| 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 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 5 | 11 4 I | 12 3 5 | 13 3 I | 14 3 6 | 15 3 I | 16 3 7 | 17 3 I | 18 3 8 | 19 3 I | 20 3 9 | 21 3 I | 22 3 10 | 23 3 I | 24 3 11 | 25 3 I | 26 3 12 | 27 3 I | 28 3 13 | 29 3 I | 30 3 14 | 31 3 I | 32 3 15 | 33 3 I | 34 3 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_77076.1_Instance_1 IL_77076.1_IL_1MZP_003_G20_C45 | G | G | A | G | C | G | C | C | G | G | U | G | A | A | A | U | A | C | ||||||||||||||||||||||||||
| IL_77076.1_Sequence_1 IL_77076.1_IL_1MZP_003_G20_C45 | G | G | A | G | * | C | G | C | C | G | G | U | G | A | A | A | U | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| IL_77076.1_Instance_2 IL_77076.1_IL_3UMY_003_G2124_C2174 | G | G | A | G | C | G | C | C | G | G | U | G | A | A | A | U | A | C | ||||||||||||||||||||||||||
| IL_77076.1_Sequence_2 IL_77076.1_IL_3UMY_003_G_2124_C_2174 | G | G | A | G | * | C | G | C | C | G | G | U | G | A | A | A | U | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 18 cWW 2 17 tSH 2 18 s55 3 6 tSS 3 17 s55 4 5 cWW 4 6 s55 4 17 tSS 5 6 s35 5 17 cSS 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 10 16 tWH 11 12 s35 11 15 tWH 12 15 s55 13 14 s35 15 16 s35 17 18 s35 8 7 7BPh 12 15 6BPh 2 16 6BPh 18 17 7BPh 17 2 6BR 14 12 7BRJAR3D SCFG/MRF model for IL_77076.1:
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 [18] // Initial node G20 - C45 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003952716,0.056367336,0.004576658,0.075011714,0.000000000],[0.006669351,0.022815069,0.080791377,0.005142338,0.000000000],[0.004519048,0.602973996,0.000833380,0.010689507,0.000000000],[0.074578555,0.037785716,0.009220848,0.004072390,0.000000000],[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 G20 - C45 cWW ClusterNode | Deletion Probability [0.000000000000000000000000000000000000152587890625000050000000] | Num Left Bases [3] | Num Right Bases [13] | Left Index [2] | Right Index [17] | Norm Constant [0.025236805498983] // Cluster node G21:G23 and C32:A44 Interaction | Interacting Bases [3,4] | 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]] // Cluster Interaction G23 - C32 cWW Interaction | Interacting Bases [2,5] | Pair Probability [[0.172411429,0.192167986,0.229920841,0.184388661,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.011541768,0.013321536,0.020537534,0.158885204,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A22 - G33 tSS Interaction | Interacting Bases [1,16] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A44 tSH Interaction | Interacting Bases [3,16] | Pair Probability [[0.027441087,0.006151523,0.007255111,0.006230281,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.680617569,0.117598954,0.118861917,0.014691247,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G23 - A44 tSS Interaction | Interacting Bases [10,14] | Pair Probability [[0.025971800,0.005446896,0.026718220,0.005446896,0.000000000],[0.054103855,0.045222361,0.036155648,0.005446896,0.000000000],[0.005446896,0.005446896,0.063745789,0.025408179,0.000000000],[0.564297448,0.005446896,0.067195854,0.058499471,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A42 tWH Interaction | Interacting Bases [9,15] | Pair Probability [[0.042142294,0.004723046,0.206685502,0.004723046,0.000000000],[0.048779144,0.021003908,0.037384201,0.004723046,0.000000000],[0.004723046,0.004723046,0.032699768,0.491912438,0.000000000],[0.022031629,0.004723046,0.019996218,0.049026621,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - U43 tWH Interaction | Interacting Bases [4,16] | Pair Probability [[0.137353716,0.027973270,0.027144157,0.027605601,0.000000000],[0.265454914,0.028129651,0.003444892,0.025860767,0.000000000],[0.146388091,0.029726665,0.026997642,0.029902458,0.000000000],[0.141951395,0.027674455,0.026559644,0.027832681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C32 - A44 cSS Interaction | Interacting Bases [6,6] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C34 Interaction | Interacting Bases [7,7] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C35 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 G36 Interaction | Interacting Bases [11,11] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G39 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 A40 Interaction | Interacting Bases [13,13] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A41 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_77076.1:
> IL_77076.1 IL_1MZP_003 G 20 C 45 GGAG*CGCCGGUGAAAUAC > IL_77076.1 IL_3UMY_003 G 2124 C 2174 GGAG*CGCCGGUGAAAUAC