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 40 Hairpin loop

Column numbers: 991-1017 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    G-------UA-A--CCAGU-------C   32

    
    G-------UA----UCAAU-------C   29

    
    G-------UA-A--UCAAU-------C   20

    
    G-------UG----AAAUU-------C   12

    
    G-------UA-A--CCAAU-------C    8

    
    G-------UA-A--CCAUU-------C    7

    
    G-------UA-A----AGU-------C    7

    
    G-------UA-A--UCAGU-------C    6

    
    A-------UA-A--CCAAU-------U    5

    
    G-------UA-A--ACAAU-------C    5

    
    G-------UA-A--GCAAU-------C    5

    
    G-------UA-A--UCAUU-------C    5

    
    C-------UG----CUAGU-------G    5

    
    GU------UA-AAUUCGCU------CC    4

    
    G-------UA-AAGGUAAU-------C    4

    
    G-------UA-A--ACAGU-------C    4

    
    G-------UA-A--GCAUU-------C    4

    
    G-------UA-A--UCAAC-------C    4

    
    G-------UA----UUAUU-------C    4

    
    G-------UU----UCAAG-------C    4

    
    G-------UA-A----AAU-------C    4

    
    G-------UA-A----AUU-------C    4

    
    G-------UAGC--AAAAU-------C    3

    
    G-------UA-G--CCAAU-------C    3

    
    G-------UA-G--CCAUU-------C    3

    
    G-------UA-G--UCAAU-------C    3

    
    G-------CA----UCAAU-------C    3

    
    G-------UA----UCAUU-------C    3

    
    G-------UACAAAAUAAU-------C    2

    
    AG------GA-A--AAGAU------CU    2

    
    A-------UA-A--CCACU-------U    2

    
    G-------CA-A--UCAAU-------C    2

    
    G-------GA-A--CCUAU-------C    2

    
    G-------UA-G--AAAGU-------C    2

    
    G-------UA-G--ACAAU-------C    2

    
    G-------UA-G--UCAUU-------C    2

    
    C-------UG----CCAAU-------G    2

    
    C-------UG----CUGGU-------G    2

    
    G-------CA----UUAAU-------C    2

    
    G-------UG----AAGUU-------C    2

    
    G-------UG----AUAUU-------C    2

    
    G----------A--UAAAU-------C    2

    
    G-------UAAA-----UC-------C    2

    
    AAUACAAAUACA--AUCUA-UUUGAUU    1

    
    G-------UAAAAAUUAAUU------C    1

    
    GA------UAAU-CUAAAC------UC    1

    
    G-------UAUGAAAAAUC-------C    1

    
    G-----UAUAAA--AGAAU-------C    1

    
    GA------UAAU--CGAGU------UC    1

    
    GA------UAAU--UAAAU------UC    1

    
    GA------UUAU--GCAAG------UC    1

    
    GG------UAAU--UUAGU------CC    1

    
    AG------GA-A--AAGGU------CU    1

    
    G-------UA-AAAAGAAU-------C    1

    
    G-------UA-AUCUGAGU-------C    1

    
    G-------UAAU-UCCAAU-------C    1

    
    G-------UAGA-AAGAGC-------C    1

    
    GC------CA-G--UAGAG------CU    1

    
    GG------UA-G--ACAUU------CC    1

    
    CG------UG-A--CCAAU------C-    1

    
    G-------UACA--UGAAU-------C    1

    
    G-------UAGA--CGAAU-------C    1

    
    A-------AA-A--CCAAU-------U    1

    
    A-------UA-A--UCAAU-------U    1

    
    G-------AA-A--CUAAU-------C    1

    
    G-------CA-A--CCAAU-------C    1

    
    G-------CA-C--UAAAU-------C    1

    
    G-------UA-A--ACAAC-------C    1

    
    G-------UA-A--CCAUC-------C    1

    
    G-------UA-A--GCAGU-------C    1

    
    G-------UA-A--UCAGC-------C    1

    
    G-------UA-A--UGAAU-------C    1

    
    G-------UA-C--UCAAU-------C    1

    
    G-------UA-C--UCAUU-------C    1

    
    G-------UA-G--UAAAU-------C    1

    
    G-------UA-G--UUAGC-------C    1

    
    G-------UC-G--CCAAG-------C    1

    
    G-------UC-G--CCGAG-------C    1

    
    G-------UC-G--CCGUG-------U    1

    
    G-------UC-G--UCGAG-------C    1

    
    G-------UG-A--AGAAU-------C    1

    
    G-------UU-G--CCAUG-------C    1

    
    G-------UU-U--ACAAU-------C    1

    
    A-------GA-G--A-GAU-------U    1

    
    C-------GA----AAGAU-------G    1

    
    C-------GA----AGGAU-------G    1

    
    C-------GA----GAGAU-------G    1

    
    G-------UA----CCAAU-------C    1

    
    G-------UA----GCAAU-------C    1

    
    G-------UA----UCAAC-------C    1

    
    G-------UA----UUAGU-------C    1

    
    G-------UA----UUGAU-------C    1

    
    G-------UC----ACAAU-------C    1

    
    G-------UC----ACAGU-------C    1

    
    G-------UG----ACAUU-------C    1

    
    G-------UU----CUAAU-------C    1

    
    G-------UU----UCGUU-------C    1

    
    U-------UA----GCAGU-------A    1

    
    U-------UG----UUGAU-------A    1

    
    C-------CA-----UCGC-------G    1

    
    G-------UA-A----AUC-------C    1

    
    G-------UG-A----AAU-------C    1

    
    --------GACA---------------    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_04171.7

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

69.66 -12.73 6 4

2

Motif group HL_38808.1

Basepair signature:
cWW-cWW

67.59 -59.64 5 3

3

Motif group HL_61996.2

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

40.00 -41.13 3 3

4

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

40.00 -90.87 2 2

T-loop with unstacked turn

5

Motif group HL_98864.1

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

33.79 -32.57 4 4

T-loop with unstacked turn

6

Motif group HL_25847.2

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

30.69 -60.21 4 4

7

Motif group HL_81545.2

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

18.97 -31.51 4 4

8

Motif group HL_20167.2

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

14.48 -58.10 4 3

9

Motif group HL_01609.3

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

11.03 -96.77 3 2

T-loop with 2 bulged bases not stacked

10

Motif group HL_08510.1

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

10.00 -214.61 7 5

11

Motif group HL_57863.1

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

7.59 -70.49 5 5

G-quadruplex fragment

12

Motif group HL_87463.1

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

7.24 -73.75 5 5

13

Motif group HL_39243.1

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

7.24 -358.09 4 3

14

Motif group HL_83808.4

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

6.90 -61.75 7 5

Pseudoknot

15

Motif group HL_77436.5

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

6.90 -95.24 3 3

T-loop related

16

Motif group HL_98252.1

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

6.55 -50.10 7 5

17

Motif group HL_02887.3

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

6.55 -54.87 6 5

T-loop with 3 stacked bulged bases

18

Motif group HL_28252.8

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

6.55 -102.08 3 3

T-loop with 2 stacked bulged bases

19

Motif group HL_15574.1

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

6.55 -219.60 3 3

20

Motif group HL_97983.1

Basepair signature:
cWW-F-F

6.21 -352.27 7 6

21

Motif group HL_68257.1

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

5.86 -46.78 6 4

22

Motif group HL_99769.3

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

5.52 -73.49 5 5

23

Motif group HL_69139.1

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

4.83 -87.74 7 5

24

Motif group HL_77600.2

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

4.83 -138.41 4 4

25

Motif group HL_93438.2

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

4.48 -49.11 6 4

26

Motif group HL_93135.1

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

4.48 -77.33 7 5

Pseudoknot

27

Motif group HL_29762.1

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

4.14 -72.63 6 5

28

Motif group HL_93324.4

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

3.10 -191.67 4 4

Pseudoknot geometry

29

Motif group HL_86012.1

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

2.76 -74.91 5 4

T-loop with unstacked turn

30

Motif group HL_73255.1

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

2.76 -86.15 6 5

31

Motif group HL_38046.1

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

2.41 -99.38 5 4

32

Motif group HL_88205.2

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

2.41 -99.95 5 4

33

Motif group HL_91939.2

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

2.41 -110.91 6 5

34

Motif group HL_73266.9

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

2.41 -125.22 5 4

35

Motif group HL_04259.3

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

2.41 -181.91 4 4

GNRA with extra cWW

36

Motif group HL_02817.2

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

2.41 -196.63 5 4

37

Motif group HL_85993.1

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

2.41 -542.09 5 4

38

Motif group HL_93383.1

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

2.41 -1106.16 5 5

39

Motif group HL_89881.5

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

2.07 -91.27 5 5

40

Motif group HL_04641.1

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

2.07 -93.91 7 5

41

Motif group HL_80008.1

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

2.07 -106.79 6 4

42

Motif group HL_13529.1

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

2.07 -121.81 4 3

43

Motif group HL_85367.2

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

2.07 -145.19 6 4

44

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

2.07 -251.66 4 3

45

Motif group HL_04725.1

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

2.07 -429.45 5 5

46

Motif group HL_60266.1

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

1.72 -67.11 5 5

47

Motif group HL_18565.1

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

1.72 -104.30 6 5

48

Motif group HL_77082.1

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

1.72 -120.71 4 4

Pseudoknot geometry

49

Motif group HL_28075.1

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

1.72 -148.56 5 4

50

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

1.72 -272.16 7 5

51

Motif group HL_53504.3

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

1.38 -92.99 5 5

52

Motif group HL_34964.1

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

1.38 -108.67 5 5

53

Motif group HL_20535.2

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

1.38 -132.72 4 4

54

Motif group HL_78197.1

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

1.38 -171.74 5 3

55

Motif group HL_99867.1

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

1.38 -2083.23 5 5

56

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

1.03 -91.60 7 5

57

Motif group HL_50860.2

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

1.03 -100.62 5 5

58

Motif group HL_80599.2

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

1.03 -107.81 6 5

59

Motif group HL_97733.1

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

1.03 -108.80 8 6

60

Motif group HL_72628.1

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

1.03 -129.44 6 5

61

Motif group HL_25061.1

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

1.03 -133.81 6 5

62

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

1.03 -134.58 6 5

tRNA anticodon loop with synthetase

63

Motif group HL_83632.1

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

1.03 -138.15 5 4

tRNA anticodon loop

64

Motif group HL_36335.1

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

0.69 -72.14 7 5

65

Motif group HL_07583.1

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

0.69 -75.22 7 6

66

Motif group HL_70658.1

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

0.69 -81.70 6 6

67

Motif group HL_18978.1

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

0.69 -102.39 7 6

68

Motif group HL_91503.7

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

0.69 -112.09 6 6

69

Motif group HL_55436.1

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

0.69 -117.09 6 5

70

Motif group HL_49941.1

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

0.69 -117.90 8 6

tRNA D-loop

71

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.69 -119.06 6 5

tRNA D-loop

72

Motif group HL_84299.4

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

0.69 -121.78 4 4

73

Motif group HL_97917.2

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

0.69 -134.71 5 4

74

Motif group HL_15802.1

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

0.69 -134.77 7 6

75

Motif group HL_10453.3

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

0.69 -163.05 3 3

tRNA anticodon loop

76

Motif group HL_81538.2

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

0.69 -188.77 4 4

GNRA with tandem sheared

77

Motif group HL_22622.1

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

0.69 -304.58 7 5

78

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

0.69 -426.55 6 4

79

Motif group HL_50779.4

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

0.69 -487.06 5 4

80

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.69 -9999.00 7 5

tRNA D-loop

81

Motif group HL_67079.1

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

0.34 -51.27 5 5

82

Motif group HL_06226.4

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

0.34 -84.35 5 5

83

Motif group HL_41464.2

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

0.34 -92.53 4 4

84

Motif group HL_64690.6

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

0.34 -112.29 4 4

85

Motif group HL_21372.1

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

0.34 -122.98 6 5

86

Motif group HL_53454.2

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

0.34 -123.64 7 5

87

Motif group HL_05304.3

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

0.34 -124.10 7 6

88

Motif group HL_87553.1

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

0.34 -153.09 5 4

89

Motif group HL_37344.1

Basepair signature:
cWW-F-F

0.34 -222.68 7 5

90

Motif group HL_37824.7

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

0.34 -313.05 3 3

GNRA

91

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

0.34 -361.51 6 5

92

Motif group HL_24792.1

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

0.34 -528.50 6 6

93

Motif group HL_13189.1

Basepair signature:
cWW-F-F

0.34 -533.01 6 6

94

Motif group HL_74292.1

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

0.34 -1875.63 5 5

95

Motif group HL_50418.1

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

0.34 -3464.69 6 5

96

Motif group HL_41543.1

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

0.00 -63.31 6 6

97

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.00 -79.75 6 4

98

Motif group HL_74379.3

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

0.00 -85.31 6 6

99

Motif group HL_29129.3

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

0.00 -85.98 5 5

100

Motif group HL_23509.1

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

0.00 -86.21 6 6

101

Motif group HL_04642.1

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

0.00 -87.04 7 5

tRNA D-loop

102

Motif group HL_85434.1

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

0.00 -87.33 5 5

103

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.00 -88.46 6 5

104

Motif group HL_90620.1

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

0.00 -91.02 7 6

105

Motif group HL_16991.1

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

0.00 -91.48 7 6

G-quadruplex fragment

106

Motif group HL_75293.5

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

0.00 -97.20 5 5

107

Motif group HL_02483.1

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

0.00 -99.72 7 6

108

Motif group HL_45785.1

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

0.00 -106.77 6 6

109

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -108.15 8 6

110

Motif group HL_58224.1

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

0.00 -108.81 7 5

111

Motif group HL_26934.1

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

0.00 -110.32 5 5

112

Motif group HL_35677.3

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

0.00 -110.98 6 5

113

Motif group HL_41902.1

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

0.00 -111.82 9 8

114

Motif group HL_80411.1

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

0.00 -114.39 9 7

tRNA D-loop

115

Motif group HL_08602.1

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

0.00 -115.66 8 7

116

Motif group HL_88558.1

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

0.00 -116.21 7 5

117

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

0.00 -118.08 5 5

118

Motif group HL_20743.5

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

0.00 -121.76 5 5

119

Motif group HL_23010.1

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

0.00 -124.21 8 6

120

Motif group HL_33983.1

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

0.00 -124.28 7 5

121

Motif group HL_84847.1

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

0.00 -124.62 7 7

122

Motif group HL_86109.1

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

0.00 -124.64 7 7

123

Motif group HL_23115.1

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

0.00 -125.26 8 7

tRNA D-loop

124

Motif group HL_19210.3

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

0.00 -126.63 5 5

125

Motif group HL_01255.1

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

0.00 -129.06 8 6

126

Motif group HL_55305.1

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

0.00 -130.76 8 6

127

Motif group HL_67407.5

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

0.00 -133.53 6 6

128

Motif group HL_38649.1

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

0.00 -136.49 5 4

129

Motif group HL_93616.2

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

0.00 -137.22 8 6

tRNA D-loop

130

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

0.00 -142.43 7 5

Other HL

131

Motif group HL_07480.2

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

0.00 -142.78 8 6

132

Motif group HL_68767.1

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

0.00 -143.44 6 6

tRNA D-loop

133

Motif group HL_81312.1

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

0.00 -145.67 8 7

134

Motif group HL_33074.4

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

0.00 -146.77 7 6

U1 small nuclear ribonucleoprotein A binding hairpin

135

Motif group HL_16398.2

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

0.00 -150.77 7 7

136

Motif group HL_74055.2

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

0.00 -150.92 9 7

137

Motif group HL_32735.2

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

0.00 -151.05 5 5

138

Motif group HL_06059.6

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

0.00 -151.31 4 3

tRNA anticodon loop

139

Motif group HL_81205.3

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

0.00 -155.04 9 8

140

Motif group HL_20751.2

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

0.00 -163.41 8 8

141

Motif group HL_47854.1

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

0.00 -164.86 5 5

142

Motif group HL_11542.1

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

0.00 -165.08 9 7

143

Motif group HL_50006.2

Basepair signature:
cWW-F-F

0.00 -167.02 4 4

144

Motif group HL_20781.1

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

0.00 -168.85 8 6

145

Motif group HL_98870.1

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

0.00 -172.80 9 8

146

Motif group HL_13971.1

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

0.00 -174.50 8 7

147

Motif group HL_47732.1

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

0.00 -176.42 8 6

148

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.00 -179.77 5 4

149

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

0.00 -181.08 4 4

150

Motif group HL_10540.1

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

0.00 -185.24 6 5

151

Motif group HL_25967.2

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

0.00 -187.48 4.5 4

152

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

0.00 -188.37 4 4

153

Motif group HL_73247.1

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

0.00 -190.78 10 8

Pseudoknot geometry

154

Motif group HL_48417.5

Basepair signature:
cWW-F-F

0.00 -193.84 4 4

155

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.00 -199.50 6 4

tRNA D-loop

156

Motif group HL_02581.1

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

0.00 -199.52 9 8

tRNA D-loop

157

Motif group HL_91641.1

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

0.00 -199.91 10 9.5

158

Motif group HL_00914.1

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

0.00 -200.43 5 5

159

Motif group HL_56131.2

Basepair signature:
cWW-F-F

0.00 -205.26 5 4

160

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 -205.69 13 11

161

Motif group HL_30680.3

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

0.00 -207.15 4 3

Pseudoknot geometry

162

Motif group HL_78347.4

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

0.00 -208.23 5 5

163

Motif group HL_73183.1

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

0.00 -208.45 9 8

Pseudoknot geometry with G-bulge

164

Motif group HL_30068.2

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

0.00 -218.32 3 3

165

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

0.00 -220.90 5 5

166

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

0.00 -225.20 5 4

167

Motif group HL_13963.3

Basepair signature:
cWW-F-F

0.00 -232.12 5 5

168

Motif group HL_31585.4

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

0.00 -237.43 4 4

Purine riboswitch

169

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

0.00 -247.06 4 4

170

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

0.00 -248.37 6 5

171

Motif group HL_10456.1

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

0.00 -250.26 12 11

172

Motif group HL_42046.2

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

0.00 -250.50 6 5

173

Motif group HL_37369.2

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

0.00 -254.21 6 4

174

Motif group HL_66482.1

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

0.00 -257.82 12 10

175

Motif group HL_29958.1

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

0.00 -268.67 9 9

176

Motif group HL_93535.1

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

0.00 -272.74 5 4

177

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

0.00 -273.17 4 4

Fab BL3-6 binding hairpin with tSW

178

Motif group HL_64292.1

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

0.00 -277.08 10 9

179

Motif group HL_47787.2

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

0.00 -277.48 6 5

180

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

0.00 -278.20 6 5

181

Motif group HL_59843.1

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

0.00 -282.84 6 5

182

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

0.00 -284.84 6 5

183

Motif group HL_51921.1

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

0.00 -287.23 13 13

184

Motif group HL_92488.1

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

0.00 -290.81 9 9

185

Motif group HL_14757.1

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

0.00 -292.58 11 10

186

Motif group HL_97756.2

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

0.00 -294.22 9 8

187

Motif group HL_27483.1

Basepair signature:
cWW-F

0.00 -300.61 6 6

188

Motif group HL_71391.1

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

0.00 -325.97 5 4

189

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.00 -362.84 5 4

UNCG

190

Motif group HL_56676.1

Basepair signature:
cWW-F-F

0.00 -363.52 6 5

191

Motif group HL_89893.1

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

0.00 -363.93 7 5

192

Motif group HL_66103.1

Basepair signature:
cWW-F-F

0.00 -439.98 6 4

193

Motif group HL_59330.1

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

0.00 -458.70 7 5

194

Motif group HL_50851.1

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

0.00 -464.64 8 8

G-quadruplex fragment

195

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

0.00 -480.34 5 4

196

Motif group HL_57875.1

Basepair signature:
cWW-F-F

0.00 -495.27 4 4

197

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

0.00 -499.18 4 4

198

Motif group HL_31581.6

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

0.00 -500.76 7 6

199

Motif group HL_15118.1

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

0.00 -527.52 7 6

200

Motif group HL_94376.1

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

0.00 -532.78 6 6

Pseudoknot geometry

201

Motif group HL_07903.1

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

0.00 -533.00 7 7

202

Motif group HL_63355.1

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

0.00 -535.66 7 7

203

Motif group HL_42998.2

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

0.00 -558.38 3 3

204

Motif group HL_65794.5

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

0.00 -759.99 4 4

Pseudoknot geometry

205

Motif group HL_46501.1

Basepair signature:
cWW-cWS

0.00 -816.43 6 5

206

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.00 -839.76 7 5

207

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

0.00 -840.68 5 5

tRNA D-loop

208

Motif group HL_80241.1

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

0.00 -900.83 6 5

209

Motif group HL_58539.1

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

0.00 -944.03 10 8

210

Motif group HL_51447.1

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

0.00 -984.07 7 5

211

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -1188.53 7 5

212

Motif group HL_38168.1

Basepair signature:
cWW-F

0.00 -1222.18 6 5

213

Motif group HL_69752.2

Basepair signature:
cWW-F

0.00 -1228.71 5 3

214

Motif group HL_70782.2

Basepair signature:
cWW-F

0.00 -1229.50 5 5

215

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

0.00 -1251.39 4 4

Pseudoknot geometry with 3' bulge

216

Motif group HL_59735.5

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

0.00 -1254.97 5 4

217

Motif group HL_75660.5

Basepair signature:
cWW-F

0.00 -1264.88 5 4

218

Motif group HL_99040.1

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

0.00 -1295.02 7 5

219

Motif group HL_48778.2

Basepair signature:
cWW-F

0.00 -1301.54 5 4

Mini UNCG

220

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.00 -1386.57 6 5

Mini UNCG

221

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

0.00 -1505.97 6 4

222

Motif group HL_56334.1

Basepair signature:
cWW-F

0.00 -1515.94 5 5

Mini UNCG

223

Motif group HL_32346.4

Basepair signature:
cWW-F

0.00 -1533.76 6 5

224

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -1536.48 5 4

225

Motif group HL_52953.3

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

0.00 -1541.52 5 5

226

Motif group HL_28791.1

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

0.00 -1544.43 7 5

227

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

0.00 -1545.39 7 6

228

Motif group HL_55195.3

Basepair signature:
cWW-F

0.00 -1551.04 6 5

229

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

0.00 -1585.23 5 5

230

Motif group HL_78284.1

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

0.00 -2226.71 7 6

231

Motif group HL_70751.1

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

0.00 -3301.59 7 5

232

Motif group HL_36684.4

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

0.00 -3388.85 5 5

233

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 -3675.30 15 13

234

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 -3834.09 15 13

235

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 -3873.15 12 10

236

Motif group HL_85461.1

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

0.00 -3981.76 12 12

237

Motif group HL_60293.1

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

0.00 -4019.29 15 14

G-quadruplex

238

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 -4026.42 17 16

G-quadruplex

239

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 -4031.37 18 17

240

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 -4052.93 18 17

G-quadruplex

241

Motif group HL_88364.2

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

0.00 -4447.05 11 9

242

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 -4470.91 31 30

243

Motif group HL_68572.1

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

0.00 -5243.97 9 7

244

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -6731.68 7 6

245

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.00 -6743.67 6 5

246

Motif group HL_78677.1

Basepair signature:
cWW-F-F

0.00 -6749.13 6 6

247

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -6776.31 8 6

248

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -6789.16 7 5

249

Motif group HL_12870.1

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

0.00 -7598.16 8 8

250

Motif group HL_81100.2

Basepair signature:
cWW

0.00 -9755.68 6 5

251

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -9787.16 7 6

252

Motif group HL_09260.2

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

0.00 -9999.00 7 7

tRNA D-loop

253

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -9999.00 6 5

Coloring options: