RNA 3D Hub

JAR3D Query RF03087-3.98 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 27 Hairpin loop

Column numbers: 781-800 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    A----GAAA----------U   94

    
    A----GGGA----------U   16

    
    G----GAAA----------C   13

    
    ACU--GAAU--------AAG   11

    
    AA---GAAA---------UU   11

    
    -----GAAA-----------   10

    
    U----GAAA----------A    9

    
    UA---GAAA---------UA    7

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

    
    AG---GAAA---------UG    6

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

    
    C----GAAA----------G    6

    
    GA---GAAA---------UC    5

    
    UG---GAAA---------CA    5

    
    G----GUAA----------C    5

    
    GUA--GAAA--------UGC    4

    
    GC---GAUCAAAA-----GC    3

    
    CA---GAAA---------UG    3

    
    UC---GUAA---------GU    3

    
    U----UAAA----------A    3

    
    -----GUAAU----------    3

    
    GCA--GAAA--------UAC    2

    
    AA---GAAA---------CU    2

    
    AA---GUGA---------UU    2

    
    CA---GUAA---------UG    2

    
    UA---GAAA---------UG    2

    
    UG---GAAA---------CG    2

    
    UG---GUGA---------CG    2

    
    UU---GAAA---------AA    2

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

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

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

    
    AAAUCAGCAGUUAA-GGUUU    1

    
    G----GAAUUGAAAA----C    1

    
    ACU--GAAUA-------AG-    1

    
    AUA--GAAA--------UAU    1

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

    
    GCU--AUCA---------GC    1

    
    UA---UAAAA--------UA    1

    
    UGC--GAAA---------GC    1

    
    UU---UAAAA--------GA    1

    
    A----CUAAA--------GU    1

    
    AC---GUAA---------GU    1

    
    AG---UAAA---------AU    1

    
    CG---GAAA---------CG    1

    
    CG---GUAA---------CG    1

    
    GA---GACA---------UC    1

    
    GA---GGGA---------UC    1

    
    GC---GAAA---------GC    1

    
    UA---GUAA---------UA    1

    
    UC---GCAA---------GA    1

    
    UG---GACA---------CA    1

    
    UG---GUAA---------CA    1

    
    UG---GUGA---------CA    1

    
    UG---GUGA---------UG    1

    
    UU---GAAA---------GA    1

    
    UU---GAAA---------UG    1

    
    U----AGGAA---------A    1

    
    A----GAUA----------U    1

    
    A----GUGA----------U    1

    
    C----GCAA----------G    1

    
    C----GGAA----------G    1

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

    
    G----ACAA----------C    1

    
    G----GCAA----------C    1

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

    
    -----GUGA-----------    1

    
    Omitted sequenced and counts

    
    --------------------    3
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_50006.2

Basepair signature:
cWW-F-F

67.25 -16.12 3 1

2

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

65.85 -9.10 2 1

3

Motif group HL_75660.5

Basepair signature:
cWW-F

64.81 -195.55 2 1

4

Motif group HL_52953.3

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

64.11 -307.53 2 1

5

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

63.76 -66.37 2 1

tRNA D-loop

6

Motif group HL_65794.5

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

63.76 -155.64 2 1

Pseudoknot geometry

7

Motif group HL_37824.7

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

63.07 -10.99 1 0

GNRA

8

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

63.07 -33.45 2 1

9

Motif group HL_56334.1

Basepair signature:
cWW-F

61.67 -236.12 3 1

Mini UNCG

10

Motif group HL_93535.1

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

59.93 -41.60 3 1

11

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

59.58 -21.49 2 0

12

Motif group HL_59843.1

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

59.23 -54.22 3 1

13

Motif group HL_13963.3

Basepair signature:
cWW-F-F

58.54 -65.41 4 2

14

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

56.45 -621.07 2 1

15

Motif group HL_47787.2

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

52.26 -90.52 2 1

16

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

51.92 -87.84 4 2

17

Motif group HL_56676.1

Basepair signature:
cWW-F-F

51.57 -90.43 3 1

18

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

49.83 -78.65 3 2

19

Motif group HL_97917.2

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

49.48 -68.70 4 2

20

Motif group HL_57875.1

Basepair signature:
cWW-F-F

49.13 -83.18 4 2

21

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

48.78 -52.84 3 2

22

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

47.74 -63.07 4 2

23

Motif group HL_38168.1

Basepair signature:
cWW-F

47.39 -234.17 3 2

24

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

44.60 -93.11 3 2

Fab BL3-6 binding hairpin with tSW

25

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

42.51 -75.82 2 1

26

Motif group HL_04259.3

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

20.56 -53.99 2 2

GNRA with extra cWW

27

Motif group HL_85993.1

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

20.56 -5189.62 3 3

28

Motif group HL_87553.1

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

15.68 -80.99 5 3

29

Motif group HL_77082.1

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

14.63 -57.08 4 2

Pseudoknot geometry

30

Motif group HL_01609.3

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

14.29 -49.36 4 2

T-loop with 2 bulged bases not stacked

31

Motif group HL_20167.2

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

14.29 -54.46 3 3

32

Motif group HL_77436.5

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

14.29 -92.90 3 2

T-loop related

33

Motif group HL_71391.1

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

14.29 -112.73 3 1

34

Motif group HL_48417.5

Basepair signature:
cWW-F-F

11.15 -45.98 3 2

35

Motif group HL_57863.1

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

11.15 -66.22 5 5

G-quadruplex fragment

36

Motif group HL_39243.1

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

11.15 -187.78 3 2

37

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

10.80 -406.54 4 3

T-loop with unstacked turn

38

Motif group HL_28791.1

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

10.45 -396.30 5 3

39

Motif group HL_13189.1

Basepair signature:
cWW-F-F

8.71 -109.20 3 2

40

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

8.01 -66.35 4 2

tRNA D-loop

41

Motif group HL_70782.2

Basepair signature:
cWW-F

7.67 -247.74 4 3

42

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

7.32 -83.35 4 3

43

Motif group HL_50860.2

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

6.97 -53.59 4 3

44

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

6.97 -631.72 3 2

Pseudoknot geometry with 3' bulge

45

Motif group HL_81100.2

Basepair signature:
cWW

6.62 -1549.08 5 3

46

Motif group HL_69752.2

Basepair signature:
cWW-F

5.92 -260.11 4 3

47

Motif group HL_33983.1

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

5.92 -359.89 5 3

48

Motif group HL_56131.2

Basepair signature:
cWW-F-F

5.57 -93.62 5 3

49

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

5.57 -146.18 3 2

UNCG

50

Motif group HL_78197.1

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

4.88 -609.47 5 3

51

Motif group HL_10540.1

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

4.53 -59.76 4 2

52

Motif group HL_66103.1

Basepair signature:
cWW-F-F

4.18 -98.07 4 2

53

Motif group HL_55195.3

Basepair signature:
cWW-F

3.83 -277.02 4 2

54

Motif group HL_78677.1

Basepair signature:
cWW-F-F

3.48 -1003.05 4 2

55

Motif group HL_59735.5

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

3.48 -6906.53 3 1

56

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

2.79 -5637.96 6 5

57

Motif group HL_61996.2

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

2.44 -83.03 5 4

58

Motif group HL_36335.1

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

2.44 -93.04 5 4

59

Motif group HL_41464.2

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

2.09 -62.32 5 3

60

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

2.09 -76.54 3 2

61

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

2.09 -90.18 6 5

62

Motif group HL_20535.2

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

2.09 -99.18 4 3

63

Motif group HL_81545.2

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

2.09 -115.54 6 5

64

Motif group HL_81538.2

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

1.74 -80.48 4 2

GNRA with tandem sheared

65

Motif group HL_18565.1

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

1.74 -85.77 4 3

66

Motif group HL_84299.4

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

1.74 -92.94 5 4

67

Motif group HL_48778.2

Basepair signature:
cWW-F

1.74 -307.62 4 2

Mini UNCG

68

Motif group HL_22622.1

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

1.74 -5288.73 5 4

69

Motif group HL_78347.4

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

1.39 -70.83 5 3

70

Motif group HL_98864.1

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

1.39 -99.80 6 6

T-loop with unstacked turn

71

Motif group HL_46501.1

Basepair signature:
cWW-cWS

1.39 -116.49 4 2

72

Motif group HL_73255.1

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

1.39 -186.83 6 6

73

Motif group HL_06226.4

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

1.39 -329.92 6 6

74

Motif group HL_38046.1

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

1.39 -431.51 5 4

75

Motif group HL_83632.1

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

1.39 -445.53 4 3

tRNA anticodon loop

76

Motif group HL_73266.9

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

1.05 -71.98 4 3

77

Motif group HL_64690.6

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

1.05 -92.13 4 4

78

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

1.05 -141.84 6 5

tRNA D-loop

79

Motif group HL_27483.1

Basepair signature:
cWW-F

1.05 -146.57 5 3

80

Motif group HL_32346.4

Basepair signature:
cWW-F

1.05 -286.64 4 2

81

Motif group HL_31585.4

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

1.05 -582.02 3 2

Purine riboswitch

82

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

1.05 -677.79 4 3

83

Motif group HL_93438.2

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

0.70 -77.89 4 4

84

Motif group HL_89893.1

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

0.70 -89.49 4 3

85

Motif group HL_47854.1

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

0.70 -90.46 5 3

86

Motif group HL_28252.8

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

0.70 -103.57 3 3

T-loop with 2 stacked bulged bases

87

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

0.70 -108.76 4 3

88

Motif group HL_75293.5

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

0.70 -116.63 4 4

89

Motif group HL_80008.1

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

0.70 -181.02 5 3

90

Motif group HL_25061.1

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

0.70 -366.30 6 4

91

Motif group HL_10453.3

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

0.70 -491.12 5 3

tRNA anticodon loop

92

Motif group HL_15574.1

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

0.70 -550.23 4 2

93

Motif group HL_93324.4

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

0.70 -659.51 4 2

Pseudoknot geometry

94

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

0.70 -713.24 6 4

95

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.70 -717.51 4 3

96

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.70 -4699.59 7 5

97

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

0.35 -58.03 4 3

98

Motif group HL_13529.1

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

0.35 -71.34 4 3

99

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

0.35 -85.62 5 4

Other HL

100

Motif group HL_68257.1

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

0.35 -94.63 6 5

101

Motif group HL_30068.2

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

0.35 -98.71 3 2

102

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.35 -123.86 6 5

103

Motif group HL_53504.3

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

0.35 -138.58 5 4

104

Motif group HL_86109.1

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

0.35 -168.11 8 7

105

Motif group HL_72628.1

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

0.35 -187.67 5 3

106

Motif group HL_68767.1

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

0.35 -190.41 8 7

tRNA D-loop

107

Motif group HL_97733.1

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

0.35 -415.26 8 6

108

Motif group HL_53454.2

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

0.35 -424.62 6 4

109

Motif group HL_00914.1

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

0.35 -446.95 4 2

110

Motif group HL_85367.2

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

0.35 -451.01 5 3

111

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.35 -496.37 4 4

112

Motif group HL_42998.2

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

0.35 -540.76 4 2

113

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.35 -617.53 5 3

Mini UNCG

114

Motif group HL_93383.1

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

0.35 -1871.38 6 4

115

Motif group HL_12870.1

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

0.35 -3348.68 9 7

116

Motif group HL_88558.1

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

0.35 -3699.27 7 6

117

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.35 -5740.67 5 5

118

Motif group HL_30680.3

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

0.35 -6791.14 4 3

Pseudoknot geometry

119

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.35 -9999.00 5 4

tRNA D-loop

120

Motif group HL_20743.5

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

0.00 -70.28 5 3

121

Motif group HL_26934.1

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

0.00 -80.30 6 4

122

Motif group HL_02887.3

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

0.00 -82.55 6 5

T-loop with 3 stacked bulged bases

123

Motif group HL_28075.1

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

0.00 -95.62 4 2

124

Motif group HL_86012.1

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

0.00 -98.88 7 5

T-loop with unstacked turn

125

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

0.00 -102.85 4 4

tRNA anticodon loop with synthetase

126

Motif group HL_04642.1

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

0.00 -104.84 7 6

tRNA D-loop

127

Motif group HL_90620.1

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

0.00 -119.15 6 5

128

Motif group HL_83808.4

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

0.00 -127.06 8 7

Pseudoknot

129

Motif group HL_37344.1

Basepair signature:
cWW-F-F

0.00 -129.87 6 4

130

Motif group HL_16991.1

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

0.00 -132.78 8 7

G-quadruplex fragment

131

Motif group HL_04171.7

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

0.00 -133.98 6 6

132

Motif group HL_67079.1

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

0.00 -133.99 6 6

133

Motif group HL_98252.1

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

0.00 -134.28 7 7

134

Motif group HL_41902.1

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

0.00 -134.60 8 7

135

Motif group HL_41543.1

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

0.00 -140.03 8 7

136

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -141.12 6 5

137

Motif group HL_60266.1

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

0.00 -147.55 7 5

138

Motif group HL_74379.3

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

0.00 -149.10 8 7

139

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

0.00 -157.79 5 4

140

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

0.00 -163.11 5 3

141

Motif group HL_70658.1

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

0.00 -166.42 7 7

142

Motif group HL_23509.1

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

0.00 -167.05 8 8

143

Motif group HL_49941.1

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

0.00 -168.30 8 7

tRNA D-loop

144

Motif group HL_25847.2

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

0.00 -168.33 7 6

145

Motif group HL_42046.2

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

0.00 -168.59 5 3

146

Motif group HL_85434.1

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

0.00 -168.93 7 5

147

Motif group HL_29129.3

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

0.00 -176.20 7 5

148

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -176.39 7 6

149

Motif group HL_07583.1

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

0.00 -193.96 8 8

150

Motif group HL_81205.3

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

0.00 -194.56 8 8

151

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.00 -195.26 5 4

152

Motif group HL_84847.1

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

0.00 -196.19 9 8

153

Motif group HL_93616.2

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

0.00 -200.36 7 6

tRNA D-loop

154

Motif group HL_74055.2

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

0.00 -209.49 10 9

155

Motif group HL_08602.1

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

0.00 -212.88 10 9

156

Motif group HL_21372.1

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

0.00 -218.60 5 4

157

Motif group HL_73247.1

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

0.00 -238.55 10 9

Pseudoknot geometry

158

Motif group HL_98870.1

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

0.00 -257.62 10 9

159

Motif group HL_91641.1

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

0.00 -272.17 11 11

160

Motif group HL_14757.1

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

0.00 -290.40 13 12

161

Motif group HL_88205.2

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

0.00 -297.23 4 4

162

Motif group HL_13971.1

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

0.00 -303.31 11 9

163

Motif group HL_87463.1

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

0.00 -310.56 6 5

164

Motif group HL_89881.5

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

0.00 -327.59 7 6

165

Motif group HL_02483.1

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

0.00 -330.58 8 6

166

Motif group HL_18978.1

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

0.00 -332.83 8 6

167

Motif group HL_45785.1

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

0.00 -344.39 9 8

168

Motif group HL_58224.1

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

0.00 -355.15 7 6

169

Motif group HL_51921.1

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

0.00 -356.44 15 15

170

Motif group HL_05304.3

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

0.00 -357.02 7 7

171

Motif group HL_04641.1

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

0.00 -359.83 6 5

172

Motif group HL_91939.2

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

0.00 -360.19 8 6

173

Motif group HL_23010.1

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

0.00 -364.99 7 6

174

Motif group HL_99040.1

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

0.00 -365.96 6 4

175

Motif group HL_15802.1

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

0.00 -370.09 6 6

176

Motif group HL_07480.2

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

0.00 -386.90 7 7

177

Motif group HL_99769.3

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

0.00 -395.19 7 7

178

Motif group HL_92488.1

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

0.00 -419.95 11 11

179

Motif group HL_02581.1

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

0.00 -428.34 10 9

tRNA D-loop

180

Motif group HL_08510.1

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

0.00 -435.30 6 6

181

Motif group HL_02817.2

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

0.00 -445.74 4 3

182

Motif group HL_55436.1

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

0.00 -446.19 6 5

183

Motif group HL_34964.1

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

0.00 -449.20 7 6

184

Motif group HL_11542.1

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

0.00 -455.41 8 7

185

Motif group HL_37369.2

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

0.00 -460.91 5 3

186

Motif group HL_38649.1

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

0.00 -469.74 7 6

187

Motif group HL_25967.2

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

0.00 -471.15 5 4

188

Motif group HL_06059.6

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

0.00 -482.41 3 3

tRNA anticodon loop

189

Motif group HL_97756.2

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

0.00 -490.99 10 10

190

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -758.00 6 4

191

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.00 -1035.78 4 3

192

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -1063.59 6 4

193

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -1073.02 6 4

194

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -1266.71 6 4

195

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -1472.87 5 3

196

Motif group HL_33074.4

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

0.00 -2687.10 8 8

U1 small nuclear ribonucleoprotein A binding hairpin

197

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 -2756.72 14 13

198

Motif group HL_10456.1

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

0.00 -2795.68 12 12

199

Motif group HL_66482.1

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

0.00 -2833.76 13 12

200

Motif group HL_20751.2

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

0.00 -3333.15 8 8

201

Motif group HL_73183.1

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

0.00 -3398.01 9 9

Pseudoknot geometry with G-bulge

202

Motif group HL_67407.5

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

0.00 -3426.50 7 6

203

Motif group HL_23115.1

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

0.00 -3560.18 8 7

tRNA D-loop

204

Motif group HL_81312.1

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

0.00 -3567.48 8 7

205

Motif group HL_19210.3

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

0.00 -3594.00 6 5

206

Motif group HL_91503.7

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

0.00 -3691.76 7 5

207

Motif group HL_55305.1

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

0.00 -3697.90 8 7

208

Motif group HL_80599.2

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

0.00 -3700.16 7 5

209

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -3739.15 4 3

210

Motif group HL_80411.1

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

0.00 -3744.66 8 7

tRNA D-loop

211

Motif group HL_01255.1

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

0.00 -3763.19 7 6

212

Motif group HL_29762.1

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

0.00 -3769.00 6 5

213

Motif group HL_32735.2

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

0.00 -3903.34 4 3

214

Motif group HL_16398.2

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

0.00 -3930.01 8 7

215

Motif group HL_93135.1

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

0.00 -3973.82 7 7

Pseudoknot

216

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 -3988.71 13 12

217

Motif group HL_85461.1

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

0.00 -4002.33 15 14

218

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 -4013.25 16 14

219

Motif group HL_50851.1

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

0.00 -4026.28 9 8

G-quadruplex fragment

220

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 -4031.16 16 14

221

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 -4036.91 17 17

G-quadruplex

222

Motif group HL_60293.1

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

0.00 -4037.36 17 16

G-quadruplex

223

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 -4058.56 18 18

224

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 -4060.44 20 19

G-quadruplex

225

Motif group HL_47732.1

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

0.00 -4064.40 8 7

226

Motif group HL_74292.1

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

0.00 -4099.61 6 5

227

Motif group HL_59330.1

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

0.00 -4119.39 7 6

228

Motif group HL_64292.1

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

0.00 -4172.38 12 11

229

Motif group HL_29958.1

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

0.00 -4239.25 9 9

230

Motif group HL_69139.1

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

0.00 -4319.84 7 7

231

Motif group HL_04725.1

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

0.00 -4323.34 9 8

232

Motif group HL_35677.3

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

0.00 -4434.38 6 5

233

Motif group HL_07903.1

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

0.00 -4481.97 10 10

234

Motif group HL_31581.6

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

0.00 -4492.53 8 8

235

Motif group HL_63355.1

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

0.00 -4525.64 9 8

236

Motif group HL_99867.1

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

0.00 -4564.81 6 5

237

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 -4630.78 34 34

238

Motif group HL_50779.4

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

0.00 -4769.91 6 5

239

Motif group HL_15118.1

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

0.00 -4822.59 8 8

240

Motif group HL_94376.1

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

0.00 -4880.93 7 6

Pseudoknot geometry

241

Motif group HL_20781.1

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

0.00 -4884.00 6 6

242

Motif group HL_88364.2

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

0.00 -4955.40 12 12

243

Motif group HL_24792.1

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

0.00 -5073.54 7 6

244

Motif group HL_78284.1

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

0.00 -5228.92 7 6

245

Motif group HL_51447.1

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

0.00 -5360.77 5 3

246

Motif group HL_70751.1

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

0.00 -5389.81 7 6

247

Motif group HL_36684.4

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

0.00 -5530.39 6 5

248

Motif group HL_50418.1

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

0.00 -5644.93 6 5

249

Motif group HL_58539.1

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

0.00 -5779.72 12 11

250

Motif group HL_68572.1

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

0.00 -5820.33 9 8

251

Motif group HL_77600.2

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

0.00 -6411.56 4 3

252

Motif group HL_80241.1

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

0.00 -6901.64 5 3

253

Motif group HL_09260.2

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

0.00 -9999.00 8 7

tRNA D-loop

Coloring options: