| 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 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 7 | 15 11 I | 16 12 8 | 17 12 I | 18 13 | 19 12 I | 20 12 9 | 21 11 I | 22 11 10 | 23 10 I | 24 10 11 | 25 9 I | 26 9 12 | 27 8 I | 28 8 13 | 29 7 I | 30 7 14 | 31 6 I | 32 5 15 | 33 2 I | 34 2 16 | 35 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_54954.1_Instance_1 IL_54954.1_IL_3U5H_005_C31_G53 | C | U | G | A | A | C | U | U | A | U | C | A | A | U | A | A | G | |||||||||||||||||||||||
| IL_54954.1_Sequence_1 IL_54954.1_IL_3U5H_005_C31_G53 | C | U | G | A | A | C | U | U | * | A | U | C | A | A | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 16 cWW 2 3 s35 3 13 s33 3 14 tSH 4 5 s35 4 12 s35 4 13 tHW 4 14 s55 5 6 s35 5 11 s33 5 12 tHH 6 7 s35 6 11 tHS 7 8 s35 7 10 cWW 8 9 cWW 9 10 s35 10 11 s35 11 12 s33 12 13 s55 14 15 s35 15 16 s35 12 5 6BPh 3 13 6BPh 14 3 6BRJAR3D SCFG/MRF model for IL_54954.1:
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 [16] // Initial node C31 - G53 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Basepair C31 - G53 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [15] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [15] // 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.051461378,0.000531940,0.002533030,0.000000000],[0.044541851,0.046686356,0.000531940,0.000531940,0.000000000],[0.382258874,0.003723579,0.018039957,0.309726994,0.000000000],[0.047988462,0.046230763,0.000531940,0.000531940,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // Basepair G33 - A51 tSH BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [4] | Right Index [13] // Basepair A34 - U50 tHW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.570891271,0.016177377,0.004000730,0.004006810,0.000000000],[0.072449192,0.000801415,0.068896252,0.056926055,0.000000000],[0.035046235,0.066498338,0.001963368,0.000801415,0.000000000],[0.034472894,0.065465821,0.000801415,0.000801415,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [12] // Basepair A35 - A48 tHH BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.067529094,0.118956523,0.149216401,0.143517090,0.000000000],[0.149836953,0.179916717,0.001700157,0.147086012,0.000000000],[0.001700157,0.001700157,0.007466133,0.001700157,0.000000000],[0.007270178,0.001700157,0.019003954,0.001700157,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [11] // Basepair C36 - C47 tHS BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.016427763,0.173116343,0.015813229,0.038072720,0.000000000],[0.020292580,0.020655153,0.023880724,0.017434414,0.000000000],[0.015507076,0.024323398,0.004977578,0.050682479,0.000000000],[0.031971055,0.018924845,0.020261855,0.507658789,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair U37 - U46 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009206316,0.020335270,0.009916234,0.209350778,0.000000000],[0.024742834,0.009627484,0.195778801,0.010479833,0.000000000],[0.009933160,0.194648267,0.002175103,0.023883287,0.000000000],[0.227411257,0.010406240,0.028134421,0.013970716,0.000000000],[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 U38 - A45 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_54954.1:
> IL_54954.1 IL_3U5H_005 C 31 G 53 CUGAACUU*AUCAAUAAG