| 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 5 4 | 9 6 I | 10 7 5 | 11 8 I | 12 13 6 | 13 13 I | 14 14 7 | 15 14 I | 16 15 | 17 14 I | 18 14 8 | 19 13 I | 20 13 9 | 21 12 I | 22 11 10 | 23 10 I | 24 9 11 | 25 4 I | 26 4 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_09129.2_Instance_1 IL_09129.2,IL_4LFB_051,U1247_G1290 | U | A | C | A | A | A | G | C | A | A | A | A | A | G | ||||||||||||||||||||||
| IL_09129.2_Sequence_1 IL_09129.24LFB_U_1247_G_1290 | U | A | C | A | A | A | G | * | C | A | A | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_09129.2_Instance_2 IL_09129.2,IL_5J7L_054,U1247_G1290 | U | A | C | A | A | A | G | C | A | U | A | A | A | G | ||||||||||||||||||||||
| IL_09129.2_Sequence_2 IL_09129.25J7L_U_1247_G_1290 | U | A | C | A | A | A | G | * | C | A | U | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 14 cWW 2 3 s35 2 13 tWH 2 14 s55 3 12 tWH 4 5 s35 4 11 s55 5 6 s35 6 7 s35 6 9 tWW 7 8 cWW 8 9 s33 9 10 s55 11 12 s35 12 13 s35 13 14 s35JAR3D SCFG/MRF model for IL_09129.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [14] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011246147,0.013983971,0.014277598,0.037274594,0.000000000],[0.302538153,0.027950744,0.042354115,0.016034133,0.000000000],[0.014590167,0.037125289,0.003306148,0.014672010,0.000000000],[0.086192816,0.014679149,0.350222612,0.013552354,0.000000000],[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 [14] // Basepair U1247 - G1290 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.381184813,0.003615770,0.318975856,0.003615770,0.000000000],[0.030948835,0.015344049,0.003615770,0.003615770,0.000000000],[0.003615770,0.008956754,0.132906372,0.038702064,0.000000000],[0.016338652,0.003615770,0.017330382,0.017617604,0.000000000],[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 [13] // Basepair A1248 - A1289 tWH BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.030717309,0.003588720,0.102662158,0.003588720,0.000000000],[0.378479886,0.026146144,0.003588720,0.003588720,0.000000000],[0.003588720,0.012529247,0.032271758,0.033080098,0.000000000],[0.036089313,0.003588720,0.016134962,0.310356803,0.000000000],[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 [12] // Basepair C1249 - A1288 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [11] // Fixed node on left for 4LFB|1|A|A|1250 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 [5] | Right Index [11] // 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 [5] | Right Index [11] // Fixed node on left for 4LFB|1|A|A|1251 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 [6] | Right Index [11] // 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 [6] | Right Index [11] // Fixed node on right for 4LFB|1|A|A|1287 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 [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // Fixed node on right for 4LFB|1|A|A|1286 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 [6] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.408702443,0.030010298,0.003890946,0.018600071,0.000000000],[0.029232420,0.014184148,0.011587973,0.014194456,0.000000000],[0.003890946,0.011604643,0.359806718,0.021928993,0.000000000],[0.018577888,0.014190992,0.021454432,0.018142633,0.000000000],[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 [6] | Right Index [9] // Basepair A1252 - A1285 tWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [7] | Right Index [8] // Basepair G1253 - C1284 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_09129.2:
> IL_09129.2 4LFB U 1247 G 1290 UACAAAG*CAAAAAG > IL_09129.2 5J7L U 1247 G 1290 UACAAAG*CAUAAAG