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 42 Hairpin loop

Column numbers: 1064-1130 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    -----------------------------GAAA----------------------------------   49

    
    C----------------------------AUUU---------------------------------G   11

    
    C----------------------------UUCG---------------------------------G    8

    
    -----------------------------UUUUA---------------------------------    8

    
    -----------------------------GCAA----------------------------------    8

    
    -----------------------------CUUUG---------------------------------    5

    
    -----------------------------GUAGA---------------------------------    4

    
    -----------------------------GUAA----------------------------------    4

    
    CGCAGCAUGG-------------------CUUAU-----------------------CC-UGUUGCG    3

    
    UACGAUAUGG-------------------CUCAA-----------------------CU-UAUUGUA    3

    
    UCCAAGCAC--------------------UUGU-------------------------GUGCGAGGA    3

    
    CGGC-------------------------GUUUGA----------------------------GUCG    3

    
    -----------------------------UUUAA---------------------------------    3

    
    -----------------------------AUUA----------------------------------    3

    
    AAUACAG----------------------UUCG---------------------------CUGUGUA    2

    
    G----------------------------UGUAUU-------------------------------C    2

    
    -----------------------------UGAAAG--------------------------------    2

    
    -----------------------------UUAAU---------------------------------    2

    
    -----------------------------UUUAU---------------------------------    2

    
    -----------------------------UUCG----------------------------------    2

    
    -----------------------------UUUA----------------------------------    2

    
    AAUUAAGG--ACGAACAUCACAAUCCAUCCGUAG---GGUGCGAGAGU-AUGUU-GUAGAAUUAAUU    1

    
    UUUAACGGUUAGGGGCGACUUAUAG----UUUAA--------CUACAAGUGGCAACAGACGGUUUAA    1

    
    AUAAUUAGUUUUCA---------------GUAA--------------------UGAAAAUCAAUUAU    1

    
    UUUGUGG-GGC------------------CGUUG----------------------GCACAAUCAAA    1

    
    -CUCCAAGCAU------------------UUGU-----------------------GUGCAAGGAGC    1

    
    UCCAAGCAC--------------------UUGU-------------------------GUGCGAAGA    1

    
    UCCAAGCGC--------------------CUUU-------------------------GCGCAAGGA    1

    
    UCCAAGCGC--------------------UUUU-------------------------GCGCAAGGA    1

    
    UUGAUAAA---------------------CAAUG-------------------------UUUAUCAG    1

    
    UAGC-------------------------GUUUGA----------------------------GCUA    1

    
    UGGA-------------------------GAGGUC----------------------------UCCA    1

    
    AUAU-------------------------CGGAC-----------------------------AU-U    1

    
    UUG--------------------------CAAAUA-----------------------------CAA    1

    
    ACC--------------------------GAAA-------------------------------GGU    1

    
    GAU--------------------------GAGA-------------------------------ACC    1

    
    GGU--------------------------GAGA-------------------------------ACC    1

    
    UGC--------------------------UUCG-------------------------------GCG    1

    
    UGC--------------------------UUCG-------------------------------GUA    1

    
    UUG--------------------------UUUU-------------------------------CAA    1

    
    GU---------------------------AGAGU-------------------------------GC    1

    
    GU---------------------------GGAAA-------------------------------AC    1

    
    -----------------------------CUUAGUGU------------------------------    1

    
    AG---------------------------CGCA--------------------------------AU    1

    
    AG---------------------------GAAA--------------------------------CU    1

    
    AG---------------------------UGUA--------------------------------CU    1

    
    CC---------------------------GAAA--------------------------------GG    1

    
    CC---------------------------UCCG--------------------------------GG    1

    
    G----------------------------GGUAUA-------------------------------C    1

    
    GG---------------------------UGUUU--------------------------------C    1

    
    UC---------------------------UUCG--------------------------------GA    1

    
    UU---------------------------UUGU--------------------------------AA    1

    
    C----------------------------CUAUG--------------------------------G    1

    
    G----------------------------UGUUU--------------------------------C    1

    
    U----------------------------AAUAU--------------------------------A    1

    
    -----------------------------UUUAUU--------------------------------    1

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

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

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

    
    C----------------------------UGGC---------------------------------G    1

    
    G----------------------------CUUG---------------------------------C    1

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

    
    U----------------------------UUAU---------------------------------A    1

    
    -----------------------------CAAAG---------------------------------    1

    
    -----------------------------CAUUG---------------------------------    1

    
    -----------------------------CUUGG---------------------------------    1

    
    -----------------------------GUAAA---------------------------------    1

    
    -----------------------------GUUCG---------------------------------    1

    
    -----------------------------GUUUC---------------------------------    1

    
    -----------------------------UAAAC---------------------------------    1

    
    -----------------------------UGUUU---------------------------------    1

    
    -----------------------------UUUGA---------------------------------    1

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

    
    -----------------------------AUUU----------------------------------    1

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

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

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

    
    -----------------------------GUUA----------------------------------    1

    
    -----------------------------GUUU----------------------------------    1

    
    -----------------------------UUAU----------------------------------    1

    
    -----------------------------UUUG----------------------------------    1

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

    
    ------------------------------AAA----------------------------------    1

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

    
    Omitted sequenced and counts

    
    -------------------------------------------------------------------   98
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

61.46 -1196.67 2 1

2

Motif group HL_56334.1

Basepair signature:
cWW-F

56.25 -1561.24 2 2

Mini UNCG

3

Motif group HL_13189.1

Basepair signature:
cWW-F-F

47.40 -1452.67 2 2

4

Motif group HL_75660.5

Basepair signature:
cWW-F

47.40 -1670.11 2 1.5

5

Motif group HL_50006.2

Basepair signature:
cWW-F-F

46.35 -1191.84 3 2

6

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

43.75 -1472.05 3 2

tRNA D-loop

7

Motif group HL_37824.7

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

41.67 -1137.61 2 1.5

GNRA

8

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

35.94 -1099.57 3 2

9

Motif group HL_38168.1

Basepair signature:
cWW-F

35.94 -1681.31 3 2

10

Motif group HL_52953.3

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

34.90 -3490.51 3 2

11

Motif group HL_47787.2

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

32.81 -1343.26 3 2

12

Motif group HL_70782.2

Basepair signature:
cWW-F

32.81 -1564.66 3 3

13

Motif group HL_48778.2

Basepair signature:
cWW-F

32.29 -1575.28 2 2

Mini UNCG

14

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

30.21 -1490.66 4 2

15

Motif group HL_48417.5

Basepair signature:
cWW-F-F

29.17 -1072.54 3 2

16

Motif group HL_32346.4

Basepair signature:
cWW-F

28.65 -1575.96 3 2

17

Motif group HL_65794.5

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

28.65 -3388.39 3 2

Pseudoknot geometry

18

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

27.60 -5836.67 3 2

19

Motif group HL_46501.1

Basepair signature:
cWW-cWS

20.83 -1479.33 3 2

20

Motif group HL_69752.2

Basepair signature:
cWW-F

20.83 -1706.53 4 3

21

Motif group HL_56131.2

Basepair signature:
cWW-F-F

19.79 -1184.97 3 3

22

Motif group HL_57875.1

Basepair signature:
cWW-F-F

17.71 -1472.62 4 2

23

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

15.10 -1232.62 3 2

24

Motif group HL_81100.2

Basepair signature:
cWW

15.10 -6345.15 5 3

25

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

14.58 -1526.50 5 4

26

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

14.58 -5864.37 5 4

27

Motif group HL_32392.1

Basepair signature:
cWW-F-F

11.46 -1512.24 4 4

28

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

9.90 -1229.28 3 2

29

Motif group HL_56676.1

Basepair signature:
cWW-F-F

9.90 -1357.67 3 2

30

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

8.33 -1236.65 5 3

31

Motif group HL_78347.4

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

7.29 -1076.73 4 3

32

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

7.29 -1231.34 4 2

33

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

6.77 -1217.21 3 2

UNCG

34

Motif group HL_78677.1

Basepair signature:
cWW-F-F

6.77 -1917.11 3 2.5

35

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

6.77 -5866.65 4 3

36

Motif group HL_37344.1

Basepair signature:
cWW-F-F

6.25 -1228.05 5 4

37

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

6.25 -1257.57 4 2

38

Motif group HL_93535.1

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

6.25 -1333.82 3 3

39

Motif group HL_55195.3

Basepair signature:
cWW-F

6.25 -1728.13 3 2

40

Motif group HL_94980.1

Basepair signature:
cWW-F-F

6.25 -2181.43 4 4

41

Motif group HL_13963.3

Basepair signature:
cWW-F-F

5.73 -1215.17 4 3

42

Motif group HL_71391.1

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

5.21 -1263.97 3 2

43

Motif group HL_66103.1

Basepair signature:
cWW-F-F

5.21 -1505.45 4 2.5

44

Motif group HL_35941.1

Basepair signature:
cWW-F

5.21 -1951.22 5 4

45

Motif group HL_31585.4

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

5.21 -5572.32 4 2

Purine riboswitch

46

Motif group HL_99040.1

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

4.69 -2971.28 5 4

47

Motif group HL_28075.1

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

3.65 -790.65 4 3

48

Motif group HL_27483.1

Basepair signature:
cWW-F

3.65 -1224.09 4 3

49

Motif group HL_59843.1

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

3.13 -1356.19 4 3

50

Motif group HL_25967.2

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

3.13 -4254.39 5 4

51

Motif group HL_26934.1

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

2.60 -718.30 6 4

52

Motif group HL_87553.1

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

2.60 -830.86 5 3

53

Motif group HL_04259.3

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

2.08 -1164.90 4 3

GNRA with extra cWW

54

Motif group HL_20535.2

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

2.08 -1251.10 4 3

55

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

2.08 -1517.12 5 3

56

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

2.08 -5842.94 3 2

Pseudoknot geometry with 3' bulge

57

Motif group HL_78197.1

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

2.08 -6984.99 5 3

58

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

2.08 -7464.91 5 5

59

Motif group HL_04171.7

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

1.56 -482.13 7 6

60

Motif group HL_75293.5

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

1.56 -663.50 6 4

61

Motif group HL_01609.3

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

1.56 -944.24 4 3

T-loop with 2 bulged bases not stacked

62

Motif group HL_42046.2

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

1.56 -992.54 5 3

63

Motif group HL_10540.1

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

1.56 -1095.21 5 4

64

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

1.56 -1253.65 4 3

65

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

1.56 -1269.80 3 2

66

Motif group HL_25061.1

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

1.56 -3811.25 6 4

67

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

1.56 -4256.66 5 3

T-loop with unstacked turn

68

Motif group HL_55436.1

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

1.56 -4443.33 6 5

69

Motif group HL_81545.2

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

1.04 -347.83 6 5

70

Motif group HL_41464.2

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

1.04 -465.57 5 4

71

Motif group HL_83808.4

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

1.04 -681.15 8 6

Pseudoknot

72

Motif group HL_77082.1

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

1.04 -824.30 4 3

Pseudoknot geometry

73

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

1.04 -1037.20 6 4

Other HL

74

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

1.04 -1084.76 4 3

Fab BL3-6 binding hairpin with tSW

75

Motif group HL_97917.2

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

1.04 -1341.89 4 3

76

Motif group HL_30068.2

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

1.04 -1391.19 3 2

77

Motif group HL_60914.1

Basepair signature:
cWW-F

1.04 -2073.85 5 4

78

Motif group HL_06226.4

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

1.04 -2487.61 7 6

79

Motif group HL_15802.1

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

1.04 -3329.34 7 5

80

Motif group HL_22622.1

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

1.04 -4087.17 6 4

81

Motif group HL_08510.1

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

1.04 -4362.26 7 5

82

Motif group HL_85367.2

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

1.04 -4828.58 5 3

83

Motif group HL_83632.1

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

1.04 -4980.66 5 3

tRNA anticodon loop

84

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

1.04 -5179.62 4 3

Mini UNCG

85

Motif group HL_85993.1

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

1.04 -5706.56 5 4

86

Motif group HL_93324.4

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

1.04 -7338.24 4 2

Pseudoknot geometry

87

Motif group HL_67079.1

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

0.52 -314.78 7 6

88

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

0.52 -457.08 5 4

89

Motif group HL_50860.2

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

0.52 -517.79 5 4

90

Motif group HL_61996.2

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

0.52 -560.46 6 4

91

Motif group HL_57863.1

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

0.52 -719.69 7 5

G-quadruplex fragment

92

Motif group HL_20743.5

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

0.52 -724.16 5 4

93

Motif group HL_73266.9

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

0.52 -760.12 5 3.5

94

Motif group HL_84299.4

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

0.52 -896.68 5 4

95

Motif group HL_18565.1

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

0.52 -903.77 6 4

96

Motif group HL_64690.6

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

0.52 -943.97 5 4

97

Motif group HL_88205.2

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

0.52 -973.47 6 4

98

Motif group HL_13529.1

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

0.52 -983.75 5 3

99

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

0.52 -1065.50 5 4

tRNA anticodon loop with synthetase

100

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.52 -1081.39 4 3

tRNA D-loop

101

Motif group HL_21372.1

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

0.52 -1166.61 6 4

102

Motif group HL_89893.1

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

0.52 -1279.00 5 4

103

Motif group HL_29129.3

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

0.52 -1785.05 7 5

104

Motif group HL_80008.1

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

0.52 -2226.88 5 4

105

Motif group HL_72628.1

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

0.52 -2249.97 6 4.5

106

Motif group HL_05304.3

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

0.52 -2409.26 9 7

107

Motif group HL_18978.1

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

0.52 -2623.89 7 6

108

Motif group HL_87463.1

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

0.52 -2927.38 7 5

109

Motif group HL_04641.1

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

0.52 -3234.95 7 6

110

Motif group HL_99769.3

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

0.52 -3412.25 7 6

111

Motif group HL_39243.1

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

0.52 -3439.72 5 3

112

Motif group HL_28791.1

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

0.52 -3549.47 5 3

113

Motif group HL_33983.1

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

0.52 -3663.09 5 4

114

Motif group HL_06059.6

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

0.52 -4030.97 5 3

tRNA anticodon loop

115

Motif group HL_97733.1

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

0.52 -4273.03 8 6

116

Motif group HL_38649.1

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

0.52 -4273.97 8 6

117

Motif group HL_59330.1

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

0.52 -4472.16 6 5

118

Motif group HL_93135.1

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

0.52 -5108.38 8 6

Pseudoknot

119

Motif group HL_35677.3

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

0.52 -5436.66 6 5

120

Motif group HL_77600.2

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

0.52 -6898.13 5 3

121

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.52 -7003.42 6 4

122

Motif group HL_30680.3

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

0.52 -7157.21 4 3

Pseudoknot geometry

123

Motif group HL_59735.5

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

0.52 -7520.68 4 3

124

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.52 -7702.52 7 5

125

Motif group HL_41902.1

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

0.00 -268.71 9 7

126

Motif group HL_70658.1

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

0.00 -282.20 9 7

127

Motif group HL_93438.2

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

0.00 -291.18 6 4

128

Motif group HL_41543.1

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

0.00 -294.06 8 7

129

Motif group HL_74379.3

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

0.00 -296.49 8 7

130

Motif group HL_68257.1

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

0.00 -305.10 7 6

131

Motif group HL_74055.2

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

0.00 -306.56 11 9

132

Motif group HL_02887.3

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

0.00 -307.59 7 5

T-loop with 3 stacked bulged bases

133

Motif group HL_81205.3

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

0.00 -307.63 10 9

134

Motif group HL_07583.1

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

0.00 -310.11 9 8

135

Motif group HL_84847.1

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

0.00 -311.09 10 8

136

Motif group HL_86109.1

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

0.00 -312.33 9 7

137

Motif group HL_90620.1

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

0.00 -313.79 8 6

138

Motif group HL_73247.1

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

0.00 -338.17 11 9

Pseudoknot geometry

139

Motif group HL_60266.1

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

0.00 -342.16 8 6

140

Motif group HL_14757.1

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

0.00 -342.72 13 12

141

Motif group HL_20167.2

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

0.00 -344.76 5 3

142

Motif group HL_23509.1

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

0.00 -346.15 8 8

143

Motif group HL_36335.1

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

0.00 -347.51 7 6

144

Motif group HL_08602.1

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

0.00 -352.00 10 8

145

Motif group HL_98870.1

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

0.00 -355.04 11 9

146

Motif group HL_91641.1

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

0.00 -358.03 13 11

147

Motif group HL_68767.1

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

0.00 -372.22 9 7

tRNA D-loop

148

Motif group HL_53504.3

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

0.00 -392.36 7 5

149

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -400.13 8 6

150

Motif group HL_77436.5

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

0.00 -433.04 4 2

T-loop related

151

Motif group HL_51921.1

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

0.00 -448.67 16 15

152

Motif group HL_98864.1

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

0.00 -500.36 7 5

T-loop with unstacked turn

153

Motif group HL_49941.1

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

0.00 -533.86 8 6

tRNA D-loop

154

Motif group HL_16991.1

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

0.00 -534.78 8 7

G-quadruplex fragment

155

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -559.18 7 5

156

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -564.87 7 6

157

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

0.00 -579.04 6 5

158

Motif group HL_28252.8

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

0.00 -585.07 5 3

T-loop with 2 stacked bulged bases

159

Motif group HL_92488.1

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

0.00 -588.32 12 11

160

Motif group HL_86012.1

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

0.00 -612.04 6.5 5

T-loop with unstacked turn

161

Motif group HL_13971.1

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

0.00 -653.28 10 9

162

Motif group HL_04642.1

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

0.00 -709.57 7 6

tRNA D-loop

163

Motif group HL_98252.1

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

0.00 -762.12 9 7

164

Motif group HL_25847.2

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

0.00 -818.76 7 6

165

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.00 -861.54 6 5

tRNA D-loop

166

Motif group HL_73255.1

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

0.00 -954.90 7 6

167

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.00 -1013.91 5 4

168

Motif group HL_97756.2

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

0.00 -1021.75 11 10

169

Motif group HL_47854.1

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

0.00 -1121.16 6 5

170

Motif group HL_81538.2

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

0.00 -1145.90 4 3

GNRA with tandem sheared

171

Motif group HL_85434.1

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

0.00 -1408.23 7 5

172

Motif group HL_93616.2

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

0.00 -1540.97 8 6

tRNA D-loop

173

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.00 -2068.54 4 4

174

Motif group HL_02581.1

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

0.00 -2277.86 11 9

tRNA D-loop

175

Motif group HL_02483.1

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

0.00 -2381.10 8 7

176

Motif group HL_91939.2

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

0.00 -2411.32 8 6

177

Motif group HL_45785.1

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

0.00 -2584.60 9 7

178

Motif group HL_89881.5

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

0.00 -2642.77 8 6

179

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -2838.87 4 3

180

Motif group HL_07480.2

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

0.00 -2882.03 8 7

181

Motif group HL_58224.1

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

0.00 -3093.43 7 6

182

Motif group HL_23010.1

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

0.00 -3113.94 8 6

183

Motif group HL_24792.1

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

0.00 -3121.39 7 6

184

Motif group HL_53454.2

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

0.00 -3136.40 6 5

185

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 -3191.80 14 13

186

Motif group HL_10456.1

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

0.00 -3210.21 14 12

187

Motif group HL_66482.1

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

0.00 -3279.81 14 12

188

Motif group HL_33074.4

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

0.00 -3449.75 9 7

U1 small nuclear ribonucleoprotein A binding hairpin

189

Motif group HL_11542.1

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

0.00 -3498.66 9 8

190

Motif group HL_34964.1

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

0.00 -3526.01 8 6

191

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 -3602.80 16 14

192

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 -3609.18 16 14

193

Motif group HL_85461.1

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

0.00 -3680.51 15 14

194

Motif group HL_60293.1

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

0.00 -3699.69 18 16

G-quadruplex

195

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 -3704.21 13 11

196

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 -3705.08 19 17

G-quadruplex

197

Motif group HL_93383.1

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

0.00 -3734.89 6 4

198

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 -3751.40 20 18

199

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 -3752.51 21 19

G-quadruplex

200

Motif group HL_80599.2

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

0.00 -3888.06 6 5

201

Motif group HL_20751.2

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

0.00 -3898.23 10 8

202

Motif group HL_73183.1

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

0.00 -3982.91 11 10

Pseudoknot geometry with G-bulge

203

Motif group HL_37369.2

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

0.00 -3998.73 5 3

204

Motif group HL_50851.1

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

0.00 -4074.25 10 8

G-quadruplex fragment

205

Motif group HL_32735.2

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

0.00 -4126.59 5 3

206

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 -4146.35 35 34

207

Motif group HL_07903.1

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

0.00 -4199.30 11 9

208

Motif group HL_63355.1

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

0.00 -4304.23 10 8

209

Motif group HL_04725.1

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

0.00 -4370.92 8 7

210

Motif group HL_88364.2

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

0.00 -4457.12 12 10

211

Motif group HL_67407.5

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

0.00 -4460.19 7 6

212

Motif group HL_02817.2

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

0.00 -4527.52 5 3

213

Motif group HL_31581.6

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

0.00 -4547.27 9 7

214

Motif group HL_88558.1

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

0.00 -4557.48 8 7

215

Motif group HL_23115.1

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

0.00 -4579.14 8 7

tRNA D-loop

216

Motif group HL_81312.1

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

0.00 -4605.83 9 7

217

Motif group HL_16398.2

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

0.00 -4662.45 9 8

218

Motif group HL_19210.3

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

0.00 -4687.20 7 5

219

Motif group HL_91503.7

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

0.00 -4724.23 7 5

220

Motif group HL_00914.1

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

0.00 -4749.44 5 4

221

Motif group HL_55305.1

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

0.00 -4755.11 8 7

222

Motif group HL_38046.1

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

0.00 -4764.73 7 5

223

Motif group HL_10453.3

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

0.00 -4794.30 4 3

tRNA anticodon loop

224

Motif group HL_80411.1

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

0.00 -4816.70 9 7

tRNA D-loop

225

Motif group HL_50779.4

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

0.00 -4848.62 6 5

226

Motif group HL_29762.1

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

0.00 -4858.76 7 5

227

Motif group HL_01255.1

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

0.00 -4878.04 8 7

228

Motif group HL_64292.1

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

0.00 -4886.75 13 11

229

Motif group HL_15118.1

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

0.00 -4890.94 9 7

230

Motif group HL_94376.1

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

0.00 -4955.60 7 6

Pseudoknot geometry

231

Motif group HL_78284.1

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

0.00 -5118.84 8 7

232

Motif group HL_47732.1

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

0.00 -5261.80 9 7

233

Motif group HL_69139.1

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

0.00 -5283.95 7 6

234

Motif group HL_70751.1

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

0.00 -5311.13 8 6

235

Motif group HL_74292.1

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

0.00 -5326.72 7 5.5

236

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.00 -5419.93 6 4

237

Motif group HL_29958.1

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

0.00 -5447.41 10 9

238

Motif group HL_36684.4

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

0.00 -5449.59 7 5

239

Motif group HL_12870.1

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

0.00 -5471.36 9 7

240

Motif group HL_50418.1

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

0.00 -5575.77 7 6

241

Motif group HL_15574.1

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

0.00 -5620.53 5 4

242

Motif group HL_68572.1

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

0.00 -5670.74 10 8

243

Motif group HL_51447.1

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

0.00 -5814.51 5 4

244

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -5891.30 4 3

245

Motif group HL_42998.2

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

0.00 -5902.70 5 4

246

Motif group HL_99867.1

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

0.00 -5905.16 6 5

247

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -6215.97 4 3

248

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.00 -6229.64 7 5

249

Motif group HL_20781.1

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

0.00 -6386.58 8 7

250

Motif group HL_80241.1

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

0.00 -7200.11 5 4

251

Motif group HL_58539.1

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

0.00 -7374.59 12 11

252

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.00 -9999.00 6 5

tRNA D-loop

253

Motif group HL_09260.2

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

0.00 -9999.00 8 7

tRNA D-loop

Coloring options: