| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 4 I | 6 5 3 | 7 6 I | 8 13 4 | 9 14 I | 10 15 | 11 14 I | 12 13 5 | 13 13 I | 14 13 6 | 15 13 I | 16 13 7 | 17 13 I | 18 13 8 | 19 13 I | 20 13 9 | 21 13 I | 22 13 10 | 23 13 I | 24 13 11 | 25 13 I | 26 13 12 | 27 13 I | 28 13 13 | 29 13 I | 30 13 14 | 31 13 I | 32 13 15 | 33 13 I | 34 13 16 | 35 13 I | 36 13 17 | 37 12 I | 38 11 18 | 39 10 I | 40 9 19 | 41 8 I | 42 7 20 | 43 2 I | 44 2 21 | 45 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_23414.1_Instance_1 IL_23414.1_IL_3Q3Z_001_G12_C75 | G | A | A | A | U | U | A | G | U | A | G | U | G | C | A | A | C | C | G | A | C | |||||||||||||||||||||||||||||
| IL_23414.1_Sequence_1 IL_23414.1_IL_3Q3Z_001_G12_C75 | G | A | A | A | * | U | U | A | G | U | A | G | U | G | C | A | A | C | C | G | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||
| IL_23414.1_Instance_2 IL_23414.1_IL_3Q3Z_003_G12_C75 | G | A | A | A | U | U | A | G | U | A | G | U | G | C | A | A | C | C | G | A | C | |||||||||||||||||||||||||||||
| IL_23414.1_Sequence_2 IL_23414.1_IL_3Q3Z_003_G12_C75 | G | A | A | A | * | U | U | A | G | U | A | G | U | G | C | A | A | C | C | G | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 21 cWW 3 4 s35 4 5 cWW 5 6 s35 7 8 s35 7 14 bif 8 9 s35 8 12 s33 8 13 tWH 10 11 s35 11 12 s35 13 14 s35 14 15 s33 15 17 s55 16 17 cSH 17 18 s35 18 19 s35 19 20 s35 20 21 s35 9 12 6BPh 7 13 7BPh 17 16 7BRJAR3D SCFG/MRF model for IL_23414.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [21] // Initial node G12 - C75 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [21] // Basepair G12 - C75 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [20] // Fixed node on left InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [20] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [20] // Fixed node on left InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [20] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [20] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [19] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [19] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [18] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [17] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000000000006103515625000001900000000000] | Num Left Bases [1] | Num Right Bases [13] | Left Index [4] | Right Index [17] | Norm Constant [0.999999999999999] // Cluster node A15:A15 and U59:C71 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009250880,0.024435597,0.009809818,0.234417244,0.000000000],[0.020082763,0.009303252,0.192231283,0.010277023,0.000000000],[0.009793103,0.193347778,0.002148094,0.027785070,0.000000000],[0.206751230,0.010349703,0.023586724,0.016430437,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A15 - U59 cWW Interaction | Interacting Bases [5,10] | Pair Probability [[0.054517083,0.004401161,0.043297051,0.004401161,0.000000000],[0.030062838,0.020071606,0.021369465,0.004401161,0.000000000],[0.004401161,0.004401161,0.459723974,0.030471216,0.000000000],[0.051507409,0.004401161,0.236641445,0.025930945,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G62 - G67 tWH Interaction | Interacting Bases [4,11] | Pair Probability [[0.034551202,0.775289325,0.007556815,0.007556815,0.000000000],[0.004751121,0.003968388,0.001079545,0.001079545,0.000000000],[0.001079545,0.001079545,0.066425872,0.091264102,0.000000000],[0.001079545,0.001079545,0.001079545,0.001079545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A61 - C68 bif Interaction | Interacting Bases [13,14] | Pair Probability [[0.107358724,0.143107315,0.006419081,0.005362531,0.000000000],[0.110490754,0.103294657,0.001234995,0.106950551,0.000000000],[0.006103550,0.006664607,0.014614084,0.106469853,0.000000000],[0.061780476,0.116710780,0.001234995,0.102203046,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A70 - C71 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U60 Interaction | Interacting Bases [6,6] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.906250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U63 Interaction | Interacting Bases [7,7] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A64 Interaction | Interacting Bases [8,8] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G65 Interaction | Interacting Bases [9,9] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U66 Interaction | Interacting Bases [12,12] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A69 InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_23414.1:
> IL_23414.1 IL_3Q3Z_001 G 12 C 75 GAAA*UUAGUAGUGCAACCGAC > IL_23414.1 IL_3Q3Z_003 G 12 C 75 GAAA*UUAGUAGUGCAACCGAC