RNA 3D Hub

JAR3D Query RF03022-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03022 maps to these 9 chains: 8UB7|1|I, 8UB8|1|I, 8UB9|1|I, 8UBA|1|I, 8UBB|1|I, 8UBC|1|I, 8UBD|1|I, 8UBE|1|I, 8UBF|1|I See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 12 Hairpin loop

Column numbers: 132-159 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    U--------GAAAU-------------A   26

    
    ---------GAAAUAU------------    6

    
    ---------CUCAU--------------    6

    
    C--------CUAGA-------------G    5

    
    CC-------CUAG-------------GG    3

    
    ---------UGAAAAU------------    3

    
    UG-------AAA--------------CA    3

    
    ---------UUAAUU-------------    3

    
    ---------GAAAU--------------    3

    
    CAA------CAUGA-----------UUG    2

    
    GC-------AGAAA------------GC    2

    
    ---------UGAAUAU------------    2

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

    
    ---------CACGU--------------    2

    
    ---------GAAUA--------------    2

    
    CACGGGCGCGGCGCGCA--GCACCCGUG    1

    
    CGGCGGUUCAGCGCA----GAACUGCCG    1

    
    UG-AGGC--CAAGG-------GCCGACA    1

    
    C-CGGGC--GCAA--------GCCCGUG    1

    
    CC-UGUG--GCGA--------CACACGG    1

    
    UG-AGGC--UGCG--------GCCAAUA    1

    
    CC-------UUUGUUGAUU-------GG    1

    
    GG-AGC---AUU----------GCUCUU    1

    
    UCAC-----CAUAUU---------GUGA    1

    
    UCAC-----UAUGUU---------GUGA    1

    
    CGGGC----UUU-----------GCCCG    1

    
    GGCG-----GCAA-----------CGCC    1

    
    CGC------UUCG------------GCG    1

    
    GCC------GCAA------------GGC    1

    
    CU-------UUAAG------------AG    1

    
    GC-------AGAAA------------GU    1

    
    CG-------CGAU-------------CG    1

    
    UG-------UAAA-------------CA    1

    
    ---------AUGCGCA------------    1

    
    ---------UGAGAAU------------    1

    
    C--------AGAAA-------------G    1

    
    C--------CACGA-------------G    1

    
    C--------CCAGA-------------G    1

    
    C--------CUAGU-------------G    1

    
    C--------CUCGA-------------G    1

    
    C--------CUGGU-------------G    1

    
    C--------CUUGA-------------G    1

    
    U--------GCAAU-------------A    1

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

    
    UG-------AGA--------------CA    1

    
    ---------AAUUAA-------------    1

    
    ---------CAGUGU-------------    1

    
    ---------UGAAAA-------------    1

    
    ---------UGAAU-------------A    1

    
    C--------GAAA--------------G    1

    
    C--------UUCU--------------G    1

    
    U--------GAAU--------------A    1

    
    ---------CAAAA--------------    1

    
    ---------GUUAU--------------    1

    
    ---------UAAAG--------------    1

    
    ---------UGAAU--------------    1

    
    C--------AGC---------------G    1

    
    ---------AAU----------------    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_53890.2

Basepair signature:
cWW-F-F-F

50.44 -605.55 2 2

2

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

42.48 -359.01 3 2

3

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

41.59 -264.72 3 2

4

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

39.82 -1002.43 4 3

5

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

39.82 -1159.14 3 2

Pseudoknot geometry with 3' bulge

6

Motif group HL_75660.5

Basepair signature:
cWW-F

39.82 -1275.49 3 2

7

Motif group HL_50006.2

Basepair signature:
cWW-F-F

37.17 -616.25 3 3

8

Motif group HL_97917.2

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

37.17 -725.49 4 3

9

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

34.51 -633.09 3 2

10

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

34.51 -1008.38 3 3

11

Motif group HL_37824.7

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

33.63 -330.84 2 2

GNRA

12

Motif group HL_65794.5

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

30.97 -2850.96 3 2

Pseudoknot geometry

13

Motif group HL_77436.5

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

30.09 -110.33 3 2

T-loop related

14

Motif group HL_59735.5

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

30.09 -2184.68 3 2

15

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

28.32 -379.71 3 3

16

Motif group HL_59843.1

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

28.32 -754.90 3 3

17

Motif group HL_39243.1

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

28.32 -2742.41 4 3

18

Motif group HL_04259.3

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

27.43 -313.10 3 2

GNRA with extra cWW

19

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

26.55 -323.74 4 3

20

Motif group HL_13529.1

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

25.66 -247.85 4 3

21

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

23.89 -664.00 3 2

22

Motif group HL_87553.1

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

15.04 -284.55 4 3

23

Motif group HL_13963.3

Basepair signature:
cWW-F-F

10.62 -650.55 5 3

24

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

10.62 -675.83 5 4

25

Motif group HL_37344.1

Basepair signature:
cWW-F-F

10.62 -695.80 6 5

26

Motif group HL_10453.3

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

9.73 -413.73 4 3

tRNA anticodon loop

27

Motif group HL_56131.2

Basepair signature:
cWW-F-F

8.85 -650.04 4 3

28

Motif group HL_31585.4

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

8.85 -757.22 3 2

Purine riboswitch

29

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

8.85 -1121.66 3 3

tRNA D-loop

30

Motif group HL_70782.2

Basepair signature:
cWW-F

8.85 -1212.07 4 4

31

Motif group HL_30680.3

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

8.85 -1671.80 4 3

Pseudoknot geometry

32

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

8.85 -2948.09 5 5

33

Motif group HL_18565.1

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

7.96 -320.30 4 4

34

Motif group HL_38168.1

Basepair signature:
cWW-F

7.96 -1296.66 4 3

35

Motif group HL_48417.5

Basepair signature:
cWW-F-F

7.08 -275.47 3 2

36

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

7.08 -565.33 5 4

Other HL

37

Motif group HL_93535.1

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

7.08 -753.20 3 3

38

Motif group HL_66103.1

Basepair signature:
cWW-F-F

7.08 -1006.71 4 3

39

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

6.19 -338.21 5 4

tRNA anticodon loop with synthetase

40

Motif group HL_20535.2

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

6.19 -370.17 4 3

41

Motif group HL_57875.1

Basepair signature:
cWW-F-F

6.19 -1012.97 4 3

42

Motif group HL_15802.1

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

5.31 -272.87 7 6

43

Motif group HL_56334.1

Basepair signature:
cWW-F

5.31 -1411.63 3 2

Mini UNCG

44

Motif group HL_69752.2

Basepair signature:
cWW-F

4.42 -1293.55 4 3

45

Motif group HL_93324.4

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

4.42 -2199.89 3 2

Pseudoknot geometry

46

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

3.54 -416.39 4 3

47

Motif group HL_37369.2

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

3.54 -531.17 5 4

48

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

3.54 -675.36 4 3

49

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

3.54 -1407.16 3 2

50

Motif group HL_83632.1

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

3.54 -1657.99 4 3

tRNA anticodon loop

51

Motif group HL_51447.1

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

3.54 -1711.30 5 4

52

Motif group HL_52953.3

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

3.54 -3144.98 3 2

53

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

2.65 -193.02 4 4

54

Motif group HL_50860.2

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

2.65 -212.60 5 4

55

Motif group HL_73266.9

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

2.65 -249.22 4 4

56

Motif group HL_30068.2

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

2.65 -771.36 3 3

57

Motif group HL_13189.1

Basepair signature:
cWW-F-F

2.65 -1029.30 3 3

58

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

2.65 -1048.79 5 3

59

Motif group HL_93383.1

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

2.65 -1107.98 5 4

60

Motif group HL_46501.1

Basepair signature:
cWW-cWS

2.65 -1151.68 4 3

61

Motif group HL_48778.2

Basepair signature:
cWW-F

2.65 -1252.33 4 3

Mini UNCG

62

Motif group HL_59330.1

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

2.65 -1311.05 7 6

63

Motif group HL_97733.1

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

2.65 -1439.03 8 6

64

Motif group HL_32346.4

Basepair signature:
cWW-F

2.65 -1443.98 4 3

65

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

2.65 -2522.79 4 3

66

Motif group HL_36335.1

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

1.77 -147.20 5 5

67

Motif group HL_20167.2

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

1.77 -154.97 4 3

68

Motif group HL_41464.2

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

1.77 -211.99 5 4

69

Motif group HL_25061.1

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

1.77 -294.21 5 4

70

Motif group HL_78347.4

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

1.77 -300.05 4 3

71

Motif group HL_33983.1

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

1.77 -501.64 5 4

72

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

1.77 -592.07 3 3

Fab BL3-6 binding hairpin with tSW

73

Motif group HL_56676.1

Basepair signature:
cWW-F-F

1.77 -812.98 3 3

74

Motif group HL_89893.1

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

1.77 -875.13 5 4

75

Motif group HL_99769.3

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

1.77 -1064.68 7 6

76

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

1.77 -1280.43 4 3

Mini UNCG

77

Motif group HL_78197.1

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

1.77 -2358.21 4 4

78

Motif group HL_86012.1

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

0.88 -199.77 6 5

T-loop with unstacked turn

79

Motif group HL_83808.4

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

0.88 -216.63 8 6

Pseudoknot

80

Motif group HL_98864.1

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

0.88 -237.06 6 5

T-loop with unstacked turn

81

Motif group HL_28252.8

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

0.88 -243.96 4 3

T-loop with 2 stacked bulged bases

82

Motif group HL_10540.1

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

0.88 -277.14 4 3

83

Motif group HL_28075.1

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

0.88 -296.63 4 3

84

Motif group HL_42046.2

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

0.88 -308.38 5 4

85

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.88 -317.65 4 3

tRNA D-loop

86

Motif group HL_64690.6

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

0.88 -351.23 5 4

87

Motif group HL_06059.6

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

0.88 -375.05 4 3

tRNA anticodon loop

88

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.88 -588.65 4 3

T-loop with unstacked turn

89

Motif group HL_47854.1

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

0.88 -612.37 5 4

90

Motif group HL_02817.2

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

0.88 -620.45 4 3

91

Motif group HL_00914.1

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

0.88 -657.65 5 3

92

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.88 -700.56 4 2

UNCG

93

Motif group HL_71391.1

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

0.88 -721.47 4 3

94

Motif group HL_47787.2

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

0.88 -776.89 3 3

95

Motif group HL_80599.2

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

0.88 -791.36 6 5

96

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.88 -1204.13 5 5

97

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

0.88 -1410.61 5 3

98

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

0.88 -1441.24 6 4

99

Motif group HL_55195.3

Basepair signature:
cWW-F

0.88 -1544.48 4 3

100

Motif group HL_85993.1

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

0.88 -1629.74 5 3

101

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.88 -1665.25 5 4

102

Motif group HL_60914.1

Basepair signature:
cWW-F

0.88 -1773.08 6 5

103

Motif group HL_50779.4

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

0.88 -1961.86 6 5

104

Motif group HL_81100.2

Basepair signature:
cWW

0.88 -2071.00 5 3

105

Motif group HL_99040.1

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

0.88 -2695.54 6 5

106

Motif group HL_22622.1

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

0.88 -3011.23 6 4

107

Motif group HL_28791.1

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

0.88 -3197.26 5 4

108

Motif group HL_55436.1

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

0.88 -4469.48 5 5

109

Motif group HL_93438.2

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

0.00 -108.16 5 4

110

Motif group HL_67079.1

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

0.00 -136.56 6 5

111

Motif group HL_02887.3

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

0.00 -146.15 5 5

T-loop with 3 stacked bulged bases

112

Motif group HL_41543.1

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

0.00 -149.24 8 7

113

Motif group HL_91939.2

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

0.00 -151.28 7 6

114

Motif group HL_90620.1

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

0.00 -151.64 7 5

115

Motif group HL_60266.1

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

0.00 -157.09 7 5

116

Motif group HL_74379.3

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

0.00 -159.01 8 7

117

Motif group HL_41902.1

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

0.00 -160.07 8 7

118

Motif group HL_70658.1

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

0.00 -160.94 8 6

119

Motif group HL_53504.3

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

0.00 -170.46 6 4

120

Motif group HL_68257.1

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

0.00 -171.48 6 5

121

Motif group HL_81545.2

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

0.00 -177.04 5 4

122

Motif group HL_86109.1

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

0.00 -179.95 8 7

123

Motif group HL_07583.1

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

0.00 -181.25 9 7

124

Motif group HL_06226.4

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

0.00 -184.13 6 5

125

Motif group HL_84847.1

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

0.00 -194.47 9 7

126

Motif group HL_81205.3

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

0.00 -201.59 9 8

127

Motif group HL_23509.1

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

0.00 -209.01 8 7

128

Motif group HL_05304.3

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

0.00 -213.26 7 6

129

Motif group HL_20743.5

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

0.00 -213.36 5 3

130

Motif group HL_74055.2

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

0.00 -215.52 9 8

131

Motif group HL_61996.2

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

0.00 -216.82 5 3

132

Motif group HL_18978.1

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

0.00 -219.54 7 6

133

Motif group HL_26934.1

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

0.00 -223.46 5 5

134

Motif group HL_04171.7

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

0.00 -224.02 6 5

135

Motif group HL_02483.1

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

0.00 -230.00 7 6

136

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -230.66 6 5

137

Motif group HL_02581.1

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

0.00 -235.76 11 9

tRNA D-loop

138

Motif group HL_57863.1

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

0.00 -237.65 6 5

G-quadruplex fragment

139

Motif group HL_98870.1

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

0.00 -242.07 10 9

140

Motif group HL_73247.1

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

0.00 -242.48 10 9

Pseudoknot geometry

141

Motif group HL_87463.1

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

0.00 -249.20 6 5

142

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -255.56 8 6

143

Motif group HL_49941.1

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

0.00 -256.81 8 7

tRNA D-loop

144

Motif group HL_91641.1

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

0.00 -259.76 11 10

145

Motif group HL_04641.1

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

0.00 -263.89 7 5

146

Motif group HL_89881.5

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

0.00 -264.60 7 5

147

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -265.63 6 6

148

Motif group HL_01609.3

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

0.00 -266.54 3 2

T-loop with 2 bulged bases not stacked

149

Motif group HL_14757.1

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

0.00 -266.88 12 11

150

Motif group HL_08602.1

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

0.00 -269.54 9 8

151

Motif group HL_58224.1

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

0.00 -270.53 7 6

152

Motif group HL_68767.1

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

0.00 -273.84 8 7

tRNA D-loop

153

Motif group HL_25847.2

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

0.00 -274.26 6 5

154

Motif group HL_16991.1

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

0.00 -274.45 7 6

G-quadruplex fragment

155

Motif group HL_04642.1

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

0.00 -275.01 7 6

tRNA D-loop

156

Motif group HL_45785.1

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

0.00 -278.91 8 7

157

Motif group HL_53454.2

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

0.00 -280.36 5 4

158

Motif group HL_13971.1

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

0.00 -283.30 9 9

159

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

0.00 -286.02 6 5

160

Motif group HL_75293.5

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

0.00 -300.13 5 3

161

Motif group HL_98252.1

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

0.00 -300.30 8 6

162

Motif group HL_23010.1

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

0.00 -309.33 8 7

163

Motif group HL_07480.2

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

0.00 -316.20 8 7

164

Motif group HL_84299.4

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

0.00 -331.15 5 3

165

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.00 -338.22 6 5

tRNA D-loop

166

Motif group HL_34964.1

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

0.00 -354.49 7 6

167

Motif group HL_51921.1

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

0.00 -369.59 14 14

168

Motif group HL_77082.1

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

0.00 -384.78 4 2

Pseudoknot geometry

169

Motif group HL_92488.1

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

0.00 -411.82 11 10

170

Motif group HL_81538.2

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

0.00 -423.03 3 2

GNRA with tandem sheared

171

Motif group HL_73255.1

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

0.00 -449.13 7 5

172

Motif group HL_97756.2

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

0.00 -463.56 10 9

173

Motif group HL_25967.2

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

0.00 -531.80 5 4

174

Motif group HL_21372.1

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

0.00 -669.11 5 5

175

Motif group HL_88205.2

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

0.00 -714.49 5 4

176

Motif group HL_27483.1

Basepair signature:
cWW-F

0.00 -716.68 5 4

177

Motif group HL_15574.1

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

0.00 -778.39 4 3

178

Motif group HL_32735.2

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

0.00 -862.41 4 3

179

Motif group HL_93616.2

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

0.00 -1095.96 7 7

tRNA D-loop

180

Motif group HL_11542.1

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

0.00 -1111.02 9 7

181

Motif group HL_85434.1

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

0.00 -1114.64 7 6

182

Motif group HL_29129.3

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

0.00 -1217.27 7 5

183

Motif group HL_10456.1

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

0.00 -1269.18 12 11

184

Motif group HL_66482.1

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

0.00 -1310.97 12 11

185

Motif group HL_20751.2

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

0.00 -1441.84 9 7

186

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -1458.00 4 3

187

Motif group HL_80008.1

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

0.00 -1533.90 5 4

188

Motif group HL_72628.1

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

0.00 -1538.03 4 4

189

Motif group HL_38046.1

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

0.00 -1587.35 5 4

190

Motif group HL_85367.2

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

0.00 -1615.67 4 3

191

Motif group HL_23115.1

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

0.00 -1635.86 8 7

tRNA D-loop

192

Motif group HL_78677.1

Basepair signature:
cWW-F-F

0.00 -1637.27 5 3

193

Motif group HL_91503.7

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

0.00 -1640.94 7 6

194

Motif group HL_88558.1

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

0.00 -1654.63 7 6

195

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -1664.51 7 5

196

Motif group HL_29762.1

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

0.00 -1688.35 6 5

197

Motif group HL_80411.1

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

0.00 -1707.48 8 7

tRNA D-loop

198

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.00 -1742.91 4 4

199

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.00 -1788.52 5 4

200

Motif group HL_93135.1

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

0.00 -1799.18 7 6

Pseudoknot

201

Motif group HL_12870.1

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

0.00 -1857.88 9 8

202

Motif group HL_69139.1

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

0.00 -1890.89 7 6

203

Motif group HL_35677.3

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

0.00 -1942.75 5 4

204

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -2174.54 6 4

205

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.00 -2451.74 6 5

206

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -2714.97 6 5

207

Motif group HL_80241.1

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

0.00 -3067.01 5 4

208

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 -3206.01 13 12

209

Motif group HL_33074.4

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

0.00 -3232.57 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

210

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 -3669.71 15 14

211

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 -3670.58 15 14

212

Motif group HL_50851.1

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

0.00 -3757.64 9 8

G-quadruplex fragment

213

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 -3794.96 12 11

214

Motif group HL_85461.1

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

0.00 -3807.02 14 13

215

Motif group HL_60293.1

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

0.00 -3844.71 16 15

G-quadruplex

216

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 -3852.97 17 17

G-quadruplex

217

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 -3868.57 19 18

G-quadruplex

218

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 -3987.54 18 17

219

Motif group HL_73183.1

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

0.00 -3999.67 9 8

Pseudoknot geometry with G-bulge

220

Motif group HL_04725.1

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

0.00 -4028.81 8 7

221

Motif group HL_07903.1

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

0.00 -4108.76 10 9

222

Motif group HL_67407.5

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

0.00 -4171.91 7 6

223

Motif group HL_63355.1

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

0.00 -4201.10 9 8

224

Motif group HL_31581.6

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

0.00 -4209.55 8 7

225

Motif group HL_38649.1

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

0.00 -4266.20 6 5

226

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 -4286.43 33 33

227

Motif group HL_81312.1

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

0.00 -4319.45 8 7

228

Motif group HL_19210.3

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

0.00 -4389.94 6 5

229

Motif group HL_88364.2

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

0.00 -4439.36 12 11

230

Motif group HL_55305.1

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

0.00 -4449.17 7 6

231

Motif group HL_15118.1

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

0.00 -4503.27 8 7

232

Motif group HL_01255.1

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

0.00 -4569.33 8 7

233

Motif group HL_94376.1

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

0.00 -4572.39 7 6

Pseudoknot geometry

234

Motif group HL_08510.1

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

0.00 -4596.53 6 5

235

Motif group HL_16398.2

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

0.00 -4644.06 8 7

236

Motif group HL_64292.1

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

0.00 -4879.14 12 10

237

Motif group HL_47732.1

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

0.00 -4917.34 8 6

238

Motif group HL_70751.1

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

0.00 -4970.35 7 6

239

Motif group HL_78284.1

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

0.00 -5033.58 7 6

240

Motif group HL_36684.4

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

0.00 -5099.21 6 5

241

Motif group HL_29958.1

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

0.00 -5106.35 10 9

242

Motif group HL_24792.1

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

0.00 -5112.70 7 5

243

Motif group HL_50418.1

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

0.00 -5209.82 6 5

244

Motif group HL_74292.1

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

0.00 -5284.78 6 5

245

Motif group HL_68572.1

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

0.00 -5312.74 9 8

246

Motif group HL_99867.1

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

0.00 -5877.82 6 5

247

Motif group HL_20781.1

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

0.00 -5962.47 7 6

248

Motif group HL_42998.2

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

0.00 -6288.41 4 3

249

Motif group HL_77600.2

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

0.00 -6699.04 4 3

250

Motif group HL_58539.1

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

0.00 -6965.98 11 10

251

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -7417.95 6 5

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 7 7

tRNA D-loop

Coloring options: