RNA 3D Hub

JAR3D Query RF03087-3.98 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 35 Hairpin loop

Column numbers: 1061-1132 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    AU------------------------------GAAA-----------------------------------G   20

    
    GC------------------------------GAAA-----------------------------------G   12

    
    UAUC----------------------------AUUU---------------------------------GAU   11

    
    C-------------------------------UUUUA-----------------------------------    7

    
    UCCC----------------------------UUCG---------------------------------GGG    5

    
    CC------------------------------GCAA-----------------------------------G    4

    
    C-------------------------------GUAGA-----------------------------------    4

    
    UA-CGCAGCAUGG-------------------CUUAU-----------------------CC-UGUUGCGAU    3

    
    UA-UACGAUAUGG-------------------CUCAA-----------------------CU-UAUUGUAAU    3

    
    AACUCCAAGCAC--------------------UUGU-------------------------GUGCGAGGAGC    3

    
    CAGCGGC-------------------------GUUUGA----------------------------GUCGUU    3

    
    GUU-----------------------------CUUUG---------------------------------AA    3

    
    GA------------------------------GAAA-----------------------------------U    3

    
    UC------------------------------GAAA-----------------------------------G    3

    
    G-------------------------------GAAA------------------------------------    3

    
    CCUAAUACAG----------------------UUCG---------------------------CUGUGUAAG    2

    
    CAGG----------------------------UGUAUU-------------------------------CCU    2

    
    UUCC----------------------------UUCG---------------------------------GGA    2

    
    GC------------------------------UUAAU----------------------------------G    2

    
    UG------------------------------UUUAU----------------------------------C    2

    
    A-------------------------------UGAAAG----------------------------------    2

    
    AA------------------------------AUUA-----------------------------------U    2

    
    AC------------------------------GUAA-----------------------------------G    2

    
    GC------------------------------GCAA-----------------------------------G    2

    
    UA------------------------------GAAA-----------------------------------U    2

    
    C-------------------------------GAAA------------------------------------    2

    
    --------------------------------GAAA------------------------------------    2

    
    CU-AAUUAAGG--ACGAACAUCACAAUCCAUCCGUAG---GGUGCGAGAGU-AUGUU-GUAGAAUUAAUUUA    1

    
    CAGUUUAACGGUUAGGGGCGACUUAUAG----UUUAA--------CUACAAGUGGCAACAGACGGUUUAACU    1

    
    UAAAUAAUUAGUUUUCA---------------GUAA--------------------UGAAAAUCAAUUAUUU    1

    
    UGGUUUGUGG-GGC------------------CGUUG----------------------GCACAAUCAAACC    1

    
    CAA-CUCCAAGCAU------------------UUGU-----------------------GUGCAAGGAGCAG    1

    
    AACUCCAAGCAC--------------------UUGU-------------------------GUGCGAAGAGC    1

    
    AACUCCAAGCGC--------------------UUUU-------------------------GCGCAAGGAGC    1

    
    -ACUCCAAGCGC--------------------CUUU-------------------------GCGCAAGGAGC    1

    
    UGAUUGAUAAA---------------------CAAUG-------------------------UUUAUCAGUU    1

    
    UGAUAGC-------------------------GUUUGA----------------------------GCUAUU    1

    
    CAAAUAU-------------------------CGGAC-----------------------------AU-UUU    1

    
    CUUUGGA-------------------------GAGGUC----------------------------UCCA--    1

    
    UUUUUG--------------------------CAAAUA-----------------------------CAAAA    1

    
    AAAUUG--------------------------UUUU-------------------------------CAAUU    1

    
    CAAUGC--------------------------UUCG-------------------------------GCGUU    1

    
    CAAUGC--------------------------UUCG-------------------------------GUAUU    1

    
    UGAACC--------------------------GAAA-------------------------------GGUUC    1

    
    UGCGAU--------------------------GAGA-------------------------------ACCGU    1

    
    UGCGGU--------------------------GAGA-------------------------------ACCGU    1

    
    AGCGU---------------------------AGAGU-------------------------------GCGC    1

    
    CCCGU---------------------------GGAAA-------------------------------ACGG    1

    
    AUCUU---------------------------UUGU--------------------------------AAGA    1

    
    CAUCC---------------------------UCCG--------------------------------GGGU    1

    
    CGG-----------------------------CUUAGUGU------------------------------CC    1

    
    GAUAG---------------------------CGCA--------------------------------AUAA    1

    
    GAUAG---------------------------UGUA--------------------------------CUAU    1

    
    GUGG----------------------------GGUAUA-------------------------------CCA    1

    
    GUUAG---------------------------GAAA--------------------------------CUAA    1

    
    GUUCC---------------------------GAAA--------------------------------GGAA    1

    
    UUGGG---------------------------UGUUU--------------------------------CCC    1

    
    UUUUC---------------------------UUCG--------------------------------GAAA    1

    
    AAGC----------------------------CUAUG--------------------------------GCU    1

    
    UGGG----------------------------UGUUU--------------------------------CCC    1

    
    UUAU----------------------------AAUAU--------------------------------AUA    1

    
    CAGC----------------------------AUAA---------------------------------GCU    1

    
    CCCC----------------------------UGGC---------------------------------GGG    1

    
    CGGU----------------------------GAAA---------------------------------ACC    1

    
    GGUG----------------------------CUUG---------------------------------CAC    1

    
    GUUA----------------------------GCAA---------------------------------UAA    1

    
    GUUC----------------------------UUCG---------------------------------GAA    1

    
    GUUU----------------------------UUAU---------------------------------AAA    1

    
    UUU-----------------------------UUUAUU--------------------------------AA    1

    
    AAG-----------------------------UUUAA---------------------------------CU    1

    
    AUA-----------------------------CUUUG---------------------------------UA    1

    
    GGG-----------------------------UGUUU---------------------------------CC    1

    
    GUU-----------------------------UUUAA---------------------------------AA    1

    
    UCU-----------------------------UUUUA---------------------------------AG    1

    
    UUA-----------------------------CAUUG---------------------------------UA    1

    
    AAC-----------------------------UUCG----------------------------------GU    1

    
    AUC-----------------------------AUUU----------------------------------GA    1

    
    CAU-----------------------------UUUU----------------------------------AU    1

    
    GAA-----------------------------GUAA----------------------------------UU    1

    
    GAU-----------------------------GAAA----------------------------------AU    1

    
    GGA-----------------------------GUGA----------------------------------UC    1

    
    GU-C----------------------------GAAA---------------------------------G-A    1

    
    UGC-----------------------------UUAU----------------------------------GC    1

    
    AU------------------------------GUAAA----------------------------------A    1

    
    CA------------------------------CAAAG----------------------------------U    1

    
    CA------------------------------UAAAC----------------------------------U    1

    
    GG------------------------------GUUCG----------------------------------C    1

    
    UC------------------------------UUUGA----------------------------------G    1

    
    UG------------------------------CUUGG----------------------------------C    1

    
    UG------------------------------GUUUC----------------------------------C    1

    
    UU------------------------------CUUUG----------------------------------A    1

    
    UU------------------------------UUUAA----------------------------------A    1

    
    AA------------------------------GUUA-----------------------------------U    1

    
    AC------------------------------GCAA-----------------------------------G    1

    
    AC------------------------------UUUG-----------------------------------G    1

    
    AU------------------------------GAAA-----------------------------------A    1

    
    CA------------------------------AUUA-----------------------------------U    1

    
    GA------------------------------AUAA-----------------------------------U    1

    
    GA------------------------------GGAA-----------------------------------U    1

    
    GC------------------------------GUUU-----------------------------------G    1

    
    GC------------------------------UUUA-----------------------------------G    1

    
    GU------------------------------UUCG-----------------------------------G    1

    
    UA------------------------------UUUA-----------------------------------U    1

    
    UC------------------------------GAGA-----------------------------------G    1

    
    UC------------------------------GUAA-----------------------------------G    1

    
    GU------------------------------UUU------------------------------------A    1

    
    UA-------------------------------AAA-----------------------------------U    1

    
    C-------------------------------GCAA------------------------------------    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_10540.1

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

27.60 -1204.72 6 4

2

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

23.44 -1530.31 4 3

3

Motif group HL_50006.2

Basepair signature:
cWW-F-F

21.35 -1654.47 4 3

4

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

20.31 -2164.03 5 4

5

Motif group HL_53890.2

Basepair signature:
cWW-F-F-F

15.10 -1702.51 4 3

6

Motif group HL_87553.1

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

14.06 -1191.22 5 3

7

Motif group HL_28075.1

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

13.02 -1233.24 4 3

8

Motif group HL_01609.3

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

11.46 -1030.98 5 4

T-loop with 2 bulged bases not stacked

9

Motif group HL_57875.1

Basepair signature:
cWW-F-F

8.85 -2138.89 4 3

10

Motif group HL_48417.5

Basepair signature:
cWW-F-F

7.81 -1294.49 4 3

11

Motif group HL_56334.1

Basepair signature:
cWW-F

7.81 -4365.03 4 3

Mini UNCG

12

Motif group HL_75660.5

Basepair signature:
cWW-F

7.29 -2958.99 4 3

13

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

6.77 -1255.56 5 4

tRNA anticodon loop with synthetase

14

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

6.77 -1516.93 4 3.5

15

Motif group HL_70782.2

Basepair signature:
cWW-F

6.25 -2947.49 5 4

16

Motif group HL_65794.5

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

6.25 -3102.52 4 3

Pseudoknot geometry

17

Motif group HL_52953.3

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

6.25 -4673.76 4 3

18

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

5.73 -712.80 7 6

19

Motif group HL_78347.4

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

5.73 -1285.00 4.5 3

20

Motif group HL_31585.4

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

5.73 -1794.35 4 3

Purine riboswitch

21

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

5.21 -1059.92 5 4

22

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

5.21 -2807.81 4 3

tRNA D-loop

23

Motif group HL_10453.3

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

4.69 -1393.31 5 3

tRNA anticodon loop

24

Motif group HL_37824.7

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

4.69 -1424.37 3 3

GNRA

25

Motif group HL_38168.1

Basepair signature:
cWW-F

4.69 -2946.98 5 4

26

Motif group HL_18565.1

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

4.17 -956.31 6 5

27

Motif group HL_37369.2

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

4.17 -1362.89 5 4

28

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

4.17 -1489.93 6 4

Other HL

29

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

4.17 -2144.64 5 4

30

Motif group HL_13189.1

Basepair signature:
cWW-F-F

4.17 -2164.85 5 4

31

Motif group HL_69752.2

Basepair signature:
cWW-F

4.17 -2966.58 5 4

32

Motif group HL_48778.2

Basepair signature:
cWW-F

4.17 -3005.31 4 3

Mini UNCG

33

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

4.17 -4468.65 4.5 3

34

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

4.17 -4487.11 6 5

35

Motif group HL_50860.2

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

3.65 -732.33 6 4

36

Motif group HL_47787.2

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

3.65 -1712.84 4 3

37

Motif group HL_93535.1

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

3.65 -1727.42 4 4

38

Motif group HL_04259.3

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

3.13 -1364.90 5 4

GNRA with extra cWW

39

Motif group HL_89893.1

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

3.13 -1665.12 6 5

40

Motif group HL_13963.3

Basepair signature:
cWW-F-F

3.13 -1676.13 5 4

41

Motif group HL_25847.2

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

2.60 -989.72 7 5

42

Motif group HL_02817.2

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

2.60 -1725.71 5 4

43

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

2.08 -723.45 6 5

44

Motif group HL_20535.2

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

2.08 -1481.07 5 4

45

Motif group HL_37344.1

Basepair signature:
cWW-F-F

2.08 -1525.89 5 4

46

Motif group HL_97917.2

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

2.08 -1656.39 5 4

47

Motif group HL_56131.2

Basepair signature:
cWW-F-F

2.08 -1678.89 4 4

48

Motif group HL_56676.1

Basepair signature:
cWW-F-F

2.08 -2090.70 4.5 3

49

Motif group HL_66103.1

Basepair signature:
cWW-F-F

2.08 -2132.45 5 4

50

Motif group HL_85993.1

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

2.08 -2745.74 6 5

51

Motif group HL_55195.3

Basepair signature:
cWW-F

2.08 -4380.24 4 3

52

Motif group HL_99867.1

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

2.08 -4539.97 6 4

53

Motif group HL_83808.4

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

1.56 -718.43 7 6

Pseudoknot

54

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

1.56 -721.04 6 5

55

Motif group HL_26934.1

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

1.56 -814.62 6 4

56

Motif group HL_77082.1

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

1.56 -1071.46 4 3

Pseudoknot geometry

57

Motif group HL_80008.1

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

1.56 -1301.52 6 5

58

Motif group HL_25967.2

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

1.56 -1409.79 5 4

59

Motif group HL_69139.1

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

1.56 -1454.97 7 6

60

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

1.56 -1679.77 5 3

61

Motif group HL_30068.2

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

1.56 -1734.01 4 3

62

Motif group HL_93324.4

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

1.56 -1984.54 4 3

Pseudoknot geometry

63

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

1.56 -2641.40 6 4

64

Motif group HL_59735.5

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

1.56 -3758.17 5 4

65

Motif group HL_78677.1

Basepair signature:
cWW-F-F

1.56 -4880.51 5 4

66

Motif group HL_67079.1

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

1.04 -352.87 6 5

67

Motif group HL_98864.1

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

1.04 -649.50 6 5

T-loop with unstacked turn

68

Motif group HL_75293.5

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

1.04 -784.57 5 4

69

Motif group HL_99769.3

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

1.04 -858.38 7 6

70

Motif group HL_73266.9

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

1.04 -870.88 5 4

71

Motif group HL_64690.6

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

1.04 -975.94 5 4

72

Motif group HL_34964.1

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

1.04 -977.88 7 6

73

Motif group HL_04171.7

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

1.04 -990.79 7 6

74

Motif group HL_41464.2

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

1.04 -1052.63 5 4

75

Motif group HL_33983.1

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

1.04 -1158.77 6 4

76

Motif group HL_38808.1

Basepair signature:
cWW-cWW

1.04 -1549.81 5.5 4

77

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

1.04 -1738.85 4 3

78

Motif group HL_59843.1

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

1.04 -1742.92 5 4

79

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

1.04 -1760.54 4 3

80

Motif group HL_59330.1

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

1.04 -2148.31 6 5

81

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

1.04 -4489.17 6 4

82

Motif group HL_68257.1

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

0.52 -272.09 7 6

83

Motif group HL_41543.1

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

0.52 -301.07 8 6

84

Motif group HL_04642.1

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

0.52 -712.62 6 5

tRNA D-loop

85

Motif group HL_49941.1

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

0.52 -728.23 7 6

tRNA D-loop

86

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.52 -745.62 7 6

87

Motif group HL_98252.1

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

0.52 -758.93 8 6.5

88

Motif group HL_36335.1

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

0.52 -775.15 7 5

89

Motif group HL_93616.2

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

0.52 -837.24 7 6

tRNA D-loop

90

Motif group HL_84299.4

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

0.52 -930.08 5 4

91

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.52 -969.86 6 5

tRNA D-loop

92

Motif group HL_25061.1

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

0.52 -972.93 6 4

93

Motif group HL_15802.1

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

0.52 -981.36 6 5

94

Motif group HL_06059.6

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

0.52 -1063.33 4 3

tRNA anticodon loop

95

Motif group HL_77436.5

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

0.52 -1065.45 4 3

T-loop related

96

Motif group HL_81538.2

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

0.52 -1226.46 4 3

GNRA with tandem sheared

97

Motif group HL_88205.2

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

0.52 -1236.06 5 5

98

Motif group HL_80599.2

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

0.52 -1277.16 5 4

99

Motif group HL_91503.7

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

0.52 -1313.48 6 5

100

Motif group HL_21372.1

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

0.52 -1357.25 5 4

101

Motif group HL_38046.1

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

0.52 -1386.07 7 5

102

Motif group HL_83632.1

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

0.52 -1440.21 5 4

tRNA anticodon loop

103

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

0.52 -1578.18 5 4

104

Motif group HL_47854.1

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

0.52 -1613.82 7 5

105

Motif group HL_93383.1

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

0.52 -2153.95 6 5

106

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

0.52 -2173.07 5 4

107

Motif group HL_39243.1

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

0.52 -2451.40 6 4

108

Motif group HL_67407.5

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

0.52 -3022.48 7 5

109

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

0.52 -3064.86 4 3

Pseudoknot geometry with 3' bulge

110

Motif group HL_19210.3

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

0.52 -3185.60 6 5

111

Motif group HL_24792.1

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

0.52 -4021.01 7 6

112

Motif group HL_36684.4

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

0.52 -4062.35 6 5

113

Motif group HL_50418.1

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

0.52 -4155.40 7 6

114

Motif group HL_32346.4

Basepair signature:
cWW-F

0.52 -4397.12 5 4

115

Motif group HL_22135.1

Basepair signature:
cWW-F-F

0.52 -4902.67 6 5

116

Motif group HL_81100.2

Basepair signature:
cWW

0.52 -5365.73 5.5 4

117

Motif group HL_09260.2

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

0.52 -9999.00 7 6

tRNA D-loop

118

Motif group HL_70658.1

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

0.00 -266.43 8 7

119

Motif group HL_41902.1

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

0.00 -274.12 8 7

120

Motif group HL_07583.1

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

0.00 -274.31 9 7

121

Motif group HL_81205.3

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

0.00 -289.10 9 8

122

Motif group HL_74379.3

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

0.00 -295.78 8 7

123

Motif group HL_84847.1

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

0.00 -299.45 9 8

124

Motif group HL_73247.1

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

0.00 -304.25 9 8

Pseudoknot geometry

125

Motif group HL_91641.1

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

0.00 -305.01 11 10

126

Motif group HL_74055.2

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

0.00 -305.41 9 8

127

Motif group HL_98870.1

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

0.00 -317.43 10 9

128

Motif group HL_14757.1

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

0.00 -328.93 12 11

129

Motif group HL_05304.3

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

0.00 -331.28 8 7

130

Motif group HL_51921.1

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

0.00 -347.98 14 14

131

Motif group HL_02581.1

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

0.00 -360.66 10 8

tRNA D-loop

132

Motif group HL_93438.2

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

0.00 -361.25 6 5

133

Motif group HL_60266.1

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

0.00 -377.32 7 6

134

Motif group HL_91939.2

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

0.00 -383.94 7 6

135

Motif group HL_86109.1

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

0.00 -466.57 8 7

136

Motif group HL_90620.1

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

0.00 -507.07 7 5

137

Motif group HL_92488.1

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

0.00 -549.99 11 10

138

Motif group HL_23509.1

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

0.00 -587.52 9 8

139

Motif group HL_02887.3

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

0.00 -622.90 7 6

T-loop with 3 stacked bulged bases

140

Motif group HL_13971.1

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

0.00 -624.88 10 9

141

Motif group HL_16991.1

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

0.00 -660.08 8 7

G-quadruplex fragment

142

Motif group HL_02483.1

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

0.00 -670.56 7 6

143

Motif group HL_08602.1

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

0.00 -683.26 9 8

144

Motif group HL_45785.1

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

0.00 -686.88 8 7

145

Motif group HL_68767.1

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

0.00 -691.06 8 7

tRNA D-loop

146

Motif group HL_06226.4

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

0.00 -691.97 7 6

147

Motif group HL_86012.1

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

0.00 -703.02 6 5

T-loop with unstacked turn

148

Motif group HL_89881.5

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

0.00 -713.55 7 6

149

Motif group HL_81545.2

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

0.00 -715.70 6 5

150

Motif group HL_57863.1

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

0.00 -720.41 7 6

G-quadruplex fragment

151

Motif group HL_18978.1

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

0.00 -742.95 6 5

152

Motif group HL_10456.1

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

0.00 -751.12 12 11

153

Motif group HL_11542.1

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

0.00 -754.43 9 8

154

Motif group HL_87463.1

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

0.00 -764.24 7 5

155

Motif group HL_07480.2

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

0.00 -814.59 8 6

156

Motif group HL_23010.1

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

0.00 -825.96 7 6

157

Motif group HL_61996.2

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

0.00 -840.00 6 4

158

Motif group HL_20743.5

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

0.00 -844.72 5 4

159

Motif group HL_53504.3

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

0.00 -851.17 6 6

160

Motif group HL_53454.2

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

0.00 -864.47 6 4.5

161

Motif group HL_20167.2

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

0.00 -867.50 5 3.5

162

Motif group HL_85434.1

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

0.00 -869.23 7 6

163

Motif group HL_28252.8

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

0.00 -885.93 5 3

T-loop with 2 stacked bulged bases

164

Motif group HL_58224.1

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

0.00 -924.35 7 5

165

Motif group HL_29129.3

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

0.00 -945.09 7 6

166

Motif group HL_97756.2

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

0.00 -971.05 10 9

167

Motif group HL_04641.1

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

0.00 -972.06 7 6

168

Motif group HL_73255.1

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

0.00 -1023.57 7 6

169

Motif group HL_66482.1

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

0.00 -1059.88 12 11

170

Motif group HL_13529.1

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

0.00 -1122.82 6 5

171

Motif group HL_20751.2

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

0.00 -1130.02 8 8

172

Motif group HL_97733.1

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

0.00 -1232.43 7 6

173

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

0.00 -1241.11 6 5

174

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

0.00 -1252.64 5 4

tRNA D-loop

175

Motif group HL_42046.2

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

0.00 -1310.15 5 4

176

Motif group HL_72628.1

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

0.00 -1323.87 6 5

177

Motif group HL_88558.1

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

0.00 -1342.32 8 6

178

Motif group HL_23115.1

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

0.00 -1386.42 7 6

tRNA D-loop

179

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

0.00 -1391.87 5 3.5

T-loop with unstacked turn

180

Motif group HL_32735.2

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

0.00 -1396.08 5 4

181

Motif group HL_85367.2

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

0.00 -1420.97 5 4

182

Motif group HL_29762.1

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

0.00 -1439.06 6.5 5

183

Motif group HL_80411.1

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

0.00 -1453.41 8 7

tRNA D-loop

184

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

0.00 -1500.31 5 4

Fab BL3-6 binding hairpin with tSW

185

Motif group HL_93135.1

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

0.00 -1535.08 7 6

Pseudoknot

186

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

0.00 -1548.34 4 3

187

Motif group HL_35677.3

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

0.00 -1587.96 6 5

188

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

0.00 -1748.50 4 3

UNCG

189

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

0.00 -1750.24 5 4

190

Motif group HL_00914.1

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

0.00 -1814.33 6 4.5

191

Motif group HL_50779.4

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

0.00 -1951.57 7 5

192

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 -1968.79 13 12

193

Motif group HL_78197.1

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

0.00 -2032.51 5 3

194

Motif group HL_27483.1

Basepair signature:
cWW-F

0.00 -2069.91 6 4

195

Motif group HL_71391.1

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

0.00 -2104.64 5 4

196

Motif group HL_15574.1

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

0.00 -2164.04 6 4.5

197

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.00 -2202.41 7 5

198

Motif group HL_33074.4

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

0.00 -2306.54 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

199

Motif group HL_73183.1

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

0.00 -2492.28 10 9

Pseudoknot geometry with G-bulge

200

Motif group HL_22622.1

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

0.00 -2561.48 6 4

201

Motif group HL_46501.1

Basepair signature:
cWW-cWS

0.00 -2812.14 5 3.5

202

Motif group HL_30680.3

