| 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 5 I | 8 8 4 | 9 8 I | 10 9 | 11 8 I | 12 8 5 | 13 7 I | 14 6 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_09530.1_Instance_1 IL_09530.1_IL_2GDI_008_U59_A80 | U | G | A | U | C | G | C | G | U | A | ||||||||||||||
| IL_09530.1_Sequence_1 IL_09530.1_IL_2GDI_008_U59_A80 | U | G | A | U | C | * | G | C | G | U | A | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_09530.1_Instance_2 IL_09530.1_IL_2GDI_004_U59_A80 | U | G | A | U | C | G | C | G | U | A | ||||||||||||||
| IL_09530.1_Sequence_2 IL_09530.1_IL_2GDI_004_U59_A80 | U | G | A | U | C | * | G | C | G | U | A | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_09530.1_Instance_3 IL_09530.1_IL_3D2V_003_U47_A68 | U | G | A | A | C | G | C | G | C | A | ||||||||||||||
| IL_09530.1_Sequence_3 IL_09530.1_IL_3D2V_003_U47_A68 | U | G | A | A | C | * | G | C | G | C | A | true | 96 | 0 | 0 | 0.51 | ||||||||
| IL_09530.1_Instance_4 IL_09530.1_IL_4LCK_005_A36_U72 | A | U | G | AUUAGCGA | C | G | G | A | U | |||||||||||||||
| IL_09530.1_Sequence_4 IL_09530.1_IL_4LCK_005_A36_U72 | A | U | G | AUUAGCGA | C | * | G | G | A | U | true | -7 | 0 | 0 | 15.07 |
1 2 s35 1 8 cWW 2 3 s33 2 7 cWH 2 8 s55 3 4 s55 4 5 cWW 5 6 s35 6 7 s33 7 8 s55JAR3D SCFG/MRF model for IL_09530.1:
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 [8] // Initial node U59 - A80 from junction BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[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 [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair U59 - A80 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.004508284,0.004508284,0.045685474,0.026411789,0.000000000],[0.004508284,0.042422116,0.209928331,0.023825784,0.000000000],[0.034825799,0.004508284,0.479674580,0.004508284,0.000000000],[0.058674243,0.004508284,0.013869760,0.037632420,0.000000000],[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 [2] | Right Index [7] // Basepair G60 - G78 cWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left InitialNode | Left Length Distribution [0.009140559,0.731244716,0.009140559,0.000457028,0.000007617,0.000007617,0.000007617,0.003046853,0.243748239,0.003046853,0.000152343] | Left Letter Distribution [0.346153846,0.115384615,0.192307692,0.346153846,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.583333333,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 [4] | Right Index [5] // Basepair C63 - G76 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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_09530.1:
> IL_09530.1 IL_2GDI_008 U 59 A 80 UGAUC*GCGUA > IL_09530.1 IL_2GDI_004 U 59 A 80 UGAUC*GCGUA > IL_09530.1 IL_3D2V_003 U 47 A 68 UGAAC*GCGCA > IL_09530.1 IL_4LCK_005 A 36 U 72 AUGAUUAGCGAC*GGAU