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The first RNA
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50 PDB ID 1E8O Signal Recognition Particle (SRP) RNA 1 G 0 2 50 1 2 G 1 3 49 2 3 G 2 4 48 3 4 C 3 5 47 4 5 C 4 6 46 5 6 G 5 7 25 6 7 G 6 8 24 7 8 G 7 9 23 8 9 C 8 10 22 9 10 G 9 11 21 10 11 C 10 12 20 11 12 G 11 13 19 12 13 G 12 14 0 13 14 U 13 15 0 14 15 G 14 16 0 15 16 G 15 17 0 16 17 C 16 18 0 17 18 G 17 19 0 18 19 C 18 20 12 19 20 G 19 21 11 20 21 C 20 22 10 21 22 G 21 23 9 22 23 C 22 24 8 23 24 C 23 25 7 24 25 U 24 26 6 25 26 G 25 27 0 26 27 U 26 28 0 27 28 A 27 29 0 28 29 G 28 30 0 29 30 U 29 31 45 30 31 C 30 32 44 31 32 C 31 33 43 32 33 C 32 34 42 33 34 A 33 35 0 34 35 G 34 36 0 35 36 C 35 37 0 36 37 U 36 38 0 37 38 A 37 39 0 38 39 C 38 40 0 39 40 U 39 41 0 40 41 C 40 42 0 41 42 G 41 43 33 42 43 G 42 44 32 43 44 G 43 45 31 44 45 A 44 46 30 45 46 G 45 47 5 46 47 G 46 48 4 47 48 C 47 49 3 48 49 U 48 50 2 49 50 C 49 51 1 50 Number of junctions with CHS: 1 Junction: Helix 1: 5-46 Helix 2: 6-25 Helix 3: 30-45 CHS: 1,3
Format of the first RNA:CT formatBpseq formatDot-bracket format
The second RNA
97 PDB ID 1LNG 7S.S SRP RNA of M. jannaschii 1 U 0 2 0 1 2 C 1 3 0 2 3 G 2 4 97 3 4 G 3 5 96 4 5 C 4 6 95 5 6 G 5 7 94 6 7 G 6 8 0 7 8 U 7 9 0 8 9 G 8 10 43 9 10 G 9 11 42 10 11 G 10 12 41 11 12 G 11 13 40 12 13 G 12 14 39 13 14 A 13 15 0 14 15 G 14 16 36 15 16 C 15 17 35 16 17 A 16 18 34 17 18 U 17 19 33 18 19 C 18 20 32 19 20 U 19 21 31 20 21 C 20 22 30 21 22 C 21 23 29 22 23 U 22 24 28 23 24 G 23 25 0 24 25 U 24 26 0 25 26 A 25 27 0 26 27 G 26 28 0 27 28 G 27 29 23 28 29 G 28 30 22 29 30 G 29 31 21 30 31 A 30 32 20 31 32 G 31 33 19 32 33 A 32 34 18 33 34 U 33 35 17 34 35 G 34 36 16 35 36 U 35 37 15 36 37 A 36 38 0 37 38 A 37 39 0 38 39 C 38 40 13 39 40 C 39 41 12 40 41 C 40 42 11 41 42 C 41 43 10 42 43 C 42 44 9 43 44 U 43 45 0 44 45 U 44 46 0 45 46 U 45 47 0 46 47 A 46 48 0 47 48 C 47 49 92 48 49 C 48 50 91 49 50 U 49 51 90 50 51 G 50 52 89 51 52 C 51 53 88 52 53 C 52 54 87 53 54 G 53 55 86 54 55 A 54 56 85 55 56 A 55 57 0 56 57 C 56 58 0 57 58 C 57 59 0 58 59 C 58 60 0 59 60 C 59 61 83 60 61 G 60 62 82 61 62 C 61 63 81 62 63 C 62 64 80 63 64 A 63 65 0 64 65 G 64 66 78 65 66 G 65 67 77 66 67 C 66 68 76 67 68 C 67 69 75 68 69 C 68 70 74 69 70 G 69 71 0 70 71 G 70 72 0 71 72 A 71 73 0 72 73 A 72 74 0 73 74 G 73 75 69 74 75 G 74 76 68 75 76 G 75 77 67 76 77 A 76 78 66 77 78 G 77 79 65 78 79 C 78 80 0 79 80 A 79 81 63 80 81 A 80 82 62 81 82 C 81 83 61 82 83 G 82 84 60 83 84 G 83 85 0 84 85 U 84 86 55 85 86 A 85 87 54 86 87 G 86 88 53 87 88 G 87 89 52 88 89 C 88 90 51 89 90 A 89 91 50 90 91 G 90 92 49 91 92 G 91 93 48 92 93 A 92 94 0 93 94 C 93 95 6 94 95 G 94 96 5 95 96 U 95 97 4 96 97 C 96 0 3 97 Number of junctions with CHS: 1 Junction: Helix 1: 6-94 Helix 2: 9-43 Helix 3: 48-92 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)