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The first RNA
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#119 PDB ID 1NBS 1 G 119 2 C 118 3 G 117 4 A 116 5 G 115 6 C 27 7 C 26 8 U 25 9 A 24 10 G 23 11 C 22 12 G 0 13 A 0 14 A 0 15 G 0 16 U 0 17 C 0 18 A 0 19 U 0 20 A 0 21 A 0 22 G 11 23 C 10 24 U 9 25 A 8 26 G 7 27 G 6 28 G 0 29 C 44 30 A 43 31 G 42 32 U 41 33 C 40 34 U 39 35 U 0 36 U 0 37 A 0 38 G 0 39 A 34 40 G 33 41 G 32 42 C 31 43 U 30 44 G 29 45 A 0 46 C 0 47 G 114 48 G 113 49 C 0 50 A 66 51 G 65 52 G 64 53 A 63 54 A 62 55 A 0 56 A 0 57 A 0 58 G 0 59 A 0 60 G 0 61 U 0 62 A 54 63 U 53 64 C 52 65 C 51 66 U 50 67 U 0 68 G 0 69 A 0 70 A 0 71 A 0 72 G 112 73 U 111 74 G 108 75 C 107 76 C 106 77 A 0 78 C 0 79 A 0 80 G 0 81 U 0 82 G 0 83 A 0 84 C 0 85 G 0 86 A 0 87 A 0 88 G 0 89 U 96 90 C 95 91 U 94 92 C 93 93 G 92 94 A 91 95 G 90 96 A 89 97 G 0 98 U 0 99 G 0 100 G 0 101 A 0 102 A 0 103 C 0 104 G 0 105 C 0 106 G 76 107 G 75 108 U 74 109 A 0 110 A 0 111 A 73 112 C 72 113 C 48 114 C 47 115 C 5 116 U 4 117 C 3 118 G 2 119 C 1 Number of junctions with CHS: 2 Junction: Helix 1: 5-115 Helix 2: 6-27 Helix 3: 29-44 Helix 4: 47-114 CHS: 2,3 CHS: 1,4 Junction: Helix 1: 48-113 Helix 2: 50-66 Helix 3: 72-112 CHS: 1,3
Format of the first RNA: CT formatBpseq formatDot-bracket format
The second RNA
#68 PDB ID 2EES 1 G 0 2 G 66 3 A 65 4 C 64 5 A 63 6 U 62 7 U 61 8 U 0 9 A 0 10 A 0 11 U 0 12 U 0 13 G 29 14 C 28 15 G 27 16 U 26 17 G 25 18 G 0 19 A 0 20 U 0 21 A 0 22 U 0 23 G 0 24 G 0 25 C 17 26 A 16 27 C 15 28 G 14 29 C 13 30 A 0 31 A 0 32 G 0 33 U 0 34 U 0 35 U 0 36 C 0 37 U 0 38 A 0 39 C 0 40 C 58 41 G 57 42 G 56 43 G 55 44 C 54 45 A 53 46 C 0 47 C 0 48 G 0 49 U 0 50 A 0 51 A 0 52 A 0 53 U 45 54 G 44 55 U 43 56 C 42 57 C 41 58 G 40 59 A 0 60 C 0 61 A 7 62 A 6 63 U 5 64 G 4 65 U 3 66 C 2 67 C 0 68 a 0 Number of junctions with CHS: 1 Junction: Helix 1: 7-61 Helix 2: 13-29 Helix 3: 40-58 CHS: 1,3
Format of the second RNA: CT formatBpseq formatDot-bracket format
Score matrix
>single-base scoring matrix: A C G U A +2.22 C -1.86 +1.16 G -1.46 -2.48 +1.03 U -1.39 -1.05 -1.74 +1.65 >base-pair scoring matrix: AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU AA -2.49 AC -7.04 -2.11 AG -8.24 -8.89 -0.80 AU -4.32 -2.04 -5.13 +4.49 CA -8.84 -9.37 -10.41 -5.56 -5.13 CC -14.37 -9.08 -14.53 -6.71 -10.45 -3.59 CG -4.68 -5.86 -4.57 1.67 -3.57 -5.71 5.36 CU -12.64 -10.45 -10.14 -5.17 -8.49 -5.77 -4.96 -2.28 GA -6.86 -9.73 -8.61 -5.33 -7.98 -12.43 -6.00 -7.71 -1.05 GC -5.03 -3.81 -5.77 2.70 -5.95 -3.70 2.11 -5.84 -4.88 5.62 GG -8.39 -11.05 -5.38 -5.61 -11.36 -12.58 -4.66 -13.69 -8.67 -4.13 -1.98 GU -5.84 -4.72 -6.60 0.59 -7.93 -7.88 -0.27 -5.61 -6.10 1.21 -5.77 3.47 UA -4.01 -5.33 -5.43 1.61 -2.42 -6.88 2.75 -4.72 -5.85 1.60 -5.75 -0.57 4.97 UC -11.32 -8.67 -8.87 -4.81 -7.08 -7.40 -4.91 -3.83 -6.63 -4.49 -12.01 -5.30 -2.98 -3.21 UG -6.16 -6.93 -5.94 -0.51 -5.63 -8.41 1.32 -7.36 -7.55 -0.08 -4.27 -2.09 1.14 -4.76 3.36 UU -9.05 -7.83 -11.07 -2.98 -8.39 -5.41 -3.67 -5.21 -11.54 -3.90 -10.79 -4.45 -3.39 -5.97 -4.28 -0.02
Gap penalty -1 -2 (default: -1)