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

0.00 -2823.11 5 3

Pseudoknot geometry

203

Motif group HL_32392.1

Basepair signature:
cWW-F-F

0.00 -2856.81 6 5

204

Motif group HL_50851.1

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

0.00 -2901.67 9 8

G-quadruplex fragment

205

Motif group HL_80241.1

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

0.00 -2905.46 5 4

206

Motif group HL_51447.1

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

0.00 -2911.98 6 5

207

Motif group HL_07903.1

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

0.00 -2939.56 10 9

208

Motif group HL_38649.1

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

0.00 -2994.55 7 6

209

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.00 -3043.24 6 4

210

Motif group HL_81312.1

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

0.00 -3050.59 8 7

211

Motif group HL_64292.1

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

0.00 -3087.23 10 10

212

Motif group HL_04725.1

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

0.00 -3113.95 8 7

213

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 -3136.87 15 14

214

Motif group HL_63355.1

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

0.00 -3142.89 9 8

215

Motif group HL_31581.6

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

0.00 -3157.21 8 7

216

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 -3173.13 15 14

217

Motif group HL_01255.1

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

0.00 -3220.18 7 6

218

Motif group HL_16398.2

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

0.00 -3246.81 8 7

219

Motif group HL_55305.1

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

0.00 -3257.98 7 6

220

Motif group HL_55436.1

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

0.00 -3263.77 6 5

221

Motif group HL_88364.2

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

0.00 -3272.37 11 10

222

Motif group HL_08510.1

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

0.00 -3400.59 7 6

223

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 -3463.85 11 10

224

Motif group HL_60293.1

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

0.00 -3467.57 16 15

G-quadruplex

225

Motif group HL_15118.1

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

0.00 -3481.90 8 7

226

Motif group HL_47732.1

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

0.00 -3492.73 8 7

227

Motif group HL_94376.1

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

0.00 -3519.89 7 6

Pseudoknot geometry

228

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 -3568.19 17 16

G-quadruplex

229

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 -3594.33 18 18

G-quadruplex

230

Motif group HL_29958.1

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

0.00 -3613.67 9 8

231

Motif group HL_85461.1

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

0.00 -3673.63 14 13

232

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 -3725.38 18 17

233

Motif group HL_78284.1

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

0.00 -3853.51 7 6

234

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 -3879.50 32 32

235

Motif group HL_99040.1

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

0.00 -3931.49 6 5

236

Motif group HL_70751.1

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

0.00 -3960.25 7 6

237

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

0.00 -3960.99 5 4

Mini UNCG

238

Motif group HL_74292.1

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

0.00 -4095.33 7 6

239

Motif group HL_12870.1

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

0.00 -4213.10 8 7

240

Motif group HL_68572.1

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

0.00 -4254.35 8 7

241

Motif group HL_20781.1

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

0.00 -4333.59 7 6

242

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

0.00 -4514.38 6 4

243

Motif group HL_28791.1

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

0.00 -4721.69 6 5

244

Motif group HL_35941.1

Basepair signature:
cWW-F

0.00 -4903.82 6 5

245

Motif group HL_60914.1

Basepair signature:
cWW-F

0.00 -4911.07 6 5

246

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

0.00 -5034.86 6 5

247

Motif group HL_42998.2

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

0.00 -5113.99 5 4

248

Motif group HL_94980.1

Basepair signature:
cWW-F-F

0.00 -5374.47 6 5

249

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.00 -5491.79 7 5

250

Motif group HL_77600.2

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

0.00 -5948.46 5 4

251

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

0.00 -6090.26 6 5

252

Motif group HL_58539.1

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

0.00 -6189.86 11 10

253

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.00 -9999.00 6 5

tRNA D-loop

Coloring options: