| 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 3 3 | 7 4 I | 8 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 | 13 6 I | 14 6 6 | 15 5 I | 16 5 7 | 17 4 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_65718.4_Instance_1 IL_65718.4,IL_8P9A_453,G1760_C1641 | G | U | A | A | C | G | C | C | C | |||||||||||||||||
| IL_65718.4_Sequence_1 IL_65718.48P9A_G_1760_C_1641 | G | U | A | A | C | * | G | C | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_65718.4_Instance_2 IL_65718.4,IL_8CRE_467,G1747_C1628 | G | U | A | A | C | G | C | C | C | |||||||||||||||||
| IL_65718.4_Sequence_2 IL_65718.48CRE_G_1747_C_1628 | G | U | A | A | C | * | G | C | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_65718.4_Instance_3 IL_65718.4,IL_5J7L_059,G1497_C1404 | G | U | A | A | C | G | C | C | C | |||||||||||||||||
| IL_65718.4_Sequence_3 IL_65718.45J7L_G_1497_C_1404 | G | U | A | A | C | * | G | C | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_65718.4_Instance_4 IL_65718.4,IL_4LFB_068,G1497_C1404 | G | U | A | A | C | G | C | C | C | |||||||||||||||||
| IL_65718.4_Sequence_4 IL_65718.44LFB_G_1497_C_1404 | G | U | A | A | C | * | G | C | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 cSH 3 4 s35 3 8 cWS 3 9 s55 4 5 s35 4 7 cWW 5 6 cWW 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for IL_65718.4:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G1760 - C1641 cWW ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [0.392332624245040] // Cluster node 8P9A|1|sR|U|1761:8P9A|1|sR|A|1762 and 8P9A|1|sR|C|1640:8P9A|1|sR|C|1640 Interaction | Interacting Bases [2,3] | Pair Probability [[0.195577420,0.251085805,0.195342865,0.191596210,0.000000000],[0.018993996,0.016859729,0.002126243,0.016434444,0.000000000],[0.017755210,0.002126243,0.052650015,0.009408353,0.000000000],[0.007701599,0.008222834,0.006550458,0.007568577,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|A|1762 - 8P9A|1|sR|C|1640 cWS Interaction | Interacting Bases [1,2] | Pair Probability [[0.100011750,0.094722610,0.004841162,0.013507039,0.000000000],[0.097683988,0.091414608,0.001039315,0.008702420,0.000000000],[0.008871102,0.001039315,0.087555151,0.085082332,0.000000000],[0.229805672,0.089188021,0.001039315,0.085496198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|1761 - 8P9A|1|sR|A|1762 cSH InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.012323344,0.391058448,0.010755562,0.028595871,0.000000000],[0.010802244,0.010352721,0.021701194,0.010688228,0.000000000],[0.010503014,0.025730213,0.002651843,0.242664219,0.000000000],[0.022759426,0.011728355,0.011216467,0.176468852,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A1763 - C1639 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 C1764 - G1638 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_65718.4:
> IL_65718.4 8P9A G 1760 C 1641 GUAAC*GCCC > IL_65718.4 8CRE G 1747 C 1628 GUAAC*GCCC > IL_65718.4 5J7L G 1497 C 1404 GUAAC*GCCC > IL_65718.4 4LFB G 1497 C 1404 GUAAC*GCCC