| 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 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 5 I | 16 6 8 | 17 6 I | 18 7 | 19 6 I | 20 6 9 | 21 5 I | 22 4 10 | 23 4 I | 24 4 11 | 25 4 I | 26 4 12 | 27 4 I | 28 4 13 | 29 3 I | 30 3 14 | 31 2 I | 32 2 15 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_28026.3_Instance_1 IL_28026.3,IL_4LFB_017,G409_C433 | G | G | A | A | G | A | A | G | U | G | U | A | A | A | C | |||||||||||||||||||||||
| IL_28026.3_Sequence_1 IL_28026.34LFB_G409_C433 | G | G | A | A | G | A | A | G | * | U | G | U | A | A | A | C | true | 98 | 0 | 0 | 0.34 | |||||||||||||||||
| IL_28026.3_Instance_2 IL_28026.3,IL_5J7L_020,U409_G433 | U | G | A | A | G | A | A | G | U | G | U | A | A | A | G | |||||||||||||||||||||||
| IL_28026.3_Sequence_2 IL_28026.35J7L_U409_G433 | U | G | A | A | G | A | A | G | * | U | G | U | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 15 cWW 2 11 s33 2 14 tSH 2 15 s55 3 5 s35 3 10 s35 3 11 s55 3 12 tWH 4 6 s35 5 10 tSS 6 7 s35 6 12 tHW 6 13 s55 7 8 s35 7 10 tHH 8 9 cWW 9 10 s33 10 12 s55 11 13 cWH 12 13 s35 13 14 s35 14 15 s35 10 6 6BPh 5 11 6BPh 2 13 6BPh 14 2 6BRJAR3D SCFG/MRF model for IL_28026.3:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[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 [15] // Basepair G409 - C433 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.046260217,0.000524565,0.002472278,0.000000000],[0.044022640,0.046153098,0.000524565,0.000524565,0.000000000],[0.386803555,0.003671957,0.017951032,0.311661837,0.000000000],[0.048778633,0.045903932,0.000524565,0.000524565,0.000000000],[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 [14] // Basepair G410 - A432 tSH ClusterNode | Deletion Probability [0.000000000000000000001953125000000000515889489244815448855715] | Num Left Bases [5] | Num Right Bases [4] | Left Index [3] | Right Index [13] | Norm Constant [0.280868878847896] // Cluster node 4LFB|1|A|A|411:4LFB|1|A|A|415 and 4LFB|1|A|G|428:4LFB|1|A|A|431 Interaction | Interacting Bases [3,6] | Pair Probability [[0.001221525,0.001022446,0.008175813,0.000734405,0.000000000],[0.000143014,0.000143014,0.088049063,0.000143014,0.000000000],[0.097318616,0.001001098,0.720376451,0.080241401,0.000000000],[0.000143014,0.000143014,0.001001098,0.000143014,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|413 - 4LFB|1|A|G|428 tSS Interaction | Interacting Bases [5,6] | Pair Probability [[0.005347053,0.006149377,0.800291450,0.094216747,0.000000000],[0.005088969,0.001115262,0.033568158,0.011931507,0.000000000],[0.009171003,0.004845667,0.007806836,0.001115262,0.000000000],[0.005355260,0.005075351,0.007806836,0.001115262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|415 - 4LFB|1|A|G|428 tHH Interaction | Interacting Bases [1,8] | 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]] // Cluster Interaction 4LFB|1|A|A|411 - 4LFB|1|A|A|430 tWH Interaction | Interacting Bases [4,8] | Pair Probability [[0.381184813,0.030948835,0.003615770,0.016338652,0.000000000],[0.003615770,0.015344049,0.008956754,0.003615770,0.000000000],[0.318975856,0.003615770,0.132906372,0.017330382,0.000000000],[0.003615770,0.003615770,0.038702064,0.017617604,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|A|414 - 4LFB|1|A|A|430 tHW Interaction | Interacting Bases [7,9] | Pair Probability [[0.003068279,0.003068279,0.013222312,0.013284346,0.000000000],[0.003068279,0.014755072,0.003068279,0.290617672,0.000000000],[0.011304130,0.003068279,0.010604660,0.003068279,0.000000000],[0.326435762,0.003068279,0.283904858,0.014393233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|429 - 4LFB|1|A|A|431 cWH Interaction | Interacting Bases [2,2] | 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]] // Left strand conserved insertion 4LFB|1|A|A|412 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 [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015839826,0.296886961,0.014317634,0.084582798,0.000000000],[0.013722760,0.012789399,0.036431816,0.014404953,0.000000000],[0.014010903,0.041562971,0.003244391,0.344046970,0.000000000],[0.036578332,0.015734627,0.014397948,0.041447713,0.000000000],[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 [8] | Right Index [9] // Basepair G416 - U427 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_28026.3:
> IL_28026.3 4LFB G 409 C 433 GGAAGAAG*UGUAAAC > IL_28026.3 5J7L U 409 G 433 UGAAGAAG*UGUAAAG