RNA 3D Hub

JAR3D Query RF00011-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF00011 maps to these 104 chains: 1NBS|1|A, 1NBS|1|B, 2A64|1|A, 3DHS|1|A, 9OV3|1|A, 9OV6|1|A, 9OV7|1|A, 9OV8|1|A, 9OVB|1|A, 9OVC|1|A, 9OWJ|1|A, 9OWK|1|A, 9OWL|1|A, 9OWM|1|A, 9OWN|1|A, 9OWO|1|A, 9OWP|1|A, 9OWQ|1|A, 9OWS|1|A, 9OWT|1|A, 9OWU|1|A, 9OWV|1|A, 9OWW|1|A, 9OWX|1|A, 9OWY|1|A, 9OY2|1|A, 9OY3|1|A, 9OY4|1|A, 9ZDV|1|A, 9ZF2|1|A, 9ZF3|1|A, 9ZF5|1|A, 9ZF9|1|A, 9ZFC|1|A, 9ZFD|1|A, 9ZGM|1|A, 9ZGN|1|A, 9ZGO|1|A, 9ZGP|1|A, 9ZGQ|1|A, 9ZGR|1|A, 9ZGS|1|A, 9ZGT|1|A, 9ZGU|1|A, 9ZGV|1|A, 9ZGW|1|A, 9ZGX|1|A, 9ZGY|1|A, 9ZGZ|1|A, 9ZH0|1|A, 9ZH1|1|A, 9ZH2|1|A, 9ZH5|1|A, 9ZH7|1|A, 9ZH9|1|A, 9ZHA|1|A, 9ZHB|1|A, 9ZHC|1|A, 9ZHD|1|A, 9ZHE|1|A, 9ZHF|1|A, 9ZHG|1|A, 9ZHI|1|A, 9ZHJ|1|A, 9ZHK|1|A, 9ZHL|1|A, 9ZHO|1|A, 9ZHP|1|A, 9ZHR|1|A, 9ZHS|1|A, 9ZHT|1|A, 9ZHU|1|A, 9ZHV|1|A, 9ZHW|1|A, 9ZHX|1|A, 9ZHZ|1|A, 9ZI0|1|A, 9ZI2|1|A, 9ZI3|1|A, 9ZI4|1|A, 9ZI5|1|A, 9ZI6|1|A, 9ZI7|1|A, 9ZI8|1|A, 9ZI9|1|A, 9ZIB|1|A, 9ZIC|1|A, 9ZID|1|A, 9ZIE|1|A, 9ZIF|1|A, 9ZIG|1|A, 9ZIH|1|A, 9ZII|1|A, 9ZIJ|1|A, 9ZIK|1|A, 9ZIL|1|A, 9ZIM|1|A, 9ZIN|1|A, 9ZIU|1|A, 9ZIV|1|A, 9ZIW|1|A, 9ZIX|1|A, 9ZIY|1|A, 9ZIZ|1|A See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Rfam family RF00011 is part of clan CL00002, which includes Rfam families RF00009, RF00373, RF02357, RF01577, RF00011, RF00010, RF00030 .
There are 130 chains in PDB that we map to these Rfam families: 1NBS|1|A, 1NBS|1|B, 1U9S|1|A, 2A2E|1|A, 2A64|1|A, 3DHS|1|A, 3OK7|1|B, 3OKB|1|B, 3Q1Q|1|B, 3Q1R|1|B, 6AGB|1|A, 6AH3|1|A, 6AHR|1|A, 6AHU|1|A, 6K0A|1|X, 6K0A|1|Y, 6K0B|1|X, 6K0B|1|Y, 6W6V|1|A, 7C79|1|A, 7C7A|1|A, 7DA7|1|C, 7DAS|1|C, 7UO0|1|B, 7UO1|1|B, 7UO2|1|B, 7UO5|1|B, 9OV3|1|A, 9OV6|1|A, 9OV7|1|A, 9OV8|1|A, 9OVB|1|A, 9OVC|1|A, 9OWJ|1|A, 9OWK|1|A, 9OWL|1|A, 9OWM|1|A, 9OWN|1|A, 9OWO|1|A, 9OWP|1|A, 9OWQ|1|A, 9OWS|1|A, 9OWT|1|A, 9OWU|1|A, 9OWV|1|A, 9OWW|1|A, 9OWX|1|A, 9OWY|1|A, 9OY2|1|A, 9OY3|1|A, 9OY4|1|A, 9UH7|1|A, 9UH9|1|A, 9UHA|1|A, 9ZDV|1|A, 9ZF2|1|A, 9ZF3|1|A, 9ZF5|1|A, 9ZF9|1|A, 9ZFC|1|A, 9ZFD|1|A, 9ZGM|1|A, 9ZGN|1|A, 9ZGO|1|A, 9ZGP|1|A, 9ZGQ|1|A, 9ZGR|1|A, 9ZGS|1|A, 9ZGT|1|A, 9ZGU|1|A, 9ZGV|1|A, 9ZGW|1|A, 9ZGX|1|A, 9ZGY|1|A, 9ZGZ|1|A, 9ZH0|1|A, 9ZH1|1|A, 9ZH2|1|A, 9ZH5|1|A, 9ZH7|1|A, 9ZH9|1|A, 9ZHA|1|A, 9ZHB|1|A, 9ZHC|1|A, 9ZHD|1|A, 9ZHE|1|A, 9ZHF|1|A, 9ZHG|1|A, 9ZHI|1|A, 9ZHJ|1|A, 9ZHK|1|A, 9ZHL|1|A, 9ZHO|1|A, 9ZHP|1|A, 9ZHR|1|A, 9ZHS|1|A, 9ZHT|1|A, 9ZHU|1|A, 9ZHV|1|A, 9ZHW|1|A, 9ZHX|1|A, 9ZHZ|1|A, 9ZI0|1|A, 9ZI2|1|A, 9ZI3|1|A, 9ZI4|1|A, 9ZI5|1|A, 9ZI6|1|A, 9ZI7|1|A, 9ZI8|1|A, 9ZI9|1|A, 9ZIB|1|A, 9ZIC|1|A, 9ZID|1|A, 9ZIE|1|A, 9ZIF|1|A, 9ZIG|1|A, 9ZIH|1|A, 9ZII|1|A, 9ZIJ|1|A, 9ZIK|1|A, 9ZIL|1|A, 9ZIM|1|A, 9ZIN|1|A, 9ZIU|1|A, 9ZIV|1|A, 9ZIW|1|A, 9ZIX|1|A, 9ZIY|1|A, 9ZIZ|1|A . See them at RNA 3D Hub by filtering on Rfam family, clan, or chain.

Loop 29 Hairpin loop

Column numbers: 511-548 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    A--------------CCUA-------------------   28

    
    U--------------CCUA------------------G    4

    
    ---------------GAAA-------------------    4

    
    G--------------CCUA-------------------    3

    
    U--------------CCUA-------------------    3

    
    ---------------GCAA-------------------    3

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

    
    CAGUGUG--------ACUA------GUGCACGUGAUGA    2

    
    GC-------------CUGA-------------------    2

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

    
    ---------------UUUU-------------------    2

    
    C--------------AGUACAACUAGUGUACGUUAUGA    1

    
    CAGU-----------GUAA---CUAGUACACAUUAUGA    1

    
    G--------------AGUGUUUCUAGUACACGUUAGCA    1

    
    G--------------AGGC---UUAGCAGCCGACGGCA    1

    
    GAGG-----------CUUA------GCAGCCGACGGCA    1

    
    GAGG-----------GAUA------CGUCCCGCUUGCA    1

    
    AAGG-----------UUGA-------CCACCGUUUGCA    1

    
    G--------------AGAU----GACCCAUCGCUUGCA    1

    
    G--------------AGGC----GAAAAGCCGUUGGCA    1

    
    G--------------AGGC----UCAUCACCGUUUGUA    1

    
    GAGG-----------UUCA-------UCACCGUUUGUA    1

    
    GAGGCG---------CAAA---------GCCGCUUGCA    1

    
    GAGGUG---------AUGA---------GCCGUUUGCA    1

    
    G--------------AGAC-----UCAGGUCGAUUGCA    1

    
    G--------------AGGC-----GAAAGCCGCUUGCA    1

    
    G--------------AGGC-----GUGGGCCGUUUGCA    1

    
    G--------------AGGC-----GUGGGCCGUUUGUA    1

    
    GAGAU----------UAAA---------AUCGUUUGCA    1

    
    GAGGCGUGGGCCGUUUGUA-------------------    1

    
    GAGGCUGGGAAG---CCAA----------------GAA    1

    
    GAGGCUGGGAAG---CCUA----------------GAA    1

    
    GAGGG----------UCAA---------ACCGUUUGCA    1

    
    GAGGCGCAAGCUGU-UUGA-------------------    1

    
    C--------------GUUU---------GCCUGAAACG    1

    
    A--------------UUUU-----------CCUGAGAA    1

    
    C--------------AGAC-----------CCUGUACU    1

    
    A--------------UUUU------------CCUGAAU    1

    
    U--------------UCUC-------------CCUGGA    1

    
    UAUGCCU--------GAUA-------------------    1

    
    A--------------UUAA--------------CCAAA    1

    
    C--------------ACGA--------------AUGUG    1

    
    CAUUGA---------UAUG-------------------    1

    
    U--------------ACCC--------------UGUAC    1

    
    U--------------ACCC--------------UGUAU    1

    
    U--------------GUGC--------------CUAGU    1

    
    U--------------UCUC--------------CCUGG    1

    
    U--------------UUCC--------------UGAAG    1

    
    UUUCCU---------GAAG-------------------    1

    
    G--------------UUCC---------------UAGU    1

    
    GAAC-----------CUAG-------------------    1

    
    GAGC-----------CUAG-------------------    1

    
    GGAC-----------CUAG-------------------    1

    
    GUGC-----------CUAG-------------------    1

    
    UUGC-----------CAAG-------------------    1

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

    
    CA-------------ACCA-------------------    1

    
    UA-------------CCUA-------------------    1

    
    C--------------CCUA-------------------    1

    
    C--------------GCCA-------------------    1

    
    G--------------AUAA-------------------    1

    
    G--------------GCCG-------------------    1

    
    U--------------ACCU-------------------    1

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

    
    ---------------AUAU-------------------    1

    
    ---------------GAGA-------------------    1

    
    ---------------UUUA-------------------    1

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

    
    -----------------UU-------------------    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_70782.2

Basepair signature:
cWW-F

41.23 -3272.50 3 3

2

Motif group HL_48417.5

Basepair signature:
cWW-F-F

38.60 -1537.33 3 2

3

Motif group HL_56131.2

Basepair signature:
cWW-F-F

37.72 -2409.68 3 3

4

Motif group HL_22135.1

Basepair signature:
cWW-F-F

35.09 -3834.67 3 3

5

Motif group HL_56334.1

Basepair signature:
cWW-F

19.30 -3470.82 2.5 2

Mini UNCG

6

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

17.54 -2913.06 4 2

7

Motif group HL_13189.1

Basepair signature:
cWW-F-F

14.04 -2546.85 4 2

8

Motif group HL_48778.2

Basepair signature:
cWW-F

13.16 -3297.24 2 2

Mini UNCG

9

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

8.77 -2845.24 3 2

10

Motif group HL_38168.1

Basepair signature:
cWW-F

7.89 -3304.49 4 3

11

Motif group HL_65794.5

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

7.89 -6855.60 3 2

Pseudoknot geometry

12

Motif group HL_37824.7

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

7.02 -1703.63 3 2

GNRA

13

Motif group HL_75660.5

Basepair signature:
cWW-F

6.14 -3308.65 3 2

14

Motif group HL_32346.4

Basepair signature:
cWW-F

6.14 -3500.24 3 3

15

Motif group HL_94980.1

Basepair signature:
cWW-F-F

6.14 -3974.79 4 4

16

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

4.39 -3223.65 4 3

tRNA D-loop

17

Motif group HL_78677.1

Basepair signature:
cWW-F-F

4.39 -4302.53 4 2

18

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

4.39 -4775.79 4 2

19

Motif group HL_46501.1

Basepair signature:
cWW-cWS

3.51 -2753.44 4 2

20

Motif group HL_13963.3

Basepair signature:
cWW-F-F

3.51 -2908.46 5 3

21

Motif group HL_50006.2

Basepair signature:
cWW-F-F

3.51 -2919.81 5 3

22

Motif group HL_47787.2

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

3.51 -2940.83 4 3

23

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

3.51 -3046.90 4 3

24

Motif group HL_69752.2

Basepair signature:
cWW-F

3.51 -3322.58 4 3

25

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

3.51 -4773.63 5 4

26

Motif group HL_52953.3

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

3.51 -7155.58 4 2

27

Motif group HL_49941.1

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

2.63 -693.81 6 5

tRNA D-loop

28

Motif group HL_93616.2

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

2.63 -2470.62 6 5

tRNA D-loop

29

Motif group HL_80411.1

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

2.63 -4598.64 7 6

tRNA D-loop

30

Motif group HL_26934.1

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

1.75 -631.58 5 4

31

Motif group HL_04642.1

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

1.75 -673.21 6 5

tRNA D-loop

32

Motif group HL_37344.1

Basepair signature:
cWW-F-F

1.75 -2239.54 5 4

33

Motif group HL_58224.1

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

1.75 -2327.77 6 5

34

Motif group HL_21372.1

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

1.75 -2397.29 5 4

35

Motif group HL_99769.3

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

1.75 -2921.37 8 7

36

Motif group HL_91503.7

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

1.75 -4118.84 7 5

37

Motif group HL_81100.2

Basepair signature:
cWW

1.75 -5620.59 4 3

38

Motif group HL_99867.1

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

1.75 -5680.73 7 6

39

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

0.88 -270.70 4 3

40

Motif group HL_04171.7

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

0.88 -332.34 6 5

41

Motif group HL_57863.1

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

0.88 -830.71 7 6

G-quadruplex fragment

42

Motif group HL_75293.5

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

0.88 -838.80 6 4

43

Motif group HL_87553.1

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

0.88 -1225.38 4 3

44

Motif group HL_45785.1

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

0.88 -1246.59 7 5

45

Motif group HL_87463.1

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

0.88 -1481.86 8 6

46

Motif group HL_85434.1

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

0.88 -2453.57 7 5

47

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

0.88 -2485.26 4 2

Fab BL3-6 binding hairpin with tSW

48

Motif group HL_59843.1

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

0.88 -2521.06 4 3

49

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.88 -2864.17 3 2

UNCG

50

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

0.88 -2929.41 4 3

51

Motif group HL_93535.1

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

0.88 -2958.97 4 3

52

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

0.88 -2969.41 4 3

53

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

0.88 -2995.13 5 3

54

Motif group HL_66103.1

Basepair signature:
cWW-F-F

0.88 -3021.58 4 3

55

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

0.88 -3057.34 5 3.5

56

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

0.88 -4589.88 4 2

Pseudoknot geometry with 3' bulge

57

Motif group HL_80008.1

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

0.88 -4601.06 7 5

58

Motif group HL_30680.3

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

0.88 -5039.01 4 3

Pseudoknot geometry

59

Motif group HL_50418.1

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

0.88 -5498.05 7 5

60

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.88 -5772.29 5 4

61

Motif group HL_09260.2

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

0.88 -9999.00 6.5 5

tRNA D-loop

62

Motif group HL_68257.1

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

0.00 -173.47 6 5

63

Motif group HL_41543.1

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

0.00 -222.15 8 7

64

Motif group HL_41902.1

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

0.00 -226.60 9 9

65

Motif group HL_08602.1

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

0.00 -228.83 8 7

66

Motif group HL_67079.1

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

0.00 -231.72 7 5

67

Motif group HL_93438.2

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

0.00 -241.23 6 5

68

Motif group HL_74055.2

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

0.00 -243.04 10 9

69

Motif group HL_07583.1

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

0.00 -249.99 10 9

70

Motif group HL_81545.2

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

0.00 -264.05 8 6

71

Motif group HL_20167.2

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

0.00 -265.87 5 4

72

Motif group HL_68767.1

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

0.00 -283.51 9 8

tRNA D-loop

73

Motif group HL_14757.1

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

0.00 -286.32 13 12

74

Motif group HL_36335.1

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

0.00 -299.26 8 7

75

Motif group HL_53504.3

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

0.00 -300.60 7 6

76

Motif group HL_41464.2

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

0.00 -328.46 7 5

77

Motif group HL_02887.3

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

0.00 -432.38 7 5

T-loop with 3 stacked bulged bases

78

Motif group HL_86012.1

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

0.00 -434.15 7 5

T-loop with unstacked turn

79

Motif group HL_23509.1

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

0.00 -441.77 9 8

80

Motif group HL_92488.1

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

0.00 -441.80 11 10

81

Motif group HL_70658.1

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

0.00 -451.97 9 8

82

Motif group HL_81205.3

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

0.00 -453.05 10 9

83

Motif group HL_74379.3

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

0.00 -456.66 9 7

84

Motif group HL_86109.1

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

0.00 -457.96 10 8

85

Motif group HL_84847.1

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

0.00 -466.01 10 9

86

Motif group HL_73247.1

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

0.00 -468.83 10 9

Pseudoknot geometry

87

Motif group HL_98870.1

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

0.00 -488.07 12 11

88

Motif group HL_91641.1

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

0.00 -488.29 12 11

89

Motif group HL_90620.1

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

0.00 -491.96 7 5.5

90

Motif group HL_51921.1

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

0.00 -499.37 16 15

91

Motif group HL_50860.2

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

0.00 -507.15 6 5

92

Motif group HL_61996.2

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

0.00 -531.22 7 5

93

Motif group HL_20743.5

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

0.00 -535.87 6 5

94

Motif group HL_60266.1

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

0.00 -541.94 9 7

95

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -545.41 7 6

96

Motif group HL_13971.1

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

0.00 -548.15 10 8

97

Motif group HL_98864.1

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

0.00 -618.68 6 4

T-loop with unstacked turn

98

Motif group HL_16991.1

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

0.00 -654.67 9 9

G-quadruplex fragment

99

Motif group HL_98252.1

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

0.00 -736.51 8 7

100

Motif group HL_78347.4

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

0.00 -737.24 4 3

101

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

0.00 -739.82 6 5

102

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -743.96 7 6

103

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -778.98 7 6

104

Motif group HL_83808.4

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

0.00 -803.06 6 5

Pseudoknot

105

Motif group HL_77436.5

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

0.00 -818.14 5 4

T-loop related

106

Motif group HL_04259.3

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

0.00 -848.86 5 3

GNRA with extra cWW

107

Motif group HL_97756.2

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

0.00 -850.62 10 9

108

Motif group HL_73266.9

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

0.00 -851.26 5 4

109

Motif group HL_28252.8

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

0.00 -874.75 6 5

T-loop with 2 stacked bulged bases

110

Motif group HL_84299.4

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

0.00 -903.57 6 4

111

Motif group HL_64690.6

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

0.00 -962.66 6 4

112

Motif group HL_02483.1

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

0.00 -1023.29 8 7

113

Motif group HL_02581.1

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

0.00 -1037.19 10 9

tRNA D-loop

114

Motif group HL_05304.3

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

0.00 -1080.72 9 9

115

Motif group HL_91939.2

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

0.00 -1097.92 8 6

116

Motif group HL_06226.4

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

0.00 -1099.72 8 7

117

Motif group HL_77082.1

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

0.00 -1102.31 4.5 3

Pseudoknot geometry

118

Motif group HL_28075.1

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

0.00 -1184.72 5 4

119

Motif group HL_81538.2

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

0.00 -1192.05 5 4

GNRA with tandem sheared

120

Motif group HL_01609.3

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

0.00 -1214.59 6 4

T-loop with 2 bulged bases not stacked

121

Motif group HL_89881.5

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

0.00 -1233.13 7 6

122

Motif group HL_18978.1

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

0.00 -1311.61 8 6

123

Motif group HL_53454.2

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

0.00 -1375.16 7 5

124

Motif group HL_13529.1

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

0.00 -1379.55 5 4

125

Motif group HL_23010.1

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

0.00 -1436.02 7 6

126

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.00 -1553.21 6 5

tRNA D-loop

127

Motif group HL_18565.1

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

0.00 -1599.03 6 4

128

Motif group HL_88205.2

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

0.00 -1718.64 6 4.5

129

Motif group HL_07480.2

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

0.00 -1798.38 8 6

130

Motif group HL_25847.2

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

0.00 -1871.02 7 6

131

Motif group HL_73255.1

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

0.00 -1889.32 6 5

132

Motif group HL_10540.1

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

0.00 -1929.90 5 3.5

133

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.00 -1973.06 5 3

tRNA D-loop

134

Motif group HL_06059.6

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

0.00 -2046.29 4 3

tRNA anticodon loop

135

Motif group HL_34964.1

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

0.00 -2208.15 8 7

136

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

0.00 -2273.75 5 4

Other HL

137

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.00 -2326.05 5 4

138

Motif group HL_25061.1

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

0.00 -2354.26 7 6

139

Motif group HL_89893.1

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

0.00 -2376.25 6 5

140

Motif group HL_42046.2

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

0.00 -2385.52 5 3

141

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

0.00 -2398.69 5 4

tRNA anticodon loop with synthetase

142

Motif group HL_47854.1

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

0.00 -2430.94 6.5 5

143

Motif group HL_04641.1

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

0.00 -2441.15 7 6

144

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 -2517.76 14 13

145

Motif group HL_30068.2

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

0.00 -2535.91 4 3

146

Motif group HL_15802.1

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

0.00 -2541.42 6 5

147

Motif group HL_27483.1

Basepair signature:
cWW-F

0.00 -2565.57 4 3

148

Motif group HL_66482.1

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

0.00 -2566.52 13 12

149

Motif group HL_10456.1

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

0.00 -2570.85 15 13

150

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

0.00 -2636.59 6 4

151

Motif group HL_56676.1

Basepair signature:
cWW-F-F

0.00 -2639.26 5 3

152

Motif group HL_80599.2

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

0.00 -2688.88 6 4

153

Motif group HL_33074.4

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

0.00 -2763.61 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

154

Motif group HL_33983.1

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

0.00 -2776.63 6 4

155

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.00 -2776.99 4 3

156

Motif group HL_93383.1

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

0.00 -2826.52 5 4

157

Motif group HL_20535.2

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

0.00 -2846.77 5 4

158

Motif group HL_32735.2

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

0.00 -2856.48 5 4

159

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

0.00 -2905.14 5 3

160

Motif group HL_97917.2

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

0.00 -2942.30 6 4

161

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

0.00 -2952.31 4 3

162

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

0.00 -2955.37 5 3

163

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

0.00 -3005.34 4 2.5

164

Motif group HL_11542.1

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

0.00 -3026.95 9 8

165

Motif group HL_57875.1

Basepair signature:
cWW-F-F

0.00 -3032.93 4 2

166

Motif group HL_37369.2

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

0.00 -3067.29 4 3

167

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 -3073.20 13 12

168

Motif group HL_71391.1

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

0.00 -3085.39 5 3

169

Motif group HL_20751.2

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

0.00 -3089.25 10 9

170

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 -3107.46 16 14

171

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 -3111.75 16 14

172

Motif group HL_85461.1

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

0.00 -3143.23 15 14

173

Motif group HL_59330.1

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

0.00 -3145.42 6 4

174

Motif group HL_73183.1

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

0.00 -3152.29 11 10

Pseudoknot geometry with G-bulge

175

Motif group HL_60293.1

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

0.00 -3193.98 18 17

G-quadruplex

176

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 -3242.72 19 18

G-quadruplex

177

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.00 -3252.13 6 4

T-loop with unstacked turn

178

Motif group HL_25967.2

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

0.00 -3267.67 5 3

179

Motif group HL_29129.3

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

0.00 -3267.85 9 7

180

Motif group HL_07903.1

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

0.00 -3277.01 11 10

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 -3278.93 21 19

G-quadruplex

182

Motif group HL_63355.1

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

0.00 -3325.66 11 9

183

Motif group HL_31581.6

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

0.00 -3487.85 8 7

184

Motif group HL_02817.2

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

0.00 -3506.07 5 4

185

Motif group HL_55195.3

Basepair signature:
cWW-F

0.00 -3519.06 4 2

186

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 -3572.88 20 18

187

Motif group HL_10453.3

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

0.00 -3620.49 4 3

tRNA anticodon loop

188

Motif group HL_88558.1

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

0.00 -3660.08 7 6

189

Motif group HL_16398.2

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

0.00 -3662.86 9 8

190

Motif group HL_00914.1

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

0.00 -3676.02 6 4

191

Motif group HL_81312.1

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

0.00 -3691.84 9 8

192

Motif group HL_38649.1

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

0.00 -3693.69 7 6

193

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 -3738.83 35 34

194

Motif group HL_88364.2

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

0.00 -3739.01 11 11

195

Motif group HL_50851.1

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

0.00 -3805.68 9 8

G-quadruplex fragment

196

Motif group HL_64292.1

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

0.00 -3838.97 12 11

197

Motif group HL_01255.1

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

0.00 -3884.69 8 6

198

Motif group HL_85993.1

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

0.00 -4023.90 6 4

199

Motif group HL_78284.1

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

0.00 -4060.55 9 7

200

Motif group HL_04725.1

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

0.00 -4089.12 8 7

201

Motif group HL_51447.1

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

0.00 -4119.02 6 4

202

Motif group HL_24792.1

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

0.00 -4171.24 7 5

203

Motif group HL_47732.1

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

0.00 -4216.22 9 8

204

Motif group HL_31585.4

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

0.00 -4227.04 5 3

Purine riboswitch

205

Motif group HL_67407.5

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

0.00 -4234.67 7 5

206

Motif group HL_69139.1

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

0.00 -4249.10 7 6

207

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.00 -4249.46 5 4

Mini UNCG

208

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -4322.57 4 3

209

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -4350.43 5 4

210

Motif group HL_15574.1

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

0.00 -4357.61 5 4

211

Motif group HL_35677.3

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

0.00 -4379.99 6 4

212

Motif group HL_23115.1

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

0.00 -4384.27 8 6

tRNA D-loop

213

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -4457.43 4 3

214

Motif group HL_19210.3

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

0.00 -4471.09 8 6

215

Motif group HL_08510.1

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

0.00 -4489.57 6 5

216

Motif group HL_97733.1

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

0.00 -4535.06 7 5

217

Motif group HL_55305.1

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

0.00 -4540.15 9 7

218

Motif group HL_15118.1

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

0.00 -4573.84 8 7

219

Motif group HL_50779.4

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

0.00 -4610.07 6 5

220

Motif group HL_72628.1

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

0.00 -4624.57 5 4

221

Motif group HL_94376.1

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

0.00 -4643.15 8 7

Pseudoknot geometry

222

Motif group HL_29762.1

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

0.00 -4672.90 8 7

223

Motif group HL_55436.1

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

0.00 -4673.52 7 5

224

Motif group HL_29958.1

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

0.00 -4721.26 10 9

225

Motif group HL_12870.1

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

0.00 -4766.84 9 7

226

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

0.00 -4788.07 5 3

227

Motif group HL_68572.1

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

0.00 -4794.54 9 8

228

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -4824.13 5 3

229

Motif group HL_77600.2

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

0.00 -4838.45 5 4

230

Motif group HL_93135.1

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

0.00 -4894.43 7 6

Pseudoknot

231

Motif group HL_38046.1

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

0.00 -5080.44 7 5

232

Motif group HL_74292.1

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

0.00 -5122.96 8 6

233

Motif group HL_85367.2

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

0.00 -5149.35 5 4

234

Motif group HL_70751.1

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

0.00 -5249.65 8 7

235

Motif group HL_83632.1

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

0.00 -5303.27 5 3

tRNA anticodon loop

236

Motif group HL_59735.5

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

0.00 -5343.08 5 3

237

Motif group HL_36684.4

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

0.00 -5391.42 7 6

238

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -5610.90 4 3.5

239

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.00 -5900.06 6 5

240

Motif group HL_99040.1

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

0.00 -5998.61 5 4

241

Motif group HL_22622.1

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

0.00 -6041.75 6 5

242

Motif group HL_20781.1

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

0.00 -6084.85 8 7

243

Motif group HL_42998.2

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

0.00 -6234.28 6 4

244

Motif group HL_80241.1

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

0.00 -6694.00 6 5

245

Motif group HL_39243.1

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

0.00 -6711.83 6 4

246

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -6828.56 7 6

247

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -7023.98 6 4

248

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

0.00 -7077.68 5 4

249

Motif group HL_58539.1

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

0.00 -7166.30 12 11

250

Motif group HL_28791.1

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

0.00 -7176.51 5 3

251

Motif group HL_78197.1

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

0.00 -7461.42 5 3.5

252

Motif group HL_93324.4

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

0.00 -7847.98 4 4

Pseudoknot geometry

253

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.00 -9999.00 6 4

tRNA D-loop

Coloring options: