RNA 3D Hub

JAR3D Query RF03072-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF03072 maps to these 6 chains: 9CXF|1|A, 9E73|1|A, 9E74|1|A, 9E75|1|A, 9ELY|1|A, 9G7C|1|A See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 13 Hairpin loop

Column numbers: 525-590 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    CUGCG------------------------------------------------------------G   24

    
    UUAAU------------------------------------------------------------U   15

    
    GCUGCGG----------------------------------------------------------C   13

    
    UUAAC------------------------------------------------------------U   11

    
    CACGAU-----------------------------------------------------------G   10

    
    CAAGU------------------------------------------------------------G   10

    
    -CAAAC------------------------------------------------------------    9

    
    -GCAA-------------------------------------------------------------    9

    
    UCUCAG-----------------------------------------------------------A    8

    
    UCUCGG-----------------------------------------------------------A    8

    
    AUGAAC-----------------------------------------------------------U    7

    
    UCUUGG-----------------------------------------------------------A    7

    
    AAGAC------------------------------------------------------------A    6

    
    CAAGC------------------------------------------------------------G    6

    
    CAAGAC-----------------------------------------------------------G    5

    
    CGGAAU-----------------------------------------------------------G    5

    
    CGUAAA-----------------------------------------------------------G    5

    
    CGAGC------------------------------------------------------------G    5

    
    GUAAU------------------------------------------------------------U    5

    
    CAAAC-------------------------------------------------------------    5

    
    CGAA-------------------------------------------------------------C    5

    
    CGUAAUU----------------------------------------------------------G    4

    
    CACGUU-----------------------------------------------------------G    4

    
    CCAUGG-----------------------------------------------------------G    4

    
    CUAUGG-----------------------------------------------------------G    4

    
    CAAAA------------------------------------------------------------G    4

    
    UCGCG------------------------------------------------------------G    4

    
    UUAAA------------------------------------------------------------U    4

    
    GAAC-------------------------------------------------------------A    4

    
    UAAA-------------------------------------------------------------G    4

    
    GCUACGG----------------------------------------------------------C    3

    
    UUCGAAU----------------------------------------------------------A    3

    
    CGGACA-----------------------------------------------------------G    3

    
    CAACA------------------------------------------------------------G    3

    
    CCGUA------------------------------------------------------------G    3

    
    CUGAG------------------------------------------------------------G    3

    
    UAUAU------------------------------------------------------------U    3

    
    UUGCG------------------------------------------------------------G    3

    
    UAAC-------------------------------------------------------------C    3

    
    CUCUGAAAA--------------------------------------------------------G    2

    
    CAUACGU----------------------------------------------------------G    2

    
    GCAAAGG----------------------------------------------------------C    2

    
    CACGAA-----------------------------------------------------------G    2

    
    CAGAC------------------------------------------------------------G    2

    
    CAGAG------------------------------------------------------------U    2

    
    CAGCA------------------------------------------------------------G    2

    
    CCAAG------------------------------------------------------------G    2

    
    CCUGA------------------------------------------------------------G    2

    
    CGAAG------------------------------------------------------------G    2

    
    CUAAG------------------------------------------------------------G    2

    
    CUGAA------------------------------------------------------------G    2

    
    GAAAA------------------------------------------------------------U    2

    
    UGAAC------------------------------------------------------------A    2

    
    UUAAG------------------------------------------------------------U    2

    
    UUAGU------------------------------------------------------------U    2

    
    -GUAAC------------------------------------------------------------    2

    
    AACA-------------------------------------------------------------U    2

    
    CAUG-------------------------------------------------------------G    2

    
    -GAAU-------------------------------------------------------------    2

    
    -GCGA-------------------------------------------------------------    2

    
    UUA--------------------------------------------------------------A    2

    
    UA---------------------------------------------------------------A    2

    
    -CACCGCCGCAGUCCCUGUGGGGCUGCGGUGCCGGUGUUGGGUCGUGUACCGCCGCCGGCGGUCC-    1

    
    -UGCCAUCAGUGGCUCCGAAGGGUCUACCGCCGGUGACGGUCGGUGCCGCCGGAGUCCGGCC----    1

    
    -UGCAAUACUCGUGCGCGCACGGU------------------------------------------    1

    
    UCGCCACGGACGUCCAG----GCG-----------------------------------------A    1

    
    CGCGGAUCA-------CCAUGAGG-----------------------------------------G    1

    
    -GAUAUAAACCUUGA---------------------------------------------------    1

    
    -GAUGCGAACACUGA---------------------------------------------------    1

    
    AGAAAGAGGGGA-----------C-----------------------------------------U    1

    
    CAACCAACAUCCC----------------------------------------------------G    1

    
    -AAAUCCAAAUUUC----------------------------------------------------    1

    
    -GCGACGAACUCAA----------------------------------------------------    1

    
    GAGCUGCGGCAC-----------------------------------------------------C    1

    
    GGCUCUGAAGUA-----------------------------------------------------C    1

    
    GUGCCGCGGCAU-----------------------------------------------------C    1

    
    UUUCUUGAGCAA-----------------------------------------------------A    1

    
    -CCCUUCAUGUCC-----------------------------------------------------    1

    
    CGGGAGAAGA-------------------------------------------------------G    1

    
    GUGGCUGCGG-------------------------------------------------------C    1

    
    CCAGAGAUG--------------------------------------------------------G    1

    
    CGAUCAAGA--------------------------------------------------------G    1

    
    CGUUCAAGA--------------------------------------------------------G    1

    
    CUAUGGAAG--------------------------------------------------------G    1

    
    CUCUGCAAA--------------------------------------------------------G    1

    
    -GAUAUCAAA--------------------------------------------------------    1

    
    CCACAACG---------------------------------------------------------G    1

    
    CCAUGUGG---------------------------------------------------------G    1

    
    CGAAAUCA---------------------------------------------------------G    1

    
    CGGCUACG---------------------------------------------------------G    1

    
    CUAUGAAG---------------------------------------------------------G    1

    
    GCAGAUAG---------------------------------------------------------C    1

    
    UGAUAUGC---------------------------------------------------------A    1

    
    UGCAGAUC---------------------------------------------------------A    1

    
    AGAGGGA----------------------------------------------------------A    1

    
    AUUGAUU----------------------------------------------------------U    1

    
    CAAAAAU----------------------------------------------------------G    1

    
    CAAGAAC----------------------------------------------------------G    1

    
    CAAUUAC----------------------------------------------------------G    1

    
    CACAAGC----------------------------------------------------------G    1

    
    CACGCUC----------------------------------------------------------A    1

    
    CAGUAAA----------------------------------------------------------G    1

    
    CCAAGAU----------------------------------------------------------G    1

    
    CCAGAAC----------------------------------------------------------G    1

    
    CCAGGAC----------------------------------------------------------G    1

    
    CCCGAAG----------------------------------------------------------G    1

    
    CCGUGCA----------------------------------------------------------G    1

    
    CCGUGUA----------------------------------------------------------G    1

    
    CGAGAAA----------------------------------------------------------G    1

    
    CGAGAGC----------------------------------------------------------G    1

    
    CGCAGCC----------------------------------------------------------G    1

    
    CGCGAAC----------------------------------------------------------G    1

    
    CGCGCAU----------------------------------------------------------G    1

    
    CGGAGAA----------------------------------------------------------G    1

    
    CGGGAGU----------------------------------------------------------G    1

    
    GCAAACG----------------------------------------------------------C    1

    
    GCAGAAA----------------------------------------------------------C    1

    
    GCAGAGG----------------------------------------------------------C    1

    
    GCAGAGU----------------------------------------------------------C    1

    
    GCCCCGG----------------------------------------------------------C    1

    
    GCCGCGG----------------------------------------------------------C    1

    
    GCUUUAG----------------------------------------------------------C    1

    
    GGCCAAC----------------------------------------------------------C    1

    
    GUUACGG----------------------------------------------------------C    1

    
    ACAAAG-----------------------------------------------------------U    1

    
    ACGAAC-----------------------------------------------------------U    1

    
    AGAGAA-----------------------------------------------------------U    1

    
    AUCUUA-----------------------------------------------------------U    1

    
    CAAAGA-----------------------------------------------------------G    1

    
    CAAUAC-----------------------------------------------------------G    1

    
    CACAUU-----------------------------------------------------------G    1

    
    CACCAA-----------------------------------------------------------G    1

    
    CACGUG-----------------------------------------------------------G    1

    
    CAGACA-----------------------------------------------------------G    1

    
    CAGCAA-----------------------------------------------------------G    1

    
    CAUGAG-----------------------------------------------------------G    1

    
    CAUGAU-----------------------------------------------------------G    1

    
    CAUUUC-----------------------------------------------------------G    1

    
    CCAAGG-----------------------------------------------------------G    1

    
    CCACGG-----------------------------------------------------------G    1

    
    CGAAAU-----------------------------------------------------------G    1

    
    CGCAAU-----------------------------------------------------------G    1

    
    CGGAAC-----------------------------------------------------------G    1

    
    CUGAAC-----------------------------------------------------------G    1

    
    CUGUAA-----------------------------------------------------------G    1

    
    GAGACA-----------------------------------------------------------C    1

    
    GUAACC-----------------------------------------------------------C    1

    
    UGAGCA-----------------------------------------------------------A    1

    
    UUGAAU-----------------------------------------------------------U    1

    
    UUUCCU-----------------------------------------------------------A    1

    
    -AAUCAA-----------------------------------------------------------    1

    
    -AUUAAA-----------------------------------------------------------    1

    
    AAAAU------------------------------------------------------------U    1

    
    AAUAC------------------------------------------------------------A    1

    
    AUAAC------------------------------------------------------------A    1

    
    AUAAU------------------------------------------------------------A    1

    
    CAAUG------------------------------------------------------------G    1

    
    CACAA------------------------------------------------------------G    1

    
    CACAG------------------------------------------------------------G    1

    
    CAGAA------------------------------------------------------------G    1

    
    CAGAG------------------------------------------------------------G    1

    
    CAGUU------------------------------------------------------------G    1

    
    CAUAC------------------------------------------------------------A    1

    
    CCAUC------------------------------------------------------------G    1

    
    CCGCG------------------------------------------------------------G    1

    
    CGAAA------------------------------------------------------------G    1

    
    CGAAC------------------------------------------------------------G    1

    
    CGGAU------------------------------------------------------------G    1

    
    CGGCA------------------------------------------------------------G    1

    
    CUACG------------------------------------------------------------G    1

    
    CUCUU------------------------------------------------------------G    1

    
    CUGUG------------------------------------------------------------G    1

    
    CUUAA------------------------------------------------------------A    1

    
    CUUAC------------------------------------------------------------G    1

    
    GAUGG------------------------------------------------------------C    1

    
    GUAAU------------------------------------------------------------A    1

    
    UAAAU------------------------------------------------------------A    1

    
    UAGAC------------------------------------------------------------A    1

    
    UAUAU------------------------------------------------------------A    1

    
    UAUAU------------------------------------------------------------C    1

    
    -CGAAC------------------------------------------------------------    1

    
    -CGUUG------------------------------------------------------------    1

    
    -GAACA------------------------------------------------------------    1

    
    -GCCAA------------------------------------------------------------    1

    
    AAAA-------------------------------------------------------------U    1

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

    
    CAAA-------------------------------------------------------------C    1

    
    CAAA-------------------------------------------------------------G    1

    
    CACA-------------------------------------------------------------G    1

    
    CACG-------------------------------------------------------------G    1

    
    CAUU-------------------------------------------------------------G    1

    
    CGAU-------------------------------------------------------------C    1

    
    CGUU-------------------------------------------------------------G    1

    
    CUUU-------------------------------------------------------------G    1

    
    GAAC-------------------------------------------------------------C    1

    
    GCCG-------------------------------------------------------------C    1

    
    GCUA-------------------------------------------------------------C    1

    
    UAAU-------------------------------------------------------------A    1

    
    UCAC-------------------------------------------------------------A    1

    
    UCGU-------------------------------------------------------------A    1

    
    -AACC-------------------------------------------------------------    1

    
    -AUUG-------------------------------------------------------------    1

    
    -GAAA-------------------------------------------------------------    1

    
    -GUAA-------------------------------------------------------------    1

    
    AAC--------------------------------------------------------------A    1

    
    AAC--------------------------------------------------------------C    1

    
    ACA--------------------------------------------------------------U    1

    
    UAU--------------------------------------------------------------A    1

    
    UGA--------------------------------------------------------------G    1

    
    CA---------------------------------------------------------------A    1

    
    Omitted sequenced and counts

    
    ------------------------------------------------------------------   53
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

50.11 -156.40 2 2

2

Motif group HL_50006.2

Basepair signature:
cWW-F-F

36.55 -160.33 3 2

3

Motif group HL_75660.5

Basepair signature:
cWW-F

35.86 -510.54 2 2

4

Motif group HL_04783.2

Basepair signature:
cWW-F-F-F

34.25 -148.85 3 2

5

Motif group HL_48417.5

Basepair signature:
cWW-F-F

33.56 -139.50 2 2

6

Motif group HL_93535.1

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

31.03 -257.65 3 2

7

Motif group HL_56334.1

Basepair signature:
cWW-F

25.75 -508.38 3 2

Mini UNCG

8

Motif group HL_56131.2

Basepair signature:
cWW-F-F

25.29 -172.40 4 3

9

Motif group HL_57176.2

Basepair signature:
cWW-F-F-F

24.60 -1017.55 3 2

Pseudoknot geometry with 3' bulge

10

Motif group HL_70782.2

Basepair signature:
cWW-F

22.53 -444.91 4 3

11

Motif group HL_86870.2

Basepair signature:
cWW-F-F-F

19.77 -190.54 3 2

12

Motif group HL_82710.2

Basepair signature:
cWW-F-F-F

19.77 -294.76 4 2

13

Motif group HL_69752.2

Basepair signature:
cWW-F

19.08 -532.55 3 3

14

Motif group HL_38901.2

Basepair signature:
cWW-F-cSH

18.62 -436.14 3 2

tRNA D-loop

15

Motif group HL_59843.1

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

18.16 -277.72 3 3

16

Motif group HL_50318.1

Basepair signature:
cWW-cSH-F-F

15.86 -315.37 5 4

17

Motif group HL_57875.1

Basepair signature:
cWW-F-F

15.17 -289.10 3 2

18

Motif group HL_38168.1

Basepair signature:
cWW-F

15.17 -530.76 3 3

19

Motif group HL_37824.7

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

14.71 -203.33 2 1

GNRA

20

Motif group HL_89199.2

Basepair signature:
cWW-F-F-F

14.71 -989.80 4 3

Mini UNCG

21

Motif group HL_13189.1

Basepair signature:
cWW-F-F

14.48 -292.57 3 3

22

Motif group HL_52953.3

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

14.48 -1937.20 3 2

23

Motif group HL_81100.2

Basepair signature:
cWW

13.56 -1551.37 4 3

24

Motif group HL_87553.1

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

13.33 -156.29 4 3

25

Motif group HL_20811.4

Basepair signature:
cWW-cWS-F

13.10 -181.52 4 3

tRNA D-loop

26

Motif group HL_89893.1

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

12.87 -288.23 4 3

27

Motif group HL_09452.1

Basepair signature:
cWW-F-F-F

12.18 -4991.03 5 4

28

Motif group HL_13963.3

Basepair signature:
cWW-F-F

11.95 -191.69 4 3

29

Motif group HL_80922.2

Basepair signature:
cWW-tSH-F

11.72 -196.28 4 3

30

Motif group HL_20535.2

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

11.26 -250.40 4 4

31

Motif group HL_46501.1

Basepair signature:
cWW-cWS

11.03 -448.72 3 3

32

Motif group HL_10540.1

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

10.80 -189.73 4 3

33

Motif group HL_62934.1

Basepair signature:
cWW-tSH-F

10.80 -211.39 3 3

34

Motif group HL_56676.1

Basepair signature:
cWW-F-F

10.34 -308.24 3 3

35

Motif group HL_99040.1

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

10.34 -1633.00 5 3

36

Motif group HL_30680.3

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

10.34 -4757.52 4 3

Pseudoknot geometry

37

Motif group HL_87954.2

Basepair signature:
cWW-tSW-F

10.11 -210.42 3 2

38

Motif group HL_55195.3

Basepair signature:
cWW-F

10.11 -611.42 3 2

39

Motif group HL_07886.3

Basepair signature:
cWW-F-F-F

9.66 -199.46 4 3

40

Motif group HL_32346.4

Basepair signature:
cWW-F

9.43 -537.62 3 2

41

Motif group HL_39243.1

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

9.20 -1721.03 5 3

42

Motif group HL_32392.1

Basepair signature:
cWW-F-F

8.97 -476.47 5 3

43

Motif group HL_35941.1

Basepair signature:
cWW-F

8.74 -717.99 4 3

44

Motif group HL_59330.1

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

8.74 -3013.28 6 5

45

Motif group HL_48778.2

Basepair signature:
cWW-F

8.51 -483.84 3 2

Mini UNCG

46

Motif group HL_60914.1

Basepair signature:
cWW-F

8.28 -805.44 4 3

47

Motif group HL_29966.1

Basepair signature:
cWW-F-F-F

8.28 -1109.71 5 3

48

Motif group HL_65794.5

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

8.05 -1840.34 3 2

Pseudoknot geometry

49

Motif group HL_37344.1

Basepair signature:
cWW-F-F

7.82 -264.72 4 4

50

Motif group HL_86769.4

Basepair signature:
cWW-cWW-cSH-F

7.59 -142.97 5 4

51

Motif group HL_34617.5

Basepair signature:
cWW-tSW-F

7.59 -236.63 3 2

UNCG

52

Motif group HL_43517.1

Basepair signature:
cWW-F-F-F

7.59 -318.07 4 3

53

Motif group HL_08100.1

Basepair signature:
cWW-F-F-F

7.13 -231.84 4 3

54

Motif group HL_80709.3

Basepair signature:
cWW-F-F-F

6.90 -1118.85 3 2

55

Motif group HL_93324.4

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

6.90 -2235.53 3 3

Pseudoknot geometry

56

Motif group HL_13529.1

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

6.67 -160.79 4 3

57

Motif group HL_18565.1

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

6.21 -208.85 5 4

58

Motif group HL_97917.2

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

6.21 -270.83 4 3

59

Motif group HL_10453.3

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

6.21 -765.17 4 3

tRNA anticodon loop

60

Motif group HL_49922.4

Basepair signature:
cWW-F-F-F

5.98 -221.88 3 2

61

Motif group HL_22622.1

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

5.52 -4572.08 4 4

62

Motif group HL_59735.5

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

5.52 -5029.05 3 3

63

Motif group HL_66103.1

Basepair signature:
cWW-F-F

5.29 -302.33 4 3

64

Motif group HL_78677.1

Basepair signature:
cWW-F-F

5.29 -724.97 4 3

65

Motif group HL_15802.1

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

4.83 -511.84 6 5

66

Motif group HL_76094.1

Basepair signature:
cWW-cWS-F-F

4.60 -2366.93 3 3

67

Motif group HL_77436.5

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

4.37 -173.86 3 3

T-loop related

68

Motif group HL_22584.6

Basepair signature:
cWW-tSW-F

4.37 -206.57 3 2

Fab BL3-6 binding hairpin with tSW

69

Motif group HL_30068.2

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

4.37 -314.14 4 3

70

Motif group HL_04259.3

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

4.14 -210.08 4 3

GNRA with extra cWW

71

Motif group HL_89567.2

Basepair signature:
cWW-F-F-F

3.91 -211.76 4 3

72

Motif group HL_47854.1

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

3.91 -254.98 5 4

73

Motif group HL_20167.2

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

3.68 -129.92 4 4

74

Motif group HL_47787.2

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

3.68 -316.99 3 2

75

Motif group HL_26631.1

Basepair signature:
cWW-F-F-F

3.68 -1331.18 4 3

76

Motif group HL_01609.3

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

3.45 -191.98 4 3

T-loop with 2 bulged bases not stacked

77

Motif group HL_99748.1

Basepair signature:
cWW-F-F-cSH

3.45 -228.45 5 4

Other HL

78

Motif group HL_65313.1

Basepair signature:
cWW-F-F-F

3.45 -1127.77 5 4

79

Motif group HL_42046.2

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

2.76 -216.96 4 4

80

Motif group HL_22135.1

Basepair signature:
cWW-F-F

2.76 -806.28 4 3

81

Motif group HL_41464.2

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

2.53 -178.98 5 4

82

Motif group HL_50537.6

Basepair signature:
cWW-F-F-F

2.53 -232.34 4 4

tRNA anticodon loop with synthetase

83

Motif group HL_25967.2

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

2.53 -654.41 5 4

84

Motif group HL_85993.1

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

2.53 -3852.01 6 4

85

Motif group HL_78347.4

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

2.30 -165.92 4 3

86

Motif group HL_27483.1

Basepair signature:
cWW-F

2.30 -230.53 4 3

87

Motif group HL_28075.1

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

1.84 -197.78 4 3

88

Motif group HL_64690.6

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

1.84 -227.79 5 4

89

Motif group HL_02817.2

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

1.84 -739.04 4 4

90

Motif group HL_00914.1

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

1.84 -769.34 5 4

91

Motif group HL_15574.1

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

1.84 -903.58 5 3

92

Motif group HL_94980.1

Basepair signature:
cWW-F-F

1.84 -1085.52 4 4

93

Motif group HL_78197.1

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

1.84 -2126.28 4 3

94

Motif group HL_71391.1

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

1.61 -242.01 4 3

95

Motif group HL_27670.2

Basepair signature:
cWW-tWH-F-F

1.61 -685.25 5 3

T-loop with unstacked turn

96

Motif group HL_86883.1

Basepair signature:
cWW-F-F-F

1.61 -1143.21 5 3

97

Motif group HL_51447.1

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

1.61 -3880.01 4 4

98

Motif group HL_88205.2

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

1.38 -412.14 5 4

99

Motif group HL_33983.1

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

1.38 -595.36 5 4

100

Motif group HL_28791.1

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

1.38 -1970.94 4 3

101

Motif group HL_84299.4

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

1.15 -223.49 5 4

102

Motif group HL_81538.2

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

1.15 -284.58 4 3

GNRA with tandem sheared

103

Motif group HL_20743.5

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

0.92 -149.28 5 4

104

Motif group HL_04641.1

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

0.92 -540.37 6 5

105

Motif group HL_31585.4

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

0.92 -896.44 3 3

Purine riboswitch

106

Motif group HL_67667.2

Basepair signature:
cWW-F-F

0.92 -2254.90 5 4

107

Motif group HL_80362.1

Basepair signature:
cWW-F-F-F

0.92 -4168.69 5 5

108

Motif group HL_50860.2

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

0.69 -123.99 5 4

109

Motif group HL_93438.2

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

0.69 -135.84 5 4

110

Motif group HL_73266.9

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

0.69 -180.27 5 4

111

Motif group HL_66853.7

Basepair signature:
cWW-cWS-F-cSH

0.69 -187.16 5 5

112

Motif group HL_06059.6

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

0.69 -719.65 4 3

tRNA anticodon loop

113

Motif group HL_80008.1

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

0.69 -1190.65 5 4

114

Motif group HL_72628.1

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

0.69 -1205.93 5 5

115

Motif group HL_38046.1

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

0.69 -1457.64 6 5

116

Motif group HL_83632.1

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

0.69 -1533.55 5 4

tRNA anticodon loop

117

Motif group HL_55436.1

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

0.69 -2727.32 5 4

118

Motif group HL_80241.1

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

0.69 -5560.81 6 4

119

Motif group HL_61996.2

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

0.46 -156.66 5 4

120

Motif group HL_57863.1

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

0.46 -178.63 6 5

G-quadruplex fragment

121

Motif group HL_18423.1

Basepair signature:
cWW-tSH-tHS-F

0.46 -183.01 7 6

122

Motif group HL_60266.1

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

0.46 -204.16 7 6

123

Motif group HL_75293.5

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

0.46 -224.22 5 5

124

Motif group HL_77082.1

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

0.46 -241.97 4 3

Pseudoknot geometry

125

Motif group HL_25061.1

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

0.46 -618.94 5 4

126

Motif group HL_37369.2

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

0.46 -635.04 4 3

127

Motif group HL_97733.1

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

0.46 -1323.44 6 6

128

Motif group HL_50779.4

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

0.46 -3790.55 6 4

129

Motif group HL_35677.3

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

0.46 -3918.13 5 5

130

Motif group HL_86012.1

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

0.23 -127.12 6 5

T-loop with unstacked turn

131

Motif group HL_26934.1

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

0.23 -148.74 6 4

132

Motif group HL_98864.1

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

0.23 -170.12 6 5

T-loop with unstacked turn

133

Motif group HL_36335.1

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

0.23 -182.50 6 5

134

Motif group HL_04171.7

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

0.23 -197.66 7 6

135

Motif group HL_01962.2

Basepair signature:
cWW-tWH-tWH-F

0.23 -202.25 7 6

136

Motif group HL_16991.1

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

0.23 -225.41 8 7

G-quadruplex fragment

137

Motif group HL_53504.3

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

0.23 -227.26 6 5

138

Motif group HL_45175.1

Basepair signature:
cWW-cWS-F-F

0.23 -251.89 5 5

tRNA D-loop

139

Motif group HL_73255.1

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

0.23 -335.29 6 5

140

Motif group HL_58224.1

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

0.23 -527.75 6 5

141

Motif group HL_93383.1

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

0.23 -1497.96 5 4

142

Motif group HL_38808.1

Basepair signature:
cWW-cWW

0.23 -1648.94 5 4

143

Motif group HL_80599.2

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

0.23 -2594.93 5 4

144

Motif group HL_08510.1

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

0.23 -2629.93 7 5

145

Motif group HL_32735.2

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

0.23 -2784.09 5 4

146

Motif group HL_93135.1

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

0.23 -3524.22 7 6

Pseudoknot

147

Motif group HL_42998.2

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

0.23 -3651.41 5 3

148

Motif group HL_16398.2

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

0.23 -4754.03 9 8

149

Motif group HL_70751.1

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

0.23 -5270.92 7 6

150

Motif group HL_78284.1

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

0.23 -5452.15 7 7

151

Motif group HL_99867.1

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

0.23 -5572.36 6 5

152

Motif group HL_77600.2

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

0.23 -6699.15 4 3

153

Motif group HL_97983.1

Basepair signature:
cWW-F-F

0.23 -7030.93 7 5

154

Motif group HL_02887.3

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

0.00 -134.76 6 5

T-loop with 3 stacked bulged bases

155

Motif group HL_83808.4

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

0.00 -156.84 6 5

Pseudoknot

156

Motif group HL_81545.2

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

0.00 -158.88 6 5

157

Motif group HL_41543.1

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

0.00 -170.59 8 7

158

Motif group HL_67079.1

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

0.00 -178.93 6 6

159

Motif group HL_41902.1

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

0.00 -182.68 8 7

160

Motif group HL_74379.3

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

0.00 -186.23 8 7

161

Motif group HL_90620.1

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

0.00 -191.44 7 6

162

Motif group HL_28252.8

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

0.00 -192.82 4 3

T-loop with 2 stacked bulged bases

163

Motif group HL_68257.1

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

0.00 -194.89 7 6

164

Motif group HL_04642.1

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

0.00 -199.12 6 5

tRNA D-loop

165

Motif group HL_70658.1

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

0.00 -203.67 8 7

166

Motif group HL_86109.1

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

0.00 -211.47 8 7

167

Motif group HL_49941.1

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

0.00 -212.80 7 6

tRNA D-loop

168

Motif group HL_40252.4

Basepair signature:
cWW-tSH-cWS-F

0.00 -218.27 7 6

169

Motif group HL_25847.2

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

0.00 -226.79 7 6

170

Motif group HL_07583.1

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

0.00 -230.63 9 8

171

Motif group HL_23509.1

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

0.00 -232.67 9 8

172

Motif group HL_81205.3

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

0.00 -235.67 9 8

173

Motif group HL_98252.1

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

0.00 -237.76 8 7

174

Motif group HL_84847.1

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

0.00 -244.20 10 9

175

Motif group HL_08602.1

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

0.00 -245.49 9 8

176

Motif group HL_74055.2

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

0.00 -248.67 10 9

177

Motif group HL_68767.1

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

0.00 -256.34 8 7

tRNA D-loop

178

Motif group HL_73247.1

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

0.00 -277.58 10 9

Pseudoknot geometry

179

Motif group HL_98870.1

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

0.00 -295.68 10 9

180

Motif group HL_13971.1

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

0.00 -309.37 10 9

181

Motif group HL_91641.1

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

0.00 -313.44 12 11

182

Motif group HL_14757.1

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

0.00 -315.03 13 12

183

Motif group HL_21372.1

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

0.00 -339.98 5 5

184

Motif group HL_51921.1

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

0.00 -409.32 15 15

185

Motif group HL_18978.1

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

0.00 -456.72 6 6

186

Motif group HL_06226.4

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

0.00 -462.80 6 6

187

Motif group HL_91939.2

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

0.00 -478.13 7 6

188

Motif group HL_02483.1

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

0.00 -479.88 7 6

189

Motif group HL_92488.1

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

0.00 -481.08 11 10

190

Motif group HL_89881.5

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

0.00 -483.39 7 6

191

Motif group HL_45785.1

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

0.00 -491.75 8 7

192

Motif group HL_97756.2

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

0.00 -495.30 10 9

193

Motif group HL_87463.1

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

0.00 -509.03 7 6

194

Motif group HL_05304.3

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

0.00 -529.11 8 7

195

Motif group HL_07480.2

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

0.00 -543.51 8 6

196

Motif group HL_02581.1

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

0.00 -545.05 10 9

tRNA D-loop

197

Motif group HL_23010.1

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

0.00 -559.45 7 6

198

Motif group HL_53454.2

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

0.00 -629.83 6 5

199

Motif group HL_34964.1

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

0.00 -658.51 8 6

200

Motif group HL_85434.1

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

0.00 -870.21 7 6

201

Motif group HL_93616.2

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

0.00 -883.92 7 6

tRNA D-loop

202

Motif group HL_29129.3

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

0.00 -986.54 7 6

203

Motif group HL_99769.3

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

0.00 -1176.22 7 6

204

Motif group HL_11542.1

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

0.00 -1264.84 9 8

205

Motif group HL_85367.2

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

0.00 -1481.16 4 4

206

Motif group HL_12870.1

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

0.00 -2398.49 9 8

207

Motif group HL_10456.1

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

0.00 -2500.25 13 12

208

Motif group HL_66482.1

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

0.00 -2517.33 12 12

209

Motif group HL_38649.1

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

0.00 -2654.37 7 6

210

Motif group HL_20751.2

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

0.00 -2967.65 9 8

211

Motif group HL_23115.1

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

0.00 -3167.81 7 7

tRNA D-loop

212

Motif group HL_33074.4

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

0.00 -3246.29 8 7

U1 small nuclear ribonucleoprotein A binding hairpin

213

Motif group HL_91503.7

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

0.00 -3290.39 7 6

214

Motif group HL_88558.1

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

0.00 -3300.17 8 7

215

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 -3303.02 14 13

216

Motif group HL_80411.1

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

0.00 -3328.36 7 7

tRNA D-loop

217

Motif group HL_29762.1

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

0.00 -3356.67 7 6

218

Motif group HL_69139.1

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

0.00 -3804.04 7 6

219

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 -3930.68 12 11

220

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 -3952.99 16 15

221

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 -3978.52 16 15

222

Motif group HL_85461.1

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

0.00 -3995.38 15 14

223

Motif group HL_60293.1

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

0.00 -4030.45 17 16

G-quadruplex

224

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 -4035.06 19 18

G-quadruplex

225

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 -4053.49 19 18

226

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 -4066.83 19 19

G-quadruplex

227

Motif group HL_73183.1

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

0.00 -4101.09 10 10

Pseudoknot geometry with G-bulge

228

Motif group HL_50851.1

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

0.00 -4145.31 9 8

G-quadruplex fragment

229

Motif group HL_67407.5

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

0.00 -4150.90 6 6

230

Motif group HL_81312.1

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

0.00 -4341.26 8 7

231

Motif group HL_19210.3

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

0.00 -4369.22 6 5

232

Motif group HL_04725.1

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

0.00 -4451.81 8 7

233

Motif group HL_55305.1

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

0.00 -4470.29 8 7

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 -4570.88 34 34

235

Motif group HL_01255.1

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

0.00 -4590.21 7 7

236

Motif group HL_07903.1

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

0.00 -4611.53 10 9

237

Motif group HL_31581.6

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

0.00 -4639.04 7 7

238

Motif group HL_63355.1

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

0.00 -4668.42 9 8

239

Motif group HL_88364.2

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

0.00 -4864.04 11 11

240

Motif group HL_47732.1

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

0.00 -4946.97 8 7

241

Motif group HL_15118.1

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

0.00 -4973.72 8 7

242

Motif group HL_64292.1

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

0.00 -5003.51 11 11

243

Motif group HL_74292.1

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

0.00 -5016.88 6 5

244

Motif group HL_94376.1

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

0.00 -5040.86 7 6

Pseudoknot geometry

245

Motif group HL_29958.1

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

0.00 -5141.08 10 9

246

Motif group HL_24792.1

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

0.00 -5146.02 7 6

247

Motif group HL_36684.4

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

0.00 -5414.50 6 5

248

Motif group HL_50418.1

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

0.00 -5531.34 6 5

249

Motif group HL_68572.1

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

0.00 -5743.00 8 8

250

Motif group HL_20781.1

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

0.00 -5948.78 7 6

251

Motif group HL_58539.1

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

0.00 -6875.96 11 10

252

Motif group HL_07951.3

Basepair signature:
cWW-F-F

0.00 -9999.00 5 5

tRNA D-loop

253

Motif group HL_09260.2

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

0.00 -9999.00 7 6

tRNA D-loop

Coloring options: