| 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 2 2 | 5 3 I | 6 4 3 | 7 5 I | 8 12 4 | 9 12 I | 10 13 5 | 11 13 I | 12 14 | 13 13 I | 14 13 6 | 15 12 I | 16 12 7 | 17 11 I | 18 10 8 | 19 9 I | 20 8 9 | 21 7 I | 22 6 10 | 23 3 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_09587.1_Instance_1 IL_09587.1_IL_2AW7_053_G1124_C1149 | G | U | U | G | C | G | A | A | C | U | C | |||||||||||||||||||
| IL_09587.1_Sequence_1 IL_09587.1_IL_2AW7_053_G_1124_C_1149 | G | U | U | G | C | * | G | A | A | C | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_09587.1_Instance_2 IL_09587.1_IL_4IOA_107_G46_C40 | G | A | A | C | U | G | C | A | C | C | C | C | ||||||||||||||||||
| IL_09587.1_Sequence_2 IL_09587.1_IL_4IOA_107_G46_C40 | G | A | A | C | U | G | * | C | A | C | C | C | C | true | 93 | 0 | 0 | 1.28 |
1 2 cSH 1 4 s35 1 7 s33 1 11 cWW 2 3 s35 2 4 s35 3 4 s35 4 5 s35 4 7 cWW 5 6 cWW 5 7 s55 6 7 s35 7 9 perp 8 9 s35 9 10 s35 10 11 s35 10 5 6BRJAR3D SCFG/MRF model for IL_09587.1:
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 [11] // Initial node G1124 - C1149 from junction ClusterNode | Deletion Probability [0.0000000079308950] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.250704046930271] // Cluster node G1124:U1125 and C1149:C1149 Interaction | Interacting Bases [1,3] | 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 G1124 - C1149 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.098479164,0.101451202,0.005532816,0.004577719,0.000000000],[0.095259415,0.110652104,0.001176781,0.111515620,0.000000000],[0.108552012,0.005261563,0.010755287,0.127482021,0.000000000],[0.008473804,0.098680881,0.001176781,0.110972829,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1124 - U1125 cSH Insertion | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node 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 [3] | Right Index [10] // Initial node U1126 - U1148 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.458333333,0.041666667,0.458333333,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // 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 [9] // 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 [9] // 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // 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 [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.027337184,0.017117650,0.175918530,0.111763840,0.000000000],[0.019469338,0.007660610,0.106704541,0.027034975,0.000000000],[0.192715421,0.106021772,0.002856825,0.019671972,0.000000000],[0.125621360,0.025689616,0.021954305,0.012462061,0.000000000],[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 [7] // Basepair G1127 - A1145 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010112949,0.018987468,0.011731285,0.192935737,0.000000000],[0.018987829,0.008487010,0.221492059,0.013594505,0.000000000],[0.011731300,0.221491395,0.002149724,0.025679421,0.000000000],[0.192935850,0.013594439,0.025679804,0.010409224,0.000000000],[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 [5] | Right Index [6] // Basepair C1128 - G1144 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_09587.1:
> IL_09587.1 IL_2AW7_053 G 1124 C 1149 GUUGC*GAACUC > IL_09587.1 IL_4IOA_107 G 46 C 40 GAACUG*CACCCC