| 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 3 I | 6 4 3 | 7 4 I | 8 7 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 6 | 13 9 I | 14 10 7 | 15 11 I | 16 12 8 | 17 12 I | 18 13 9 | 19 13 I | 20 14 | 21 13 I | 22 13 10 | 23 12 I | 24 12 11 | 25 9 I | 26 9 12 | 27 8 I | 28 8 13 | 29 7 I | 30 7 14 | 31 6 I | 32 5 15 | 33 4 I | 34 4 16 | 35 3 I | 36 3 17 | 37 2 I | 38 2 18 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_76095.3_Instance_1 IL_76095.3_IL_1M5O_005_G19_C64 | G | A | G | A | A | A | C | A | C | G | G | U | A | U | A | U | U | A | C | C | ||||||||||||||||||||||||
| IL_76095.3_Sequence_1 IL_76095.3_IL_1M5O_005_G19_C64 | G | A | G | A | A | A | C | A | C | * | G | G | U | A | U | A | U | U | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| IL_76095.3_Instance_2 IL_76095.3_IL_2P7D_001_G19_C45 | G | A | G | A | A | A | C | A | C | G | G | U | A | C | A | U | U | A | C | C | ||||||||||||||||||||||||
| IL_76095.3_Sequence_2 IL_76095.3_IL_2P7D_001_G19_C45 | G | A | G | A | A | A | C | A | C | * | G | G | U | A | C | A | U | U | A | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 18 cWW 2 3 s35 2 17 cWW 3 14 s33 3 16 tSH 4 5 s35 4 14 tHW 4 16 s55 5 6 s35 5 13 tHW 5 15 perp 6 7 s35 6 12 tWH 7 8 s35 8 9 s35 8 11 cWW 9 10 cWW 10 11 s35 12 13 s35 13 14 s35 14 15 perp 16 17 s35 17 18 s35 17 16 7BPh 16 3 6BR 3 14 6BRJAR3D SCFG/MRF model for IL_76095.3:
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 [18] // Initial node G19 - C64 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 [18] // Basepair G19 - C64 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.004239289,0.704559841,0.003968692,0.011130938,0.000000000],[0.003985917,0.023716009,0.007830734,0.003917236,0.000000000],[0.003875504,0.066182996,0.000978503,0.087912340,0.000000000],[0.009148129,0.030421125,0.004101169,0.034031578,0.000000000],[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 [2] | Right Index [17] // Basepair A20 - C63 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.054858579,0.063944697,0.000660976,0.003147483,0.000000000],[0.055346656,0.058011367,0.000660976,0.000660976,0.000000000],[0.350095800,0.003304880,0.016011447,0.274899622,0.000000000],[0.059629333,0.057445257,0.000660976,0.000660976,0.000000000],[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 [3] | Right Index [16] // Basepair G21 - A62 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [4] | Right Index [15] // 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 [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.025971800,0.054103855,0.005446896,0.564297448,0.000000000],[0.005446896,0.045222361,0.005446896,0.005446896,0.000000000],[0.026718220,0.036155648,0.063745789,0.067195854,0.000000000],[0.005446896,0.005446896,0.025408179,0.058499471,0.000000000],[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 [4] | Right Index [14] // Basepair A22 - U60 tHW BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.418144609,0.031463906,0.003985368,0.019002964,0.000000000],[0.003985368,0.014640658,0.003985368,0.003985368,0.000000000],[0.341751342,0.022813077,0.049366656,0.023593614,0.000000000],[0.003985368,0.003985368,0.035560217,0.019750751,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Left Index [5] | Right Index [13] // Basepair A23 - A59 tHW BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [6] | Right Index [12] // Basepair A24 - A57 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [7] | Right Index [11] // 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 [8] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.194909758,0.012133405,0.318763646,0.013661711,0.000000000],[0.011848504,0.004569762,0.016221879,0.034517612,0.000000000],[0.287416726,0.016428681,0.002991558,0.013487720,0.000000000],[0.013638432,0.036717533,0.013189215,0.009503858,0.000000000],[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 [8] | Right Index [11] // Basepair A26 - G55 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [9] | Right Index [10] // Basepair C27 - G54 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_76095.3:
> IL_76095.3 IL_1M5O_005 G 19 C 64 GAGAAACAC*GGUAUAUUACC > IL_76095.3 IL_2P7D_001 G 19 C 45 GAGAAACAC*GGUACAUUACC