------GCUGCA-------CA    3

    
    UGUUGAUUUCAAGGC----------------AUACG---------------------------------------------------------------------------------GCCUUG-------CA    3

    
    C------------------------------AUGAA-----------------------------------------------------------------------------------------------G    3

    
    U------------------------------AAAAA-----------------------------------------------------------------------------------------------A    3

    
    -------------------------------UUGUAU-----------------------------------------------------------------------------------------------    3

    
    A------------------------------GAAA------------------------------------------------------------------------------------------------U    3

    
    A------------------------------GAGA------------------------------------------------------------------------------------------------U    3

    
    -------------------------------AUAAA------------------------------------------------------------------------------------------------    3

    
    -------------------------------GUAAA------------------------------------------------------------------------------------------------    3

    
    -------------------------------UAUAA------------------------------------------------------------------------------------------------    3

    
    G------------------------------AAA-------------------------------------------------------------------------------------------------U    3

    
    -------------------------------AAAG-------------------------------------------------------------------------------------------------    3

    
    -------------------------------GAGA-------------------------------------------------------------------------------------------------    3

    
    -------------------------------AA---------------------------------------------------------------------------------------------------    3

    
    CG-UUCUACUUUC-UUUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    2

    
    CGGUCGUUUCCGCGGCC--------------AUCCA-------------------------------------------------------------------------------GGCCGC------C--UG    2

    
    UGUUAUAACAAA--------------GAGACAAAGG-----------------------------------------------------------------GUCUC-----------------------GCA    2

    
    -------CCGGCGACC---------------CAGAU--------------------------------------------------------------------------------GGUUGCCGUCC-----    2

    
    -------------------------------ACCCUAAUAGGUUAUAACAA---------------------------------------------------------------------------------    2

    
    -------------------------------AUAAAAAUUGAG-----------------------------------------------------------------------------------------    2

    
    AU-G--C------------------------GGAA------------------------------------------------------------------------------------------G---CAU    2

    
    GC-----------------------------CCAG-----------------------------------------------------------------------------------------------GC    2

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

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

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

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

    
    -------------------------------AUUUAA-----------------------------------------------------------------------------------------------    2

    
    -------------------------------GCAA-------------------------------------------------------------------------------------------------    2

    
    -------------------------------GCGA-------------------------------------------------------------------------------------------------    2

    
    -------------------------------UAAG-------------------------------------------------------------------------------------------------    2

    
    -------------------------------UAUA-------------------------------------------------------------------------------------------------    2

    
    UUUUCAUGG----------------------AACCGUAAGGAAGGACGCUACAAGAAUCCCCGCUUUUCUAUGCCGUGGAUCCAGCGACUCCCCAAGGAUG----------------------CCAA--AAA    1

    
    UU-A-GGAAAAUAAUA-AUCUAUUCCAGUCUAGUACAUAGUACUUA-------------------------------------------------------AGGCU--AAUUGAU--GUUAUUUUGC--UGG    1

    
    GG----UGGUAU--GGAAGGUU-AAGAUGUACAUGGAUAUUAUCCUA------------------------------------------------------UGAGUUUCAAACUUUCCGAUUACUG----CU    1

    
    UUGGGA--AGUGGG-----------------AGGCGGGAAAGUUCCGCCAACGAGUUUCUUGCACUGA--------------------------------------------------UCCAUUGUAAUCA-    1

    
    CA------CUUGC------------------UUUGUAGGAAAGACAAACUUCGGUUGCGCAUCCGUCAAAU------------------------------------------------GUAAG-----AUU    1

    
    CA------CUUGC------------------UUUGUAGGAAAGACAAACUUCGGUUGGGCAUCCGUCAAAU------------------------------------------------GUAAG-----AUU    1

    
    CA----CUUGC--------------------UUUGUAGGAAAGACAAACUUCGGUUGGGCAUCCGUCAAAU--------------------------------------------------GUAAG---AUU    1

    
    CGCG--GGUGCUG------------------CUCUUACUAUAGGCGCGGGGACGAGACACCCCGA------------------------------------------------------CAUCAUU---GCG    1

    
    CGUGUGGCCGA-UGGU-ACGGUA--------GAUAAUACGGGG------------------------------------------------------------------UGCUGUCAUCAGUUGGUUG-CCG    1

    
    GGGAAGGAAGGA---------CAUGCCGGCGUAA-------------------------------------------------------------------CGGCGGCAUGGGCCGG---UCAUUCU--UUU    1

    
    CG-UUCUAUUUUUCUUUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    1

    
    CGUCGCUACUUUUUUGAGGCA----------AUACG---------------------------------------------------------------------------UGCCUCG------------CG    1

    
    CGUUCUACUUUUU--UUGGGGC---------AAUUACC------------------------------------------------------------------------GCCUC--------------GCG    1

    
    CG-UUCUACUUUCU-UUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    1

    
    CGUCGCACUUUUUU-----------GAGGCAAUACG-----------------------------------------------------------------UGCCUC----------------------GCG    1

    
    CGUCUUAUUCUUUU-----------GAGGCAAUAGG-----------------------------------------------------------------UGUCUC----------------------GCG    1

    
    CGUUCUACUUUUU--UUGGGGC---------AAUACC-------------------------------------------------------------------------GCCUC--------------GCG    1

    
    UG-UAUUACAUAUAAAUGCAGC---------AUAGG--------------------------------------------------------------------------GCUGC--------------GCA    1

    
    CG-C-UGACAUUUUCGCGGC-----------ACGGAC---------------------------------------------------------------------------GCCGCGA-----------CG    1

    
    CG-GUGGUAAAUUU-----------------CUCAAGU--------------------------------------------------------------------------------GAAUUUAUUA-UGG    1

    
    CG-UCAUACACACUGAGGCA-----------AUAGG----------------------------------------------------------------------------UGCCUC-----------GCG    1

    
    CGCUGACAUUUUCGCGGC-------------ACGGAC-----------------------------------------------------------------------------GCCGUG---------ACG    1

    
    CGUCAUACACACU------------GAGGCAAUAGG-----------------------------------------------------------------UGCCUC----------------------GCG    1

    
    CG-GAGAUUGUUUUGCGGC------------GUGGU-----------------------------------------------------------------------------GCUGCA----------CCG    1

    
    UGUUAUAUCACAAA------------GAGACAAAGG-----------------------------------------------------------------GUCUC-----------------------GCA    1

    
    CAACGAUAAGC--------------AAGGACGUGGG-----------------------------------------------------------------GUCCU-----------------------GCG    1

    
    CG-AAACCAAGCCGAGGC-------------GUCCA------------------------------------------------------------------------------GCCUC-------A---CG    1

    
    CGACGAUAAGC--------------AAGGACGUGGG-----------------------------------------------------------------GUCCU-----------------------GCG    1

    
    CGACGAUAAGCAAGGAC--------------GUGGG-------------------------------------------------------------------------------GUCCU---------GCG    1

    
    CGUCAGACUGAA--------------GAGGCAUACC-----------------------------------------------------------------GCCUC-----------------------GCG    1

    
    CGUUUAUACGA---------------GCGGCAUACC-----------------------------------------------------------------GUCGC---------------------G-ACG    1

    
    UG-UUACACAUAAAAGAC-------------AUAGG------------------------------------------------------------------------------GUCUU----------GCA    1

    
    UG-UUAUAUAAAUGAGAC-------------AAAGG------------------------------------------------------------------------------GUCUC----------GCA    1

    
    UGUA-AUAUCAAAGAGAC-------------AAAGG------------------------------------------------------------------------------GUCUC----------GCA    1

    
    UGUAAAUU--GC-------------AGCGACAUACG-----------------------------------------------------------------GUCG----------------CA------ACG    1

    
    UGUUAA-ACAUAAAAGAC-------------AUAGG------------------------------------------------------------------------------GUCUU----------GCA    1

    
    UGUUAUACUCAAAAGGC--------------AUCCC-------------------------------------------------------------------------------GCCUU---------GCA    1

    
    CG-GCCGAUUUUUGCGG--------------CAACG-------------------------------------------------------------------------------CCGCA---------CUG    1

    
    CGUCAUACUCAGAGGC---------------AUACG--------------------------------------------------------------------------------GCCUC--------GCG    1

    
    UGAUCGGCUUU---------------GGGGCAAAGA-----------------------------------------------------------------GCCCC-----------------------ACA    1

    
    UGAUCGGCUUUGGGGC---------------AAAGA--------------------------------------------------------------------------------GCCCC--------ACA    1

    
    CG-GGUUUUAUGCGAC---------------AUAGG--------------------------------------------------------------------------------GUUGCA--------CG    1

    
    CG-GUGGUUUUGCGAC---------------AAGUG--------------------------------------------------------------------------------GUCGC--------CCG    1

    
    CGGGUUUUAUGCAAC----------------AUAGG---------------------------------------------------------------------------------GUUGCA-------CG    1

    
    CGUCAGUCAAGAGGC----------------AUCCG---------------------------------------------------------------------------------GCCUC-------GCG    1

    
    CGUUAGACAAGAGGC----------------AUACG---------------------------------------------------------------------------------GCCUC-------GCG    1

    
    CGUUAGAUGAGAGGC----------------ACGGG---------------------------------------------------------------------------------GCCUC-------GCG    1

    
    CGUUCC-------------------------AGAAGAGGGCAUGCGCCCC-------------------------------------------------------------------------------GCG    1

    
    CGUUUA-CACGCGAC----------------AUGGU---------------------------------------------------------------------------------GCCGCG------GCG    1

    
    UGAUAUAUUUGAGAC----------------AGGUA---------------------------------------------------------------------------------GUCUCA-------CA    1

    
    --AC--UGAGGG-----------------UCCCGAU-----------------------------------------------------------------GU-----------------CCCUCAU--GAC    1

    
    CG-UUUCUA-----------------GGGGUAAUUCC----------------------------------------------------------------GCCCC-----------------------GCG    1

    
    CGAU--UACAGUCGC----------------AUCCC---------------------------------------------------------------------------------GCGGCU------UCG    1

    
    CGUUCA------------------GGGUCGCAUCCC-----------------------------------------------------------------GCGAUCC----------------------CG    1

    
    GC--CCUCCCGU-------------------CAGAU------------------------------------------------------------------------------------ACGGGAACCAGC    1

    
    ---------------------GCGGCUUUGCAUUCU-----------------------------------------------------------------GCGAGGCUGC----------------G----    1

    
    -G-C--CGGGGGAU-----------------CAGAC----------------------------------------------------------------------------------AUCCUCCG---GUC    1

    
    CA---CACGCCG------------------UCCGAC-----------------------------------------------------------------A------------------CGGCGUCA--GG    1

    
    CG----GAGGG--------------------UCCAGAUGU---------------------------------------------------------------------------------CCCUCAU-GAC    1

    
    CGCGU--UAUGCAGC----------------AGAGG---------------------------------------------------------------------------------GCUGCA-------CG    1

    
    GUGG--ACGGGU-------------------CCGAU------------------------------------------------------------------------------------GCCCGUCG-CUC    1

    
    UC---CCGGCCGU------------------CAGAU-----------------------------------------------------------------------------------GCGGUCGUC--GG    1

    
    UG----------------------GGAGGGCCCGAU-----------------------------------------------------------------GCCCUCCGG-------------------ACA    1

    
    UGUUGA--UGGCAAC----------------AUAGU---------------------------------------------------------------------------------GUUGC-------GCA    1

    
    ------CCGGAGGCC----------------CAGAU---------------------------------------------------------------------------------GACCUCCGACC----    1

    
    ------CCGGGGAGC----------------CAGAU---------------------------------------------------------------------------------GUUCCUCGCCA----    1

    
    ------CCGGGGGAU----------------ACCGA---------------------------------------------------------------------------------GUUCCCCGCCC----    1

    
    ------CCGGGGGGC----------------CGGAU---------------------------------------------------------------------------------GUCCCCCGUAC----    1

    
    ------CCGGGGGUC----------------CGGAU---------------------------------------------------------------------------------GUCCCCCGUAC----    1

    
    A------------------------------GAAUUAUACAUAAUAGUAAUUUA-----------------------------------------------------------------------------U    1

    
    A------------------------------GAAUUAUACAUAUAGUUAAUUUA-----------------------------------------------------------------------------U    1

    
    A----CG--GAGGGC----------------CCGAU---------------------------------------------------------------------------------GCCCUCCAC----CC    1

    
    CGAAAUUGCAGC-------------------AUGGG------------------------------------------------------------------------------------GCUGCA----CG    1

    
    CGUUAU-------------------GGGCGCAUAGG-----------------------------------------------------------------GCGCCC-----------------------CG    1

    
    U------CACGACAU----------------CAGAU---------------------------------------------------------------------------------GUGUCGUGU----GC    1

    
    U-----CGGAGG-U-----------------CCAGAU---------------------------------------------------------------------------------GUCCUCUGCA---A    1

    
    CGAU--CGGCCG-------------------ACCCU------------------------------------------------------------------------------------CGGCCC---GGG    1

    
    GGUG----AAGCGGC----------------AUAGG---------------------------------------------------------------------------------GCUGCU-------CU    1

    
    GUUG--CUCCCG-------------------GCUCU------------------------------------------------------------------------------------CGGGGG---AGC    1

    
    U------------------------------UUAAGUAAUUAAAGUACAUAAU------------------------------------------------------------------------------A    1

    
    UC-G--GUAGGU-------------------CCGAC------------------------------------------------------------------------------------ACCUAC---CGG    1

    
    CG----GCAUUC-------------------AAAACC-----------------------------------------------------------------------------------GAAUGC----GG    1

    
    CG----GCAUUC-------------------AAAAUC-----------------------------------------------------------------------------------GAAUGC----GG    1

    
    CG----GCAUUC-------------------CGAAUC-----------------------------------------------------------------------------------GAAUGC----GG    1

    
    G-----AUUG---------------------AUCAAAG------------------------------------------------------------------------------------UGGUCAUCCC    1

    
    ----GUGUGACC-------------------AAAGU------------------------------------------------------------------------------------GGUCAUGG----    1

    
    UGUCUU----G--------------------AUAGACAAAAU---------------------------------------------------------------------------------------UUU    1

    
    UUAU--UAGCU--------------------ACGUC-------------------------------------------------------------------------------------AGCUA----GA    1

    
    -------------------------------ACCCUAACAGGUUAGAACAA---------------------------------------------------------------------------------    1

    
    -------------------------------ACCUUAACGGGUUAGAACAA---------------------------------------------------------------------------------    1

    
    -------------------------------ACCUUAAUUGGUGAUAAUAA---------------------------------------------------------------------------------    1

    
    AC-----------------------------CUUAAUUGGUGAUAA-----------------------------------------------------------------------------------UAA    1

    
    --------UAUU-------------------CAAA-------------------------------------------------------------------------------------AAUAAAUU-CCA    1

    
    AAAUACUAAAAA-----------------------------------------------------------------------------------------------------------------ACACAUG    1

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

    
    C------------------------------CCGGUAAAGAAAUUU-------------------------------------------------------------------------------------G    1

    
    GCACCG-------------------------GGCACG------------------------------------------------------------------------------------------G-GGU    1

    
    UU-U--AU-----------------------CCUGU----------------------------------------------------------------------------------------AU---AAA    1

    
    -------------------------------AAAAAAAAUUAUGG---------------------------------------------------------------------------------------    1

    
    A--C--GCC----------------------GUA-----------------------------------------------------------------------------------------GGC---GAU    1

    
    -------------------------------GGAAAAUACUAUA----------------------------------------------------------------------------------------    1

    
    -------------------------------GGACUAUACUAUA----------------------------------------------------------------------------------------    1

    
    UG----CGU----------------------AAU-----------------------------------------------------------------------------------------ACA----CA    1

    
    -------------------------------AAAAAAUUAUGG-----------------------------------------------------------------------------------------    1

    
    AU-G--C------------------------GAGA------------------------------------------------------------------------------------------G---CAU    1

    
    -------------------------------AAAAAAUAAUG------------------------------------------------------------------------------------------    1

    
    -------------------------------ACGAUAUUCUG------------------------------------------------------------------------------------------    1

    
    GC-A---------------------------UCUU----------------------------------------------------------------------------------------------UGC    1

    
    -------------------------------AUAAUAAUA--------------------------------------------------------------------------------------------    1

    
    AU-----------------------------GUAAA----------------------------------------------------------------------------------------------AU    1

    
    GA-----------------------------CUCGG----------------------------------------------------------------------------------------------UC    1

    
    GG-----------------------------CGCAG----------------------------------------------------------------------------------------------CC    1

    
    A------------------------------CGGCGA----------------------------------------------------------------------------------------------U    1

    
    AC-----------------------------AACG-----------------------------------------------------------------------------------------------AU    1

    
    CC-----------------------------UUAC-----------------------------------------------------------------------------------------------GG    1

    
    GC-----------------------------CUCG-----------------------------------------------------------------------------------------------GC    1

    
    GC-----------------------------GCAA-----------------------------------------------------------------------------------------------GC    1

    
    GC-----------------------------GCAG-----------------------------------------------------------------------------------------------GC    1

    
    U------------------------------AAAAA----------------------------------------------------------------------------------------------AA    1

    
    U------------------------------CAUAAA----------------------------------------------------------------------------------------------A    1

    
    UC-----------------------------AUAAA-----------------------------------------------------------------------------------------------A    1

    
    -------------------------------ACAAUCA----------------------------------------------------------------------------------------------    1

    
    -------------------------------CGUUAGU----------------------------------------------------------------------------------------------    1

    
    -------------------------------GGUUAAA----------------------------------------------------------------------------------------------    1

    
    A------------------------------GACCA-----------------------------------------------------------------------------------------------U    1

    
    AU-----------------------------AGU------------------------------------------------------------------------------------------------AU    1

    
    C------------------------------AGACA-----------------------------------------------------------------------------------------------G    1

    
    C------------------------------GAAAA-----------------------------------------------------------------------------------------------G    1

    
    C------------------------------GGAAA-----------------------------------------------------------------------------------------------G    1

    
    G------------------------------CAUGA-----------------------------------------------------------------------------------------------C    1

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

    
    UU-----------------------------AAA------------------------------------------------------------------------------------------------AG    1

    
    -------------------------------AGAAAA-----------------------------------------------------------------------------------------------    1

    
    -------------------------------GAAAAA-----------------------------------------------------------------------------------------------    1

    
    -------------------------------GGAAAA-----------------------------------------------------------------------------------------------    1

    
    -------------------------------UGAGAU-----------------------------------------------------------------------------------------------    1

    
    -------------------------------UUAGGU-----------------------------------------------------------------------------------------------    1

    
    -------------------------------UUAUAU-----------------------------------------------------------------------------------------------    1

    
    A------------------------------GCAA------------------------------------------------------------------------------------------------U    1

    
    A------------------------------GCGA------------------------------------------------------------------------------------------------U    1

    
    A------------------------------UUCU------------------------------------------------------------------------------------------------U    1

    
    A------------------------------UUUA------------------------------------------------------------------------------------------------U    1

    
    C------------------------------GACA------------------------------------------------------------------------------------------------G    1

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

    
    U------------------------------CUUA------------------------------------------------------------------------------------------------A    1

    
    U------------------------------GAAA------------------------------------------------------------------------------------------------A    1

    
    U------------------------------UAAA------------------------------------------------------------------------------------------------A    1

    
    -------------------------------AAAUU------------------------------------------------------------------------------------------------    1

    
    -------------------------------ACAAA------------------------------------------------------------------------------------------------    1

    
    -------------------------------AUCAA------------------------------------------------------------------------------------------------    1

    
    -------------------------------AUGUA------------------------------------------------------------------------------------------------    1

    
    -------------------------------AUUCC------------------------------------------------------------------------------------------------    1

    
    -------------------------------CGUGU------------------------------------------------------------------------------------------------    1

    
    -------------------------------CUUGC------------------------------------------------------------------------------------------------    1

    
    -------------------------------UCUUU------------------------------------------------------------------------------------------------    1

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

    
    -------------------------------UUUAG------------------------------------------------------------------------------------------------    1

    
    -------------------------------AAAU-------------------------------------------------------------------------------------------------    1

    
    -------------------------------AAGA-------------------------------------------------------------------------------------------------    1

    
    -------------------------------AUAA-------------------------------------------------------------------------------------------------    1

    
    -------------------------------CAGA-------------------------------------------------------------------------------------------------    1

    
    -------------------------------GGAA-------------------------------------------------------------------------------------------------    1

    
    -------------------------------GUGU-------------------------------------------------------------------------------------------------    1

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

    
    -------------------------------UUAG-------------------------------------------------------------------------------------------------    1

    
    -------------------------------UUCG-------------------------------------------------------------------------------------------------    1

    
    -------------------------------UUUU-------------------------------------------------------------------------------------------------    1

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

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

    
    -------------------------------UUU--------------------------------------------------------------------------------------------------    1

    
    A------------------------------A---------------------------------------------------------------------------------------------------U    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_75660.5

Basepair signature:
cWW-F

38.52 -4691.16 3 2

2

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

35.86 -3476.85 3 2

3

Motif group HL_38168.1

Basepair signature:
cWW-F

34.84 -4696.21 3 3

4

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

32.38 -3439.08 3 2

5

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

28.48 -3588.88 4 3

6

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

27.05 -3735.94 3 2

tRNA D-loop

7

Motif group HL_56334.1

Basepair signature:
cWW-F

15.98 -4064.09 3 3

Mini UNCG

8

Motif group HL_50006.2

Basepair signature:
cWW-F-F

13.73 -3492.48 4 3

9

Motif group HL_48417.5

Basepair signature:
cWW-F-F

13.52 -3330.57 3 2

10

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

12.91 -5244.66 3 2

11

Motif group HL_13189.1

Basepair signature:
cWW-F-F

12.50 -3534.10 4 4

12

Motif group HL_70782.2

Basepair signature:
cWW-F

12.09 -4015.19 4 4

13

Motif group HL_69752.2

Basepair signature:
cWW-F

12.09 -4728.73 4 3

14

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

11.48 -3564.18 4 2

15

Motif group HL_48778.2

Basepair signature:
cWW-F

11.48 -4033.12 3 3

Mini UNCG

16

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

10.04 -5192.10 3 2

Pseudoknot geometry with 3' bulge

17

Motif group HL_32346.4

Basepair signature:
cWW-F

9.84 -4073.78 3 3

18

Motif group HL_37824.7

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

9.63 -3368.35 2 2

GNRA

19

Motif group HL_93535.1

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

7.99 -4190.57 4 2

20

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

7.79 -3499.72 4 3

21

Motif group HL_65794.5

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

7.38 -7155.60 3 2

Pseudoknot geometry

22

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

5.94 -4585.66 4 3

23

Motif group HL_52953.3

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

5.94 -7476.51 3 2

24

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

5.74 -5260.72 5 4

25

Motif group HL_46501.1

Basepair signature:
cWW-cWS

5.53 -3689.47 4 3

26

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

5.12 -3563.25 6 4

27

Motif group HL_20535.2

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

5.12 -4128.60 5 3

28

Motif group HL_59843.1

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

5.12 -4187.93 4 3

29

Motif group HL_47787.2

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

4.92 -4176.83 3 2

30

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

4.30 -3493.22 4 3

31

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

4.30 -3562.04 4 3

32

Motif group HL_56131.2

Basepair signature:
cWW-F-F

4.10 -3424.93 4 4

33

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

4.10 -3489.46 4 3

34

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

4.10 -3548.72 3 3

35

Motif group HL_22135.1

Basepair signature:
cWW-F-F

4.10 -4750.12 4 4

36

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

3.89 -3627.12 5 4

37

Motif group HL_02817.2

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

3.89 -4376.25 5 3

38

Motif group HL_39243.1

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

3.69 -7007.88 4 3

39

Motif group HL_57875.1

Basepair signature:
cWW-F-F

3.48 -3592.30 4 3

40

Motif group HL_97917.2

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

3.48 -4168.15 5 3

41

Motif group HL_13529.1

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

3.07 -2808.68 5 3

42

Motif group HL_13963.3

Basepair signature:
cWW-F-F

3.07 -3504.72 5 4

43

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

2.87 -2975.94 4 3

Fab BL3-6 binding hairpin with tSW

44

Motif group HL_87553.1

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

2.87 -3170.77 5 4

45

Motif group HL_66103.1

Basepair signature:
cWW-F-F

2.87 -3616.24 5 3

46

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

2.66 -2687.87 5 4

47

Motif group HL_78677.1

Basepair signature:
cWW-F-F

2.66 -4113.16 4 4

48

Motif group HL_56676.1

Basepair signature:
cWW-F-F

2.66 -4245.53 4 3

49

Motif group HL_31585.4

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

2.46 -5376.79 4 3

Purine riboswitch

50

Motif group HL_47854.1

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

2.25 -3349.08 5 4

51

Motif group HL_15574.1

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

2.25 -5419.68 4 3

52

Motif group HL_59735.5

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

2.25 -6809.12 4 3

53

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

1.84 -3499.38 6 4

tRNA anticodon loop with synthetase

54

Motif group HL_30068.2

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

1.84 -4180.98 4 3

55

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

1.64 -2292.22 6 5

56

Motif group HL_77436.5

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

1.64 -2553.36 4 3

T-loop related

57

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

1.64 -3184.79 6 4

Other HL

58

Motif group HL_94980.1

Basepair signature:
cWW-F-F

1.64 -4871.99 5 5

59

Motif group HL_18565.1

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

1.43 -2626.00 5 4

60

Motif group HL_04259.3

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

1.43 -3235.12 4 3

GNRA with extra cWW

61

Motif group HL_32392.1

Basepair signature:
cWW-F-F

1.43 -3737.68 5 5

62

Motif group HL_10453.3

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

1.43 -4597.87 5 3

tRNA anticodon loop

63

Motif group HL_38046.1

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

1.43 -5233.57 6 5

64

Motif group HL_30680.3

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

1.43 -6367.72 5 4

Pseudoknot geometry

65

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

1.43 -6894.06 6 5

66

Motif group HL_28075.1

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

1.23 -3061.41 5 3

67

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

1.23 -3247.89 4 3

tRNA D-loop

68

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

1.23 -3488.33 5 3

69

Motif group HL_37344.1

Basepair signature:
cWW-F-F

1.23 -3735.69 6 4

70

Motif group HL_15802.1

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

1.02 -2839.00 7 6

71

Motif group HL_10540.1

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

1.02 -3167.87 5 3

72

Motif group HL_28791.1

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

1.02 -7537.34 6 5

73

Motif group HL_93324.4

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

1.02 -8052.32 4 3

Pseudoknot geometry

74

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.82 -2731.40 5 3

75

Motif group HL_64690.6

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

0.82 -2934.37 5 4

76

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

0.82 -5293.90 6 5

77

Motif group HL_81100.2

Basepair signature:
cWW

0.82 -6046.58 6 4

78

Motif group HL_73266.9

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

0.61 -2128.42 5 4

79

Motif group HL_78347.4

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

0.61 -3203.07 5 4

80

Motif group HL_89893.1

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

0.61 -3323.76 5 4

81

Motif group HL_77082.1

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

0.61 -3390.95 5 3

Pseudoknot geometry

82

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.61 -3454.07 4 3

UNCG

83

Motif group HL_71391.1

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

0.61 -3621.43 4 3

84

Motif group HL_55195.3

Basepair signature:
cWW-F

0.61 -4804.89 4 3

85

Motif group HL_83632.1

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

0.61 -5479.56 5 4

tRNA anticodon loop

86

Motif group HL_01609.3

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

0.41 -2581.81 5 3

T-loop with 2 bulged bases not stacked

87

Motif group HL_41464.2

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

0.41 -2673.26 6 4

88

Motif group HL_42046.2

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

0.41 -2915.97 6 4

89

Motif group HL_37369.2

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

0.41 -3451.71 5 3

90

Motif group HL_27483.1

Basepair signature:
cWW-F

0.41 -3528.39 5 4

91

Motif group HL_25967.2

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

0.41 -3654.96 5 4

92

Motif group HL_59330.1

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

0.41 -3957.04 8 6

93

Motif group HL_35941.1

Basepair signature:
cWW-F

0.41 -4142.83 5 5

94

Motif group HL_00914.1

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

0.41 -4594.47 5 3

95

Motif group HL_38649.1

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

0.41 -4847.19 8 6

96

Motif group HL_85993.1

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

0.41 -5031.85 6 4

97

Motif group HL_22622.1

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

0.41 -6474.19 6 4

98

Motif group HL_83808.4

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

0.20 -1805.37 9 7

Pseudoknot

99

Motif group HL_98864.1

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

0.20 -1901.69 7 6

T-loop with unstacked turn

100

Motif group HL_04642.1

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

0.20 -2152.29 8 6

tRNA D-loop

101

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.20 -2611.95 7 5

tRNA D-loop

102

Motif group HL_84299.4

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

0.20 -2728.47 5 4

103

Motif group HL_58224.1

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

0.20 -3011.68 8 6

104

Motif group HL_04641.1

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

0.20 -3126.42 7 6

105

Motif group HL_33983.1

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

0.20 -3541.08 6 4

106

Motif group HL_81538.2

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

0.20 -3584.40 4 3

GNRA with tandem sheared

107

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.20 -4108.45 5 4

T-loop with unstacked turn

108

Motif group HL_80008.1

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

0.20 -4807.78 6 4

109

Motif group HL_16398.2

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

0.20 -4906.11 9 8

110

Motif group HL_51447.1

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

0.20 -5273.75 6 4

111

Motif group HL_78284.1

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

0.20 -5296.15 8 7

112

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.20 -5743.62 7 5

113

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.20 -5952.71 6 5

114

Motif group HL_42998.2

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

0.20 -6756.09 5 3

115

Motif group HL_14757.1

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

0.00 -444.96 14 12

116

Motif group HL_81205.3

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

0.00 -471.13 10 9

117

Motif group HL_73247.1

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

0.00 -478.72 11 9

Pseudoknot geometry

118

Motif group HL_84847.1

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

0.00 -481.95 10 9

119

Motif group HL_91641.1

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

0.00 -486.56 12 11

120

Motif group HL_07583.1

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

0.00 -486.78 10 8

121

Motif group HL_98870.1

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

0.00 -494.25 11 9

122

Motif group HL_74055.2

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

0.00 -632.10 11 9

123

Motif group HL_41902.1

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

0.00 -710.31 9 7

124

Motif group HL_51921.1

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

0.00 -722.48 16 14

125

Motif group HL_70658.1

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

0.00 -756.66 9 7

126

Motif group HL_74379.3

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

0.00 -807.57 8 7

127

Motif group HL_41543.1

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

0.00 -825.22 9 8

128

Motif group HL_68257.1

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

0.00 -1081.93 7 6

129

Motif group HL_92488.1

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

0.00 -1179.89 12 11

130

Motif group HL_86109.1

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

0.00 -1224.32 9 7

131

Motif group HL_93438.2

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

0.00 -1282.96 6 5

132

Motif group HL_60266.1

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

0.00 -1286.15 7 6

133

Motif group HL_02581.1

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

0.00 -1303.29 11 9

tRNA D-loop

134

Motif group HL_67079.1

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

0.00 -1313.09 8 6

135

Motif group HL_13971.1

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

0.00 -1407.81 11 10

136

Motif group HL_90620.1

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

0.00 -1411.77 7 6

137

Motif group HL_08602.1

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

0.00 -1456.26 10 9

138

Motif group HL_68767.1

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

0.00 -1492.87 9 7

tRNA D-loop

139

Motif group HL_02887.3

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

0.00 -1563.47 7 6

T-loop with 3 stacked bulged bases

140

Motif group HL_23509.1

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

0.00 -1650.53 9 8

141

Motif group HL_05304.3

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

0.00 -1666.84 9 7

142

Motif group HL_86012.1

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

0.00 -1671.79 7 6

T-loop with unstacked turn

143

Motif group HL_91939.2

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

0.00 -1681.22 8 6

144

Motif group HL_81545.2

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

0.00 -1708.43 6 5

145

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -1710.63 8 6

146

Motif group HL_36335.1

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

0.00 -1767.02 7 5

147

Motif group HL_49941.1

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

0.00 -1786.49 9 7

tRNA D-loop

148

Motif group HL_50860.2

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

0.00 -1856.84 5 4

149

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -1873.09 7 6

150

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -1876.27 7 6

151

Motif group HL_16991.1

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

0.00 -1899.94 9 8

G-quadruplex fragment

152

Motif group HL_53504.3

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

0.00 -1911.80 7 5

153

Motif group HL_20167.2

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

0.00 -1962.02 5 4

154

Motif group HL_61996.2

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

0.00 -1968.16 6 5

155

Motif group HL_26934.1

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

0.00 -1989.84 6 5

156

Motif group HL_20743.5

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

0.00 -2022.68 6 4

157

Motif group HL_28252.8

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

0.00 -2071.34 5 4

T-loop with 2 stacked bulged bases

158

Motif group HL_97756.2

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

0.00 -2138.28 11 10

159

Motif group HL_57863.1

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

0.00 -2167.20 7 5

G-quadruplex fragment

160

Motif group HL_06226.4

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

0.00 -2206.08 7 6

161

Motif group HL_25847.2

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

0.00 -2261.70 7 6

162

Motif group HL_98252.1

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

0.00 -2261.82 9 7

163

Motif group HL_18978.1

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

0.00 -2274.82 8 7

164

Motif group HL_88205.2

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

0.00 -2341.02 6 5

165

Motif group HL_02483.1

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

0.00 -2407.15 8 7

166

Motif group HL_04171.7

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

0.00 -2441.27 8 6

167

Motif group HL_07480.2

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

0.00 -2459.66 8 7

168

Motif group HL_89881.5

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

0.00 -2478.15 8 7

169

Motif group HL_45785.1

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

0.00 -2505.97 9 8

170

Motif group HL_75293.5

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

0.00 -2507.92 6 5

171

Motif group HL_10456.1

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

0.00 -2517.73 14 12

172

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 -2640.16 15 13

173

Motif group HL_73255.1

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

0.00 -2679.63 8 6

174

Motif group HL_87463.1

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

0.00 -2754.30 7 6

175

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 -2864.27 16 14

176

Motif group HL_23010.1

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

0.00 -2918.51 8 6

177

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 -2959.96 16 14

178

Motif group HL_60293.1

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

0.00 -3009.08 18 16

G-quadruplex

179

Motif group HL_34964.1

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

0.00 -3010.40 8 7

180

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 -3025.83 19 17

G-quadruplex

181

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 -3034.56 20 18

G-quadruplex

182

Motif group HL_53454.2

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

0.00 -3049.62 6 5

183

Motif group HL_93616.2

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

0.00 -3263.35 8 7

tRNA D-loop

184

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 -3271.95 19 17

185

Motif group HL_85434.1

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

0.00 -3326.30 8 6

186

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 -3378.06 34 33

187

Motif group HL_66482.1

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

0.00 -3386.58 14 12

188

Motif group HL_80599.2

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

0.00 -3417.82 7 5

189

Motif group HL_21372.1

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

0.00 -3457.19 6 5

190

Motif group HL_93383.1

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

0.00 -3526.87 6 4

191

Motif group HL_73183.1

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

0.00 -3600.99 11 10

Pseudoknot geometry with G-bulge

192

Motif group HL_33074.4

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

0.00 -3605.44 10 8

U1 small nuclear ribonucleoprotein A binding hairpin

193

Motif group HL_32735.2

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

0.00 -3637.26 5.5 4

194

Motif group HL_85461.1

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

0.00 -3670.50 15 14

195

Motif group HL_25061.1

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

0.00 -3681.63 7 5

196

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 -3687.17 13 11

197

Motif group HL_11542.1

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

0.00 -3722.09 10 8

198

Motif group HL_06059.6

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

0.00 -3797.90 5 4

tRNA anticodon loop

199

Motif group HL_29129.3

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

0.00 -3887.00 7 6

200

Motif group HL_20751.2

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

0.00 -3897.92 10 9

201

Motif group HL_99769.3

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

0.00 -3929.93 8 7

202

Motif group HL_88364.2

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

0.00 -4135.40 13 12

203

Motif group HL_07903.1

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

0.00 -4197.97 11 10

204

Motif group HL_50851.1

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

0.00 -4208.42 10 9

G-quadruplex fragment

205

Motif group HL_04725.1

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

0.00 -4517.57 9 8

206

Motif group HL_63355.1

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

0.00 -4555.72 10 9

207

Motif group HL_24792.1

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

0.00 -4560.05 8 7

208

Motif group HL_31581.6

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

0.00 -4609.90 10 8

209

Motif group HL_23115.1

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

0.00 -4610.23 9 7

tRNA D-loop

210

Motif group HL_88558.1

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

0.00 -4640.82 8 7

211

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.00 -4658.03 5 4

Mini UNCG

212

Motif group HL_97733.1

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

0.00 -4687.91 8 7

213

Motif group HL_67407.5

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

0.00 -4701.50 7 6

214

Motif group HL_50779.4

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

0.00 -4770.15 6 5

215

Motif group HL_91503.7

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

0.00 -4779.36 7 6

216

Motif group HL_64292.1

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

0.00 -4797.55 12 11

217

Motif group HL_81312.1

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

0.00 -4815.43 9 7

218

Motif group HL_72628.1

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

0.00 -4831.32 6 4

219

Motif group HL_12870.1

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

0.00 -4845.53 10 8

220

Motif group HL_80411.1

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

0.00 -4846.78 9 7

tRNA D-loop

221

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -4848.58 5 5

222

Motif group HL_29762.1

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

0.00 -4895.76 7 6

223

Motif group HL_08510.1

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

0.00 -4925.77 8 7

224

Motif group HL_19210.3

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

0.00 -4947.15 7 5

225

Motif group HL_15118.1

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

0.00 -5046.97 10 8

226

Motif group HL_55305.1

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

0.00 -5055.11 8 7

227

Motif group HL_01255.1

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

0.00 -5098.73 8 7

228

Motif group HL_94376.1

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

0.00 -5119.30 8 6

Pseudoknot geometry

229

Motif group HL_93135.1

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

0.00 -5142.12 9 7

Pseudoknot

230

Motif group HL_55436.1

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

0.00 -5161.68 6 5

231

Motif group HL_70751.1

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

0.00 -5295.72 8 6

232

Motif group HL_85367.2

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

0.00 -5301.47 5 4

233

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -5304.56 5 4

234

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -5319.22 5 4

235

Motif group HL_69139.1

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

0.00 -5393.55 8 7

236

Motif group HL_36684.4

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

0.00 -5445.97 7 6

237

Motif group HL_47732.1

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

0.00 -5484.23 9 7

238

Motif group HL_50418.1

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

0.00 -5560.32 7 6

239

Motif group HL_68572.1

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

0.00 -5563.51 10 8

240

Motif group HL_35677.3

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

0.00 -5575.29 7 5

241

Motif group HL_74292.1

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

0.00 -5635.23 7 5

242

Motif group HL_29958.1

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

0.00 -5770.58 11 10

243

Motif group HL_99867.1

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

0.00 -6264.27 6 5

244

Motif group HL_99040.1

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

0.00 -6297.81 6 5

245

Motif group HL_77600.2

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

0.00 -6574.75 5 4

246

Motif group HL_20781.1

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

0.00 -6722.94 8 6

247

Motif group HL_80241.1

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

0.00 -6947.67 6 4

248

Motif group HL_78197.1

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

0.00 -7687.30 5 4

249

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -7711.80 6 5

250

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -7906.36 7 6

251

Motif group HL_58539.1

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

0.00 -7937.18 12 11

252

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.00 -9999.00 6 5

tRNA D-loop

253

Motif group HL_09260.2

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

0.00 -9999.00 9 7

tRNA D-loop

Coloring options: