| 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 4 I | 6 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 10 I | 16 11 8 | 17 11 I | 18 12 | 19 11 I | 20 11 9 | 21 10 I | 22 9 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_31707.1_Instance_1 IL_31707.1_IL_1ET4_001_C211_G230 | C | G | C | A | U | A | A | C | G | C | G | |||||||||||||||||||
| IL_31707.1_Sequence_1 IL_31707.1_IL_1ET4_001_C211_G230 | C | G | C | A | U | A | A | C | * | G | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_31707.1_Instance_2 IL_31707.1_IL_1ET4_003_C311_G330 | C | G | C | A | U | A | A | C | G | C | G | |||||||||||||||||||
| IL_31707.1_Sequence_2 IL_31707.1_IL_1ET4_003_C311_G330 | C | G | C | A | U | A | A | C | * | G | C | G | true | 100 | 0 | 0 | 0.00 |
1 4 perp 1 5 s55 1 11 cWW 2 3 s35 3 4 s33 5 10 cWW 6 7 s35 7 8 s35 7 10 bif 8 9 cWW 9 10 s35 10 11 s33 3 1 7BRJAR3D SCFG/MRF model for IL_31707.1:
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 C211 - G230 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 [11] // Basepair C211 - G230 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | 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 [3] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.875000000,0.041666667,0.041666667,0.000000000] | 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 [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | 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 [5] | Right Index [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [10] | Norm Constant [0.398999573027921] // Cluster node U215:A217 and C229:C229 Interaction | Interacting Bases [1,4] | Pair Probability [[0.037709894,0.016489402,0.045568617,0.017888108,0.000000000],[0.014863033,0.008107799,0.022909058,0.308140468,0.000000000],[0.042838384,0.024047847,0.003712699,0.018379192,0.000000000],[0.017762489,0.390877773,0.016589484,0.014115752,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U215 - C229 cWW Interaction | Interacting Bases [3,4] | Pair Probability [[0.020935056,0.568882952,0.005492751,0.005492751,0.000000000],[0.024173820,0.283797663,0.005492751,0.005492751,0.000000000],[0.005492751,0.005492751,0.020832258,0.005492751,0.000000000],[0.005492751,0.005492751,0.026450739,0.005492751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A217 - C229 bif 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 A216 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 [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 C218 - G228 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_31707.1:
> IL_31707.1 IL_1ET4_001 C 211 G 230 CGCAUAAC*GCG > IL_31707.1 IL_1ET4_003 C 311 G 330 CGCAUAAC*GCG