| 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 5 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 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 11 I | 26 10 12 | 27 9 I | 28 9 13 | 29 8 I | 30 8 14 | 31 7 I | 32 6 15 | 33 3 I | 34 3 16 | 35 2 I | 36 2 17 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_94744.1_Instance_1 IL_94744.1_IL_3D0U_003_G19_C67 | G | A | U | G | A | G | U | A | G | U | G | A | A | A | G | G | C | |||||||||||||||||||||||||
| IL_94744.1_Sequence_1 IL_94744.1_IL_3D0U_003_G19_C67 | G | A | U | G | A | G | U | A | G | * | U | G | A | A | A | G | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||
| IL_94744.1_Instance_2 IL_94744.1_IL_3DIR_003_G22_C70 | G | A | U | G | A | G | U | A | G | U | G | A | A | A | G | G | C | |||||||||||||||||||||||||
| IL_94744.1_Sequence_2 IL_94744.1_IL_3DIR_003_G22_C70 | G | A | U | G | A | G | U | A | G | * | U | G | A | A | A | G | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 17 cWW 2 3 s35 2 16 cWW 3 4 s35 4 5 s33 4 13 s33 4 14 tSH 5 6 s55 5 7 s55 5 12 s53 5 13 tHH 6 7 cSH 6 11 s33 7 8 s35 7 11 s33 7 12 tWH 8 9 s35 8 11 tHS 8 12 s55 9 10 cWW 10 11 s35 12 13 s35 13 14 s35 14 15 s35 15 16 s35 16 17 s35 11 7 6BPh 6 12 6BPh 5 13 6BPh 14 4 6BR 11 6 6BR 8 11 6BRJAR3D SCFG/MRF model for IL_94744.1:
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 [17] // Initial node G19 - C67 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 [17] // Basepair G19 - C67 cWW 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 [2] | Right Index [16] // Basepair A20 - G66 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [3] | Right Index [15] // 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 [15] // 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 [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 [[0.111901106,0.130435065,0.001348266,0.006420269,0.000000000],[0.112896691,0.118332196,0.001348266,0.001348266,0.000000000],[0.154434405,0.001348266,0.006532064,0.112148628,0.000000000],[0.121632542,0.117177440,0.001348266,0.001348266,0.000000000],[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 G22 - A64 tSH BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.562260899,0.109540081,0.027089699,0.027130866,0.000000000],[0.010011575,0.000775219,0.066644223,0.055065299,0.000000000],[0.004842953,0.064324690,0.001899191,0.000775219,0.000000000],[0.004763724,0.063325924,0.000775219,0.000775219,0.000000000],[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 [5] | Right Index [13] // Basepair A23 - A63 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [6] | Right Index [12] | Norm Constant [0.464443704046994] // Cluster node G24:U25 and A62:A62 Interaction | Interacting Bases [2,3] | 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 U25 - A62 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.055133713,0.056797613,0.003097555,0.002562843,0.000000000],[0.053331132,0.061948753,0.000658823,0.062432193,0.000000000],[0.037706404,0.020619858,0.042149551,0.480783711,0.000000000],[0.004744073,0.055246645,0.000658823,0.062128311,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G24 - U25 cSH 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 [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] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.044105167,0.388315159,0.047517987,0.000000000],[0.050956855,0.046228647,0.003687073,0.045777520,0.000000000],[0.000526725,0.000526725,0.017863095,0.000526725,0.000000000],[0.002508196,0.000526725,0.306690455,0.000526725,0.000000000],[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 - G61 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 G27 - U60 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_94744.1:
> IL_94744.1 IL_3D0U_003 G 19 C 67 GAUGAGUAG*UGAAAGGC > IL_94744.1 IL_3DIR_003 G 22 C 70 GAUGAGUAG*UGAAAGGC