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 31 Hairpin loop

Column numbers: 542-559 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    ----UUGGCGU-------   20

    
    AU--GUAGCA------GU   13

    
    GC--GUAGCA------GU   12

    
    ---GGUGAUAG-------   11

    
    ----GUGAGAA-------    8

    
    GU--GUGAGAG-----AC    7

    
    U---GUGGCA-------A    7

    
    G--UUUGAGAC------C    6

    
    ----GGGGAC--------    6

    
    G--CGUGAGAAA-----C    5

    
    ----CUGGUAA-------    5

    
    ----GUGGUA--------    5

    
    ----GUGGUG--------    5

    
    GU--GUGAAAG-----AC    4

    
    ---CGUCGAAAA------    4

    
    ----CUGGUGA-------    4

    
    ----GUGGAAG-------    4

    
    ----CCGCAA--------    4

    
    ----GUGGAA--------    4

    
    AG--GCGGAAAA----CU    3

    
    GG--CUGAUUA-----CC    3

    
    UU--AGGGAU------AA    3

    
    C--UGUGGUG-------G    3

    
    ---GGUGGAAG-------    3

    
    U---GUGGCA-------G    3

    
    -----GGGAUGC------    3

    
    ----GUAGCA--------    3

    
    G--CCUGAGAAA-----C    2

    
    G--CGUGAGAGA-----C    2

    
    GC--GUAGCA------GC    2

    
    GC--GUAGCG------GU    2

    
    U---GUGAGAG------A    2

    
    ---CUUGGCCG-------    2

    
    ---UGUGGCAA-------    2

    
    ---UGUGGCAG-------    2

    
    C---UUGGCC-------G    2

    
    U---UUGGCA-------A    2

    
    ----CUGGUUA-------    2

    
    ----GUGAGAG-------    2

    
    ----UUGGCAU-------    2

    
    ----UUGGCUU-------    2

    
    ----UUGGUGA-------    2

    
    ----UUGGUUA-------    2

    
    ---UGUGGUG--------    2

    
    ---UUUGCGG--------    2

    
    ----AGGGAU--------    2

    
    ----GUGGCA--------    2

    
    ----UGGGAG--------    2

    
    ----UUGGCA--------    2

    
    ----GUGGAAUGUUACAG    1

    
    GU-UAUGGGAAUA---GC    1

    
    UG-GGAGAUGAA----CG    1

    
    GC--AUGAGAAC----GC    1

    
    UCUAGGGAUA------GA    1

    
    ----GUGGAAUGU---UA    1

    
    A--CCUGAAGAA-----U    1

    
    AG--CUGGUGC-----UU    1

    
    AG-CUGGUAA------CU    1

    
    AU-UAUGGUG------AU    1

    
    G--CGUAGGAAA-----C    1

    
    G--CGUCGAAAA-----C    1

    
    GU--GUGAGAA-----GC    1

    
    GU--GUGAGAG-----GC    1

    
    GU-GUGAGAG------AC    1

    
    UU--GUGGCAU-----AA    1

    
    UU--GUGGCAU-----GA    1

    
    ----UUGGUACCCU----    1

    
    A---GUGGGAGC-----U    1

    
    AU--GGGGAC------AU    1

    
    AU--GGGGGC------AU    1

    
    AU--GUGGUA------GU    1

    
    G--GGUGAGAG------C    1

    
    GC--GUGGUU------GU    1

    
    GG--GUGGAA------CC    1

    
    GU--GUAGCA------AC    1

    
    GU--GUGAGA------GC    1

    
    UC--AGAGAU------GA    1

    
    ---CCUGAGAAA------    1

    
    ---CGUAGAAAA------    1

    
    ---CGUCGAAA------A    1

    
    ---CGUCGAAAC------    1

    
    ---CGUGAGAGA------    1

    
    --AAUGAGAGA-------    1

    
    --CCGUGGAAC-------    1

    
    --UAGAGGUAU-------    1

    
    A---UUGGUAA------C    1

    
    U---GUGAGAGA------    1

    
    ----UGUGGCAG------    1

    
    ---CGUGGCAA-------    1

    
    ---CUUGAUAA-------    1

    
    ---GGUGGUAG-------    1

    
    ---UGUGGUAG-------    1

    
    ---UUUGAGAC-------    1

    
    ---UUUGGUAC-------    1

    
    --GGUGAUAG--------    1

    
    -U--GUGGCA------G-    1

    
    C---GUAGCU-------G    1

    
    C---GUGGCA-------G    1

    
    G---GUGACA-------C    1

    
    G---GUGGAA-------C    1

    
    G---GUGGUG-------C    1

    
    U---AGGGAU-------A    1

    
    U---GUGACA-------A    1

    
    U---GUGGAA-------A    1

    
    U---UUGGCG-------A    1

    
    -----GGGGUGC------    1

    
    ----CCGCAAG-------    1

    
    ----CUAACGA-------    1

    
    ----CUGAGAA-------    1

    
    ----CUGCAAA-------    1

    
    ----CUGGUGC-------    1

    
    ----GUAGCAA-------    1

    
    ----GUGAUAG-------    1

    
    ----GUGGAAU-------    1

    
    ----GUGGGAA-------    1

    
    ----GUUGCAG-------    1

    
    ----UUGGUAA-------    1

    
    ----UUGGUAC-------    1

    
    ----UUGGUCG-------    1

    
    ---GUGAGAG--------    1

    
    ---GUUGCAG--------    1

    
    ---UUUGCAG--------    1

    
    ---UUUGGCA--------    1

    
    G---GUGGUG--------    1

    
    -----GGGAUA-------    1

    
    ----AUGGGG--------    1

    
    ----AUGGUG--------    1

    
    ----GUGACA--------    1

    
    ----GUGAGA--------    1

    
    ----GUGGCU--------    1

    
    ----UGGGUG--------    1

    
    -----GGGAU--------    1

    
    Omitted sequenced and counts

    
    ------------------    5
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_25061.1

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

23.16 -41.18 4 3

2

Motif group HL_75293.5

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

15.44 -60.25 5 3

3

Motif group HL_81538.2

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

10.88 -87.36 3 3

GNRA with tandem sheared

4

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

7.72 -67.31 5 4

tRNA anticodon loop with synthetase

5

Motif group HL_78197.1

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

7.37 -140.77 4 3

6

Motif group HL_41543.1

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

7.02 -77.63 6 5

7

Motif group HL_85367.2

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

6.67 -102.86 4 3

8

Motif group HL_36684.4

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

6.67 -4446.19 5 4

9

Motif group HL_33983.1

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

5.26 -61.70 5 4

10

Motif group HL_29129.3

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

4.91 -83.43 5 4

11

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

4.56 -96.37 4 4

12

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

3.86 -138.73 5 4

13

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

3.86 -1415.78 5 4

14

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

3.51 -72.40 5 4

tRNA D-loop

15

Motif group HL_41464.2

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

3.16 -75.82 4 4

16

Motif group HL_50418.1

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

3.16 -4553.38 6 5

17

Motif group HL_13963.3

Basepair signature:
cWW-F-F

2.81 -112.54 4 4

18

Motif group HL_83632.1

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

2.81 -115.41 5 3

tRNA anticodon loop

19

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

2.81 -120.50 4 4

tRNA D-loop

20

Motif group HL_88205.2

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

2.81 -217.29 5 4

21

Motif group HL_87463.1

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

2.46 -62.10 5 4

22

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

2.46 -63.37 5 4

23

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

2.46 -321.83 3 4

tRNA D-loop

24

Motif group HL_93135.1

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

2.46 -961.39 6 5

Pseudoknot

25

Motif group HL_04642.1

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

2.11 -62.32 6 5

tRNA D-loop

26

Motif group HL_86012.1

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

2.11 -72.91 6 5

T-loop with unstacked turn

27

Motif group HL_78347.4

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

2.11 -101.42 4 4

28

Motif group HL_06059.6

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

2.11 -107.53 4 3

tRNA anticodon loop

29

Motif group HL_87553.1

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

2.11 -112.80 4 4

30

Motif group HL_50006.2

Basepair signature:
cWW-F-F

2.11 -112.83 4 4

31

Motif group HL_19210.3

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

2.11 -2369.84 6 4

32

Motif group HL_84299.4

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

1.75 -79.98 4 3

33

Motif group HL_56131.2

Basepair signature:
cWW-F-F

1.75 -117.67 4 4

34

Motif group HL_28075.1

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

1.75 -121.67 5 4

35

Motif group HL_22622.1

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

1.75 -1422.53 5 4

36

Motif group HL_55436.1

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

1.75 -1799.19 5 4

37

Motif group HL_58224.1

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

1.40 -66.33 6 5

38

Motif group HL_16991.1

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

1.40 -76.31 6 5

G-quadruplex fragment

39

Motif group HL_20167.2

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

1.40 -78.75 4 3

40

Motif group HL_31585.4

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

1.40 -121.67 3 3

Purine riboswitch

41

Motif group HL_00914.1

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

1.40 -129.96 5 4

42

Motif group HL_59330.1

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

1.40 -1060.51 6 4

43

Motif group HL_08510.1

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

1.40 -1739.33 5 4

44

Motif group HL_18565.1

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

1.05 -60.70 5 4

45

Motif group HL_98864.1

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

1.05 -76.79 5 5

T-loop with unstacked turn

46

Motif group HL_21372.1

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

1.05 -113.50 5 4

47

Motif group HL_07480.2

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

1.05 -156.53 7 6

48

Motif group HL_59843.1

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

1.05 -185.34 5 5

49

Motif group HL_74292.1

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

1.05 -3033.83 6 5

50

Motif group HL_18978.1

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

0.70 -72.79 6 5

51

Motif group HL_01609.3

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

0.70 -86.07 3 3

T-loop with 2 bulged bases not stacked

52

Motif group HL_97917.2

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

0.70 -100.91 4 4

53

Motif group HL_20743.5

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

0.70 -105.16 5 5

54

Motif group HL_99769.3

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

0.70 -110.26 6 4

55

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

0.70 -134.33 5 4

56

Motif group HL_04259.3

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

0.70 -135.21 4 3

GNRA with extra cWW

57

Motif group HL_37369.2

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

0.70 -164.30 4 4

58

Motif group HL_99867.1

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

0.70 -3358.16 5 4

59

Motif group HL_57863.1

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

0.35 -67.77 6 5

G-quadruplex fragment

60

Motif group HL_50860.2

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

0.35 -68.10 4 3

61

Motif group HL_61996.2

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

0.35 -74.19 5 4

62

Motif group HL_02887.3

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

0.35 -84.27 7 6

T-loop with 3 stacked bulged bases

63

Motif group HL_93438.2

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

0.35 -85.78 6 5

64

Motif group HL_20535.2

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

0.35 -92.57 5 4

65

Motif group HL_89881.5

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

0.35 -97.41 6 5

66

Motif group HL_06226.4

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

0.35 -97.91 6 5

67

Motif group HL_10453.3

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

0.35 -106.31 4 4

tRNA anticodon loop

68

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

0.35 -122.84 4 4

69

Motif group HL_80008.1

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

0.35 -123.94 5 4

70

Motif group HL_48417.5

Basepair signature:
cWW-F-F

0.35 -124.61 4 4

71

Motif group HL_10540.1

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

0.35 -125.79 5 4

72

Motif group HL_13529.1

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

0.35 -143.47 5 5

73

Motif group HL_34964.1

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

0.35 -154.70 6 5

74

Motif group HL_93324.4

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

0.35 -174.32 4 3

Pseudoknot geometry

75

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

0.35 -220.28 6 5

76

Motif group HL_20751.2

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

0.35 -881.52 8 7

77

Motif group HL_80599.2

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

0.35 -900.12 5 4

78

Motif group HL_35677.3

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

0.35 -1106.68 6 5

79

Motif group HL_85993.1

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

0.35 -1373.07 6 5

80

Motif group HL_51447.1

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

0.35 -1542.59 5 5

81

Motif group HL_32346.4

Basepair signature:
cWW-F

0.35 -1800.50 4 4

82

Motif group HL_55305.1

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

0.35 -2428.35 7 6

83

Motif group HL_42998.2

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

0.35 -2437.47 5 4

84

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.35 -3776.85 6 5

85

Motif group HL_78284.1

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

0.35 -3902.97 7 6

86

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.35 -9999.00 5 4

tRNA D-loop

87

Motif group HL_15802.1

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

0.00 -69.19 6 5

88

Motif group HL_26934.1

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

0.00 -87.52 5 4

89

Motif group HL_04641.1

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

0.00 -92.15 7 6

90

Motif group HL_83808.4

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

0.00 -92.26 6 5

Pseudoknot

91

Motif group HL_97733.1

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

0.00 -95.57 6 5

92

Motif group HL_53454.2

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

0.00 -95.66 5 4

93

Motif group HL_67079.1

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

0.00 -96.20 6 5

94

Motif group HL_49941.1

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

0.00 -98.23 6 5

tRNA D-loop

95

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

0.00 -99.66 6 5

Other HL

96

Motif group HL_23010.1

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

0.00 -100.48 7 5

97

Motif group HL_02483.1

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

0.00 -103.78 7 6

98

Motif group HL_68257.1

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

0.00 -106.10 7 6

99

Motif group HL_77436.5

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

0.00 -107.01 4 3

T-loop related

100

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.00 -107.77 5 4

101

Motif group HL_64690.6

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

0.00 -108.83 5 4

102

Motif group HL_28252.8

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

0.00 -110.24 4 3

T-loop with 2 stacked bulged bases

103

Motif group HL_45785.1

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

0.00 -111.06 8 7

104

Motif group HL_41902.1

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

0.00 -111.54 7 6

105

Motif group HL_81545.2

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

0.00 -111.61 6 5

106

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.00 -112.47 4 4

T-loop with unstacked turn

107

Motif group HL_36335.1

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

0.00 -114.84 7 6

108

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -117.97 7 5

109

Motif group HL_73266.9

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

0.00 -118.41 5 4

110

Motif group HL_74379.3

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

0.00 -118.59 8 7

111

Motif group HL_86109.1

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

0.00 -118.68 7 6

112

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -119.19 7 6

113

Motif group HL_77082.1

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

0.00 -119.62 5 4

Pseudoknot geometry

114

Motif group HL_98252.1

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

0.00 -120.28 8 7

115

Motif group HL_04171.7

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

0.00 -121.44 6 6

116

Motif group HL_90620.1

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

0.00 -122.31 8 6

117

Motif group HL_05304.3

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

0.00 -124.29 8 6

118

Motif group HL_60266.1

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

0.00 -125.05 7 6

119

Motif group HL_70658.1

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

0.00 -126.40 8 6

120

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -127.40 6 5

121

Motif group HL_85434.1

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

0.00 -127.49 7 6

122

Motif group HL_25847.2

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

0.00 -132.27 7 6

123

Motif group HL_91939.2

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

0.00 -132.43 7 6

124

Motif group HL_37344.1

Basepair signature:
cWW-F-F

0.00 -132.94 5 4

125

Motif group HL_38046.1

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

0.00 -140.60 7 6

126

Motif group HL_47854.1

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

0.00 -143.46 6 5

127

Motif group HL_42046.2

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

0.00 -145.94 4 4

128

Motif group HL_72628.1

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

0.00 -148.48 6 5

129

Motif group HL_07583.1

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

0.00 -148.98 8 7

130

Motif group HL_23509.1

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

0.00 -150.06 9 8

131

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

0.00 -150.75 5 4

132

Motif group HL_93616.2

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

0.00 -152.08 6 5

tRNA D-loop

133

Motif group HL_53504.3

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

0.00 -158.16 7 5

134

Motif group HL_81205.3

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

0.00 -158.78 8 7

135

Motif group HL_25967.2

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

0.00 -162.21 6 5

136

Motif group HL_68767.1

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

0.00 -164.33 7 6

tRNA D-loop

137

Motif group HL_93535.1

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

0.00 -168.31 4 4

138

Motif group HL_84847.1

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

0.00 -171.84 9 8

139

Motif group HL_73255.1

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

0.00 -172.89 7 6

140

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

0.00 -173.49 5 4

141

Motif group HL_02817.2

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

0.00 -173.95 6 5

142

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

0.00 -175.75 4 4

143

Motif group HL_08602.1

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

0.00 -176.45 9 8

144

Motif group HL_11542.1

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

0.00 -177.79 8 7

145

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

0.00 -180.54 4 4

146

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

0.00 -182.54 5 4

147

Motif group HL_30068.2

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

0.00 -184.62 4 4

148

Motif group HL_98870.1

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

0.00 -187.71 9 7

149

Motif group HL_89893.1

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

0.00 -190.63 5 5

150

Motif group HL_73247.1

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

0.00 -191.99 9 8

Pseudoknot geometry

151

Motif group HL_15574.1

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

0.00 -192.97 5 5

152

Motif group HL_13971.1

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

0.00 -197.48 9 8

153

Motif group HL_74055.2

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

0.00 -197.83 9 8

154

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

0.00 -199.00 5 5

155

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

0.00 -204.42 4 4

156

Motif group HL_02581.1

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

0.00 -208.68 9 8

tRNA D-loop

157

Motif group HL_37824.7

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

0.00 -216.79 3 3

GNRA

158

Motif group HL_47787.2

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

0.00 -217.06 4 4

159

Motif group HL_27483.1

Basepair signature:
cWW-F

0.00 -217.15 5 5

160

Motif group HL_56676.1

Basepair signature:
cWW-F-F

0.00 -217.32 4 4

161

Motif group HL_71391.1

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

0.00 -217.46 5 4

162

Motif group HL_91641.1

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

0.00 -220.64 11 9

163

Motif group HL_66103.1

Basepair signature:
cWW-F-F

0.00 -232.09 5 4

164

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

0.00 -234.78 5 5

Fab BL3-6 binding hairpin with tSW

165

Motif group HL_57875.1

Basepair signature:
cWW-F-F

0.00 -252.71 4 4

166

Motif group HL_39243.1

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

0.00 -259.26 6 5

167

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.00 -260.23 4 4

UNCG

168

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

0.00 -261.35 5 4

169

Motif group HL_13189.1

Basepair signature:
cWW-F-F

0.00 -265.24 4 4

170

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

0.00 -283.26 5 5

171

Motif group HL_14757.1

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

0.00 -289.79 12 11

172

Motif group HL_51921.1

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

0.00 -309.05 14 13

173

Motif group HL_46501.1

Basepair signature:
cWW-cWS

0.00 -313.37 4 4

174

Motif group HL_65794.5

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

0.00 -318.56 3 4

Pseudoknot geometry

175

Motif group HL_97756.2

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

0.00 -337.45 10 8

176

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.00 -346.81 5 5

177

Motif group HL_92488.1

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

0.00 -374.53 11 10

178

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -465.04 5 5

179

Motif group HL_70782.2

Basepair signature:
cWW-F

0.00 -472.24 4 4

180

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

0.00 -478.58 4 4

Pseudoknot geometry with 3' bulge

181

Motif group HL_69752.2

Basepair signature:
cWW-F

0.00 -482.56 5 5

182

Motif group HL_38168.1

Basepair signature:
cWW-F

0.00 -484.54 5 4

183

Motif group HL_75660.5

Basepair signature:
cWW-F

0.00 -487.46 4 4

184

Motif group HL_48778.2

Basepair signature:
cWW-F

0.00 -570.24 4 4

Mini UNCG

185

Motif group HL_10456.1

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

0.00 -834.61 12 10

186

Motif group HL_66482.1

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

0.00 -847.89 11 10

187

Motif group HL_23115.1

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

0.00 -886.80 7 6

tRNA D-loop

188

Motif group HL_91503.7

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

0.00 -905.73 5 4

189

Motif group HL_29762.1

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

0.00 -930.12 6 5

190

Motif group HL_80411.1

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

0.00 -941.26 7 6

tRNA D-loop

191

Motif group HL_88558.1

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

0.00 -968.91 8 7

192

Motif group HL_32735.2

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

0.00 -1008.46 5 5

193

Motif group HL_69139.1

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

0.00 -1069.45 7 6

194

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.00 -1196.43 6 5

195

Motif group HL_93383.1

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

0.00 -1382.17 6 5

196

Motif group HL_99040.1

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

0.00 -1500.56 5 4

197

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.00 -1568.53 5 4

Mini UNCG

198

Motif group HL_30680.3

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

0.00 -1644.99 4 3

Pseudoknot geometry

199

Motif group HL_56334.1

Basepair signature:
cWW-F

0.00 -1761.60 4 4

Mini UNCG

200

Motif group HL_38649.1

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

0.00 -1765.41 6 5

201

Motif group HL_55195.3

Basepair signature:
cWW-F

0.00 -1767.24 4 4

202

Motif group HL_33074.4

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

0.00 -1788.74 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

203

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

0.00 -1804.58 6 6

204

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

0.00 -1806.80 4 4

205

Motif group HL_52953.3

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

0.00 -1806.81 4 4

206

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

0.00 -1817.50 7 6

207

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -1821.28 6 5

208

Motif group HL_28791.1

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

0.00 -1826.01 5 5

209

Motif group HL_50779.4

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

0.00 -1832.29 6 5

210

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 -1849.41 13 11

211

Motif group HL_59735.5

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

0.00 -2045.36 5 5

212

Motif group HL_67407.5

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

0.00 -2246.33 6 5

213

Motif group HL_73183.1

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

0.00 -2284.98 9 8

Pseudoknot geometry with G-bulge

214

Motif group HL_81312.1

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

0.00 -2370.92 8 7

215

Motif group HL_01255.1

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

0.00 -2497.75 8 7

216

Motif group HL_16398.2

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

0.00 -2619.91 8 7

217

Motif group HL_80241.1

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

0.00 -2705.55 6 5

218

Motif group HL_47732.1

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

0.00 -2717.91 9 7

219

Motif group HL_50851.1

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

0.00 -2733.57 8 7

G-quadruplex fragment

220

Motif group HL_64292.1

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

0.00 -2794.66 11 9

221

Motif group HL_29958.1

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

0.00 -2805.29 8 6

222

Motif group HL_04725.1

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

0.00 -2953.34 8 7

223

Motif group HL_31581.6

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

0.00 -3071.96 7 6

224

Motif group HL_07903.1

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

0.00 -3079.98 9 8

225

Motif group HL_63355.1

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

0.00 -3109.21 8 7

226

Motif group HL_20781.1

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

0.00 -3243.58 8 7

227

Motif group HL_15118.1

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

0.00 -3286.89 8 7

228

Motif group HL_94376.1

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

0.00 -3325.13 6 5

Pseudoknot geometry

229

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -3554.78 5 5

230

Motif group HL_78677.1

Basepair signature:
cWW-F-F

0.00 -3560.48 4 5

231

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -3568.70 5 5

232

Motif group HL_24792.1

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

0.00 -3604.30 7 6

233

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.00 -3609.48 5 6

234

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -3618.21 5 6

235

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 -3959.85 15 14

236

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 -3978.09 11 10

237

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 -4002.12 15 14

238

Motif group HL_85461.1

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

0.00 -4002.15 13 12

239

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 -4028.91 16 15

G-quadruplex

240

Motif group HL_60293.1

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

0.00 -4033.30 15 14

G-quadruplex

241

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 -4044.63 17 16

242

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 -4065.52 18 17

G-quadruplex

243

Motif group HL_81100.2

Basepair signature:
cWW

0.00 -4186.06 5 5

244

Motif group HL_77600.2

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

0.00 -4234.11 4 3

245

Motif group HL_88364.2

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

0.00 -4288.82 10 9

246

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -4329.92 5 6

247

Motif group HL_70751.1

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

0.00 -4356.41 7 6

248

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 -4566.29 32 31

249

Motif group HL_12870.1

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

0.00 -4719.10 8 7

250

Motif group HL_58539.1

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

0.00 -4927.86 11 9

251

Motif group HL_68572.1

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

0.00 -5024.66 8 6

252

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -6240.70 6 6

253

Motif group HL_09260.2

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

0.00 -9999.00 6 5

tRNA D-loop

Coloring options: