RNA 3D Hub

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

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

Loop 3 Hairpin loop

Column numbers: 52-65 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    ---GUGACA-----   21

    
    ---UGCUC------   20

    
    A--AGAGCA----U   12

    
    U--UUUC------A   12

    
    A--AGACCA----U    9

    
    UU-UUUC-----AG    7

    
    U--UAGUC-----A    7

    
    ---GUGAUA-----    7

    
    AUUUCGCA---GAU    5

    
    U--GUCA------G    5

    
    ---CUAACAA----    4

    
    ---GUGUCAA----    4

    
    A--UGACU-----U    4

    
    C--UUGCU-----G    4

    
    U--UACUC-----A    4

    
    ---UGGUCA-----    4

    
    U--GCCA------G    4

    
    ---UAAUC------    4

    
    A--CUGAUAA---U    3

    
    AU-GCGAU----GU    3

    
    A--AUGCCA----U    3

    
    A--AUUCCA----U    3

    
    U--UUUUCA----G    3

    
    ---CUAACCA----    3

    
    A--UGACC-----U    3

    
    G--UGACA-----C    3

    
    ---AUAUCA-----    3

    
    ---UUAAUC-----    3

    
    C--GCCA------G    3

    
    U--GGUC------A    3

    
    ---UGUCA------    3

    
    GUGUCGAC---CAC    2

    
    UC-CUGACA---GG    2

    
    U--CUAAUCA---A    2

    
    U--GUGACAA---G    2

    
    UU-UAACA----AA    2

    
    A--ACACCA----U    2

    
    U--AUGACA----G    2

    
    UU-AAUC-----AA    2

    
    ---CUAAUCA----    2

    
    ---CUGACAA----    2

    
    ---CUUGUCA----    2

    
    ---GUGACGA----    2

    
    C--UGACU-----G    2

    
    G--CUCCA-----C    2

    
    U--UGUCA-----A    2

    
    ---CUGUCA-----    2

    
    U--AAUC------A    2

    
    ---UAGUC------    2

    
    ---UUGCU------    2

    
    ---ACAC-------    2

    
    ---GUCA-------    2

    
    ---UGCA-------    2

    
    GUCGCGCA---GAU    1

    
    AA-CCAACA---UU    1

    
    GG-AUACCG---CC    1

    
    GG-GAGACA---CC    1

    
    GUUUUCA----GAC    1

    
    ---CAUAACCAA--    1

    
    AU-UCGAU----GU    1

    
    AUUAAUC----AA-    1

    
    CU-UUUCA----AC    1

    
    G--UAAACUG---C    1

    
    GU-UGUCA----AC    1

    
    U--CUAACAA---A    1

    
    UC-UGGCA----GA    1

    
    ---GAUGAAAA---    1

    
    A--AGACAA----U    1

    
    A--AUGCAA----U    1

    
    A--UUGACA----A    1

    
    C--CUGACA----G    1

    
    G--AUACCA----C    1

    
    G--CAAUAU----C    1

    
    U--CUGAAC----A    1

    
    U--CUGGCA----G    1

    
    U--UUGACA----A    1

    
    UU--AAUC----AA    1

    
    ---CCAGUCA----    1

    
    ---CUAGUCC----    1

    
    ---GUAAGCA----    1

    
    ---GUAGUUA----    1

    
    ---GUGACAA----    1

    
    ---UUAACCA----    1

    
    ---UUAGCAA----    1

    
    ---UUGACAA----    1

    
    A--GCUAC-----U    1

    
    C--GGUCA-----G    1

    
    U--GAACC-----A    1

    
    U--UAACC-----A    1

    
    U--UAGUU-----A    1

    
    U--UGAAC-----A    1

    
    U--UGACC-----G    1

    
    U--UGAUA-----A    1

    
    ---AAGCCA-----    1

    
    ---ACACCA-----    1

    
    ---AGACCA-----    1

    
    ---AGAGCA-----    1

    
    ---AGGCUA-----    1

    
    ---AUGACA-----    1

    
    ---AUGCCA-----    1

    
    ---AUGUUA-----    1

    
    ---GUGAU-----A    1

    
    ---UGUCAA-----    1

    
    ---UGUUAC-----    1

    
    ---UUAGUC-----    1

    
    ---UUUGUC-----    1

    
    U--GAGA------A    1

    
    U--UUAC------A    1

    
    ---CUGCU------    1

    
    ---UAACA------    1

    
    ---UAUCA------    1

    
    ---UGCAA------    1

    
    ---UGUUA------    1

    
    ---UUACA------    1

    
    U---AAUC------    1

    
    U--GUC-------A    1

    
    ---GACA-------    1

    
    ---GCAA-------    1

    
    ---UGAC-------    1

    
    ---UGAU-------    1

    
    ---UGUC-------    1

    
    ---GUU--------    1

    
    ---UAC--------    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

36.21 -48.58 3 3

2

Motif group HL_50006.2

Basepair signature:
cWW-F-F

18.97 -41.88 4 3

3

Motif group HL_38168.1

Basepair signature:
cWW-F

16.90 -152.00 4 3

4

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

15.86 -43.85 3 2

5

Motif group HL_64690.6

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

15.86 -142.32 4 3

6

Motif group HL_67667.2

Basepair signature:
cWW-F-F

12.07 -1770.71 4 3.5

7

Motif group HL_56131.2

Basepair signature:
cWW-F-F

11.72 -54.89 3 3

8

Motif group HL_31585.4

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

11.72 -557.28 3 2

Purine riboswitch

9

Motif group HL_65794.5

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

11.03 -1544.01 2 2

Pseudoknot geometry

10

Motif group HL_56334.1

Basepair signature:
cWW-F

10.69 -368.29 3 2

Mini UNCG

11

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

10.34 -61.77 4 2

12

Motif group HL_87553.1

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

9.66 -90.26 4 3

13

Motif group HL_13529.1

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

9.31 -78.77 4 3

14

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

9.31 -98.52 3 3

tRNA D-loop

15

Motif group HL_77082.1

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

9.31 -159.40 4 3

Pseudoknot geometry

16

Motif group HL_32346.4

Basepair signature:
cWW-F

9.31 -409.13 3 3

17

Motif group HL_78197.1

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

9.31 -1860.04 4 3

18

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

8.62 -103.26 3 3

19

Motif group HL_48778.2

Basepair signature:
cWW-F

8.62 -123.36 2 3

Mini UNCG

20

Motif group HL_93535.1

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

8.62 -142.79 4 2

21

Motif group HL_75660.5

Basepair signature:
cWW-F

8.62 -167.43 3 3

22

Motif group HL_78347.4

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

7.93 -67.32 4 3

23

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

7.93 -97.53 4 3

24

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

7.93 -117.15 5 3

tRNA anticodon loop with synthetase

25

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

6.90 -63.76 4 3

26

Motif group HL_13189.1

Basepair signature:
cWW-F-F

6.90 -87.92 3 3

27

Motif group HL_57875.1

Basepair signature:
cWW-F-F

6.90 -98.96 4 3

28

Motif group HL_89893.1

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

6.90 -132.20 5 4

29

Motif group HL_33983.1

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

6.90 -371.23 5 4

30

Motif group HL_32392.1

Basepair signature:
cWW-F-F

6.55 -129.79 4 3

31

Motif group HL_47787.2

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

6.55 -195.03 3 3

32

Motif group HL_48417.5

Basepair signature:
cWW-F-F

6.21 -65.09 3 2

33

Motif group HL_81100.2

Basepair signature:
cWW

6.21 -1789.26 5 4

34

Motif group HL_04259.3

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

5.86 -104.30 4 3

GNRA with extra cWW

35

Motif group HL_20535.2

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

5.86 -142.66 5 3

36

Motif group HL_26934.1

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

5.52 -50.00 4 3

37

Motif group HL_46501.1

Basepair signature:
cWW-cWS

5.52 -97.95 4 3

38

Motif group HL_13963.3

Basepair signature:
cWW-F-F

5.17 -74.61 5 3

39

Motif group HL_78677.1

Basepair signature:
cWW-F-F

5.17 -634.77 4 3

40

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

4.83 -83.53 5 3

41

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

4.83 -90.05 4 3

42

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

4.83 -106.15 5 4

43

Motif group HL_56676.1

Basepair signature:
cWW-F-F

4.83 -199.92 4 3

44

Motif group HL_59330.1

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

4.83 -2147.26 5 4

45

Motif group HL_51447.1

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

4.83 -2760.13 5 3

46

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

4.83 -3317.62 6 4

47

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

4.48 -99.94 4 3

48

Motif group HL_30068.2

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

4.48 -167.57 3 3

49

Motif group HL_83632.1

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

4.48 -1336.47 5 3

tRNA anticodon loop

50

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

4.14 -139.41 3 2

UNCG

51

Motif group HL_81538.2

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

4.14 -168.96 4 3

GNRA with tandem sheared

52

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

4.14 -826.45 6 4

53

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

4.14 -3997.94 5 4

54

Motif group HL_28075.1

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

3.79 -102.09 5 3

55

Motif group HL_66103.1

Basepair signature:
cWW-F-F

3.45 -89.99 5 3

56

Motif group HL_18565.1

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

3.45 -120.39 5 4

57

Motif group HL_80599.2

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

3.45 -1942.86 5 4

58

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

3.10 -108.96 4 3

Fab BL3-6 binding hairpin with tSW

59

Motif group HL_84299.4

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

3.10 -137.44 5 3

60

Motif group HL_06059.6

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

3.10 -472.00 4 3

tRNA anticodon loop

61

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

3.10 -715.06 4 3

Mini UNCG

62

Motif group HL_38808.1

Basepair signature:
cWW-cWW

3.10 -1448.12 5 4

63

Motif group HL_20167.2

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

2.76 -84.11 5 3

64

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

2.76 -122.84 6 4

Other HL

65

Motif group HL_25061.1

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

2.76 -413.03 6 4

66

Motif group HL_10453.3

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

2.76 -487.76 4 3

tRNA anticodon loop

67

Motif group HL_52953.3

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

2.76 -1889.59 4 3

68

Motif group HL_37824.7

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

2.41 -134.16 2 2

GNRA

69

Motif group HL_59843.1

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

2.41 -172.52 4 3

70

Motif group HL_55195.3

Basepair signature:
cWW-F

2.41 -487.70 4 3

71

Motif group HL_22135.1

Basepair signature:
cWW-F-F

2.41 -739.91 4 4

72

Motif group HL_28791.1

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

2.41 -1914.74 5 4

73

Motif group HL_41464.2

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

2.07 -86.65 5 4

74

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

2.07 -98.22 4 3

75

Motif group HL_71391.1

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

2.07 -119.20 4 3

76

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

2.07 -508.00 4 3

Pseudoknot geometry with 3' bulge

77

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

2.07 -812.03 4 3

78

Motif group HL_93324.4

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

2.07 -1984.26 4 3

Pseudoknot geometry

79

Motif group HL_30680.3

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

2.07 -3568.45 4 3

Pseudoknot geometry

80

Motif group HL_01609.3

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

1.72 -105.63 4 3

T-loop with 2 bulged bases not stacked

81

Motif group HL_61996.2

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

1.72 -111.71 5 4

82

Motif group HL_69752.2

Basepair signature:
cWW-F

1.72 -177.90 4 3

83

Motif group HL_21372.1

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

1.72 -192.08 5 4

84

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

1.72 -3373.94 5 4

85

Motif group HL_86012.1

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

1.38 -72.59 5 4

T-loop with unstacked turn

86

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

1.38 -97.88 5 3

87

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

1.38 -108.21 4 3

88

Motif group HL_42046.2

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

1.38 -115.21 5 3

89

Motif group HL_77436.5

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

1.38 -119.49 4 3

T-loop related

90

Motif group HL_28252.8

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

1.38 -127.58 4 3

T-loop with 2 stacked bulged bases

91

Motif group HL_75293.5

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

1.38 -168.41 5 4

92

Motif group HL_25967.2

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

1.38 -418.04 4 4

93

Motif group HL_15574.1

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

1.38 -592.46 5 3

94

Motif group HL_80008.1

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

1.38 -1107.16 5 4

95

Motif group HL_38046.1

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

1.38 -1282.01 6 4

96

Motif group HL_50860.2

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

1.03 -84.45 5 4

97

Motif group HL_02887.3

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

1.03 -89.06 6 5

T-loop with 3 stacked bulged bases

98

Motif group HL_10540.1

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

1.03 -114.69 5 4

99

Motif group HL_73266.9

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

1.03 -120.84 5 4

100

Motif group HL_97917.2

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

1.03 -141.74 5 3

101

Motif group HL_18978.1

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

1.03 -280.01 6 4

102

Motif group HL_35941.1

Basepair signature:
cWW-F

1.03 -646.55 5 4

103

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

1.03 -818.90 5 4

104

Motif group HL_72628.1

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

1.03 -1134.29 6 4

105

Motif group HL_97733.1

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

1.03 -1158.46 7 5

106

Motif group HL_22622.1

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

1.03 -3724.01 5 4

107

Motif group HL_07951.3

Basepair signature:
cWW-F-F

1.03 -9999.00 6 4

tRNA D-loop

108

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

0.69 -82.67 4 3

109

Motif group HL_27483.1

Basepair signature:
cWW-F

0.69 -124.60 5 4

110

Motif group HL_37344.1

Basepair signature:
cWW-F-F

0.69 -153.51 5 4

111

Motif group HL_37369.2

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

0.69 -404.30 4 3

112

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.69 -1090.17 5 4

113

Motif group HL_39243.1

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

0.69 -1571.91 5 4

114

Motif group HL_35677.3

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

0.69 -3207.76 5 4

115

Motif group HL_42998.2

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

0.69 -3301.67 5 3

116

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.34 -93.83 4 3

tRNA D-loop

117

Motif group HL_93438.2

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

0.34 -94.69 5 4

118

Motif group HL_41543.1

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

0.34 -118.29 7 6

119

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.34 -454.92 4 3

T-loop with unstacked turn

120

Motif group HL_02817.2

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

0.34 -492.98 5 4

121

Motif group HL_85367.2

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

0.34 -1302.83 5 3

122

Motif group HL_55436.1

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

0.34 -2603.41 6 5

123

Motif group HL_50779.4

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

0.34 -3507.45 6 4

124

Motif group HL_59735.5

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

0.34 -3627.24 5 4

125

Motif group HL_24792.1

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

0.34 -4935.25 7 6

126

Motif group HL_83808.4

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

0.00 -80.16 6 5

Pseudoknot

127

Motif group HL_20743.5

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

0.00 -105.30 6 5

128

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

0.00 -108.43 5 3

129

Motif group HL_81545.2

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

0.00 -120.60 6 5

130

Motif group HL_67079.1

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

0.00 -122.86 6 5

131

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

0.00 -131.40 6 4

132

Motif group HL_98864.1

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

0.00 -132.27 6 5

T-loop with unstacked turn

133

Motif group HL_57863.1

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

0.00 -133.81 6 5

G-quadruplex fragment

134

Motif group HL_04642.1

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

0.00 -136.39 6 5

tRNA D-loop

135

Motif group HL_49941.1

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

0.00 -138.15 6 5

tRNA D-loop

136

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -139.21 7 6

137

Motif group HL_36335.1

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

0.00 -141.70 7 6

138

Motif group HL_25847.2

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

0.00 -142.75 7 6

139

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -144.95 6 5

140

Motif group HL_74379.3

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

0.00 -149.14 8 7

141

Motif group HL_90620.1

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

0.00 -150.08 7 6

142

Motif group HL_41902.1

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

0.00 -151.78 8 7

143

Motif group HL_68257.1

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

0.00 -153.30 7 6

144

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.00 -157.00 5 4

tRNA D-loop

145

Motif group HL_04171.7

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

0.00 -160.38 7 6

146

Motif group HL_70658.1

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

0.00 -165.65 8 7

147

Motif group HL_60266.1

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

0.00 -166.73 7 6

148

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -167.06 7 6

149

Motif group HL_47854.1

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

0.00 -171.46 6 4

150

Motif group HL_98252.1

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

0.00 -177.67 8 6

151

Motif group HL_53504.3

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

0.00 -180.42 7 5

152

Motif group HL_86109.1

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

0.00 -180.70 9 7

153

Motif group HL_16991.1

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

0.00 -183.50 8 7

G-quadruplex fragment

154

Motif group HL_08602.1

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

0.00 -191.93 8 7

155

Motif group HL_23509.1

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

0.00 -192.39 8 7

156

Motif group HL_07583.1

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

0.00 -195.79 9 8

157

Motif group HL_84847.1

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

0.00 -198.35 9 7

158

Motif group HL_81205.3

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

0.00 -199.15 9 8

159

Motif group HL_74055.2

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

0.00 -215.21 9 8

160

Motif group HL_68767.1

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

0.00 -222.32 9 7

tRNA D-loop

161

Motif group HL_73255.1

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

0.00 -225.56 6 5

162

Motif group HL_73247.1

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

0.00 -231.20 10 8

Pseudoknot geometry

163

Motif group HL_13971.1

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

0.00 -241.43 9 8

164

Motif group HL_98870.1

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

0.00 -247.67 10 9

165

Motif group HL_91641.1

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

0.00 -279.78 12 11

166

Motif group HL_14757.1

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

0.00 -288.99 12 11

167

Motif group HL_88205.2

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

0.00 -293.02 5 4

168

Motif group HL_15802.1

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

0.00 -318.09 6 5

169

Motif group HL_89881.5

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

0.00 -332.68 6 5

170

Motif group HL_87463.1

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

0.00 -337.01 6 5

171

Motif group HL_45785.1

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

0.00 -340.11 7 6

172

Motif group HL_06226.4

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

0.00 -340.80 7 6

173

Motif group HL_91939.2

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

0.00 -358.45 7 6

174

Motif group HL_58224.1

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

0.00 -358.61 6 5

175

Motif group HL_02483.1

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

0.00 -364.65 8 6

176

Motif group HL_04641.1

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

0.00 -368.37 6 5

177

Motif group HL_51921.1

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

0.00 -371.69 15 13

178

Motif group HL_07480.2

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

0.00 -391.98 8 6

179

Motif group HL_97756.2

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

0.00 -397.11 10 9

180

Motif group HL_05304.3

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

0.00 -399.51 8 7

181

Motif group HL_23010.1

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

0.00 -405.71 8 6

182

Motif group HL_02581.1

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

0.00 -421.02 10 8.5

tRNA D-loop

183

Motif group HL_92488.1

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

0.00 -432.60 12 10

184

Motif group HL_34964.1

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

0.00 -458.34 7 6

185

Motif group HL_53454.2

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

0.00 -461.53 6 5

186

Motif group HL_00914.1

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

0.00 -497.97 5 4

187

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -743.94 5 4

188

Motif group HL_85434.1

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

0.00 -829.39 6 4.5

189

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -832.52 4 4

190

Motif group HL_93616.2

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

0.00 -853.38 7 6

tRNA D-loop

191

Motif group HL_29129.3

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

0.00 -944.26 6 5

192

Motif group HL_99769.3

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

0.00 -1075.59 7 6

193

Motif group HL_11542.1

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

0.00 -1158.33 9 8

194

Motif group HL_93383.1

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

0.00 -1499.37 6 5

195

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -1503.57 5 4

196

Motif group HL_99040.1

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

0.00 -1571.85 4 3

197

Motif group HL_32735.2

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

0.00 -2089.32 5 4

198

Motif group HL_66482.1

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

0.00 -2110.56 13 11

199

Motif group HL_10456.1

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

0.00 -2111.21 13 12

200

Motif group HL_08510.1

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

0.00 -2425.29 6 4

201

Motif group HL_20751.2

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

0.00 -2485.61 10 8

202

Motif group HL_38649.1

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

0.00 -2528.29 7 6

203

Motif group HL_23115.1

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

0.00 -2587.90 8 6

tRNA D-loop

204

Motif group HL_91503.7

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

0.00 -2694.81 6 6

205

Motif group HL_80411.1

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

0.00 -2716.51 8 6

tRNA D-loop

206

Motif group HL_88558.1

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

0.00 -2717.50 8 6

207

Motif group HL_29762.1

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

0.00 -2738.81 7 6

208

Motif group HL_85993.1

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

0.00 -2768.13 5 4

209

Motif group HL_33074.4

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

0.00 -2829.06 7 6

U1 small nuclear ribonucleoprotein A binding hairpin

210

Motif group HL_93135.1

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

0.00 -2861.42 7 5

Pseudoknot

211

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 -2915.86 14 13

212

Motif group HL_69139.1

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

0.00 -3135.10 7 6

213

Motif group HL_12870.1

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

0.00 -3206.76 9 8

214

Motif group HL_67407.5

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

0.00 -3605.38 6 5

215

Motif group HL_73183.1

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

0.00 -3621.36 10 10

Pseudoknot geometry with G-bulge

216

Motif group HL_81312.1

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

0.00 -3779.36 7 6

217

Motif group HL_19210.3

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

0.00 -3795.64 6 4

218

Motif group HL_55305.1

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

0.00 -3895.75 7 6

219

Motif group HL_50851.1

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

0.00 -3934.02 9 8

G-quadruplex fragment

220

Motif group HL_01255.1

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

0.00 -4004.72 8 6

221

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 -4004.83 12 11

222

Motif group HL_85461.1

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

0.00 -4011.25 14 13

223

Motif group HL_60293.1

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

0.00 -4051.91 17 16

G-quadruplex

224

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 -4053.69 15 14

225

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 -4054.04 18 17

G-quadruplex

226

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 -4066.12 19 18

227

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 -4083.81 20 19

G-quadruplex

228

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 -4086.02 15 14

229

Motif group HL_16398.2

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

0.00 -4177.73 8.5 7

230

Motif group HL_04725.1

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

0.00 -4218.83 8 7

231

Motif group HL_47732.1

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

0.00 -4312.72 8 7

232

Motif group HL_07903.1

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

0.00 -4393.19 10 8

233

Motif group HL_31581.6

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

0.00 -4394.71 7 6

234

Motif group HL_64292.1

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

0.00 -4408.28 11 10

235

Motif group HL_63355.1

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

0.00 -4448.04 9 8

236

Motif group HL_29958.1

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

0.00 -4489.83 9 8

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 -4631.80 33 32

238

Motif group HL_74292.1

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

0.00 -4676.60 7 6

239

Motif group HL_15118.1

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

0.00 -4700.62 7 6

240

Motif group HL_94376.1

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

0.00 -4763.76 6 5

Pseudoknot geometry

241

Motif group HL_88364.2

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

0.00 -4894.02 11 10

242

Motif group HL_70751.1

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

0.00 -5011.47 7 6

243

Motif group HL_80241.1

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

0.00 -5073.94 5 4

244

Motif group HL_36684.4

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

0.00 -5149.79 6 5

245

Motif group HL_99867.1

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

0.00 -5172.77 6 4

246

Motif group HL_20781.1

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

0.00 -5182.34 8 6

247

Motif group HL_50418.1

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

0.00 -5255.41 6 5

248

Motif group HL_78284.1

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

0.00 -5458.70 7 6

249

Motif group HL_77600.2

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

0.00 -5592.00 4 3

250

Motif group HL_68572.1

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

0.00 -5758.63 9 8

251

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -6032.03 7 5

252

Motif group HL_58539.1

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

0.00 -6196.51 11 10

253

Motif group HL_09260.2

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

0.00 -9999.00 7 6

tRNA D-loop

Coloring options: