| 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 3 I | 12 3 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_86843.1_Instance_1 HL_86843.1_HL_1U0B_001_A12_U23 | A | A | A | G | C | GGUU | A | U | ||||||||||||
| HL_86843.1_Sequence_1 HL_86843.1_HL_1U0B_001_A12_U23 | A | A | A | G | C | GGUU | A | U | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_86843.1_Instance_2 HL_86843.1_HL_5X6B_001_C12_G22 | C | U | A | G | G | GGCU | A | G | ||||||||||||
| HL_86843.1_Sequence_2 HL_86843.1_HL_5X6B_001_C12_G22 | C | U | A | G | G | GGCU | A | G | true | 97 | 0 | 0 | 0.49 |
1 2 s35 1 7 cWW 2 6 tSH 3 4 s35 3 6 s55 4 5 s35 6 7 s35JAR3D SCFG/MRF model for HL_86843.1:
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 [7] // Initial node A12 - U23 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009409752,0.019555960,0.010438919,0.211256183,0.000000000],[0.018897284,0.009646494,0.211374635,0.012074740,0.000000000],[0.010490831,0.199877935,0.002065453,0.038339992,0.000000000],[0.198695040,0.012157589,0.024891932,0.010827262,0.000000000],[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 [7] // Basepair A12 - U23 cWW BasepairNode | Deletion Probability [0.0000000000000148] | Pair Probability [[0.170633068,0.018769317,0.001608291,0.009807274,0.000000000],[0.155944887,0.063880246,0.001608291,0.001608291,0.000000000],[0.133975908,0.001608291,0.013970829,0.035102001,0.000000000],[0.243751236,0.144515485,0.001608291,0.001608291,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.050000000,0.150000000,0.450000000,0.350000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair A13 - A22 tSH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A14:C16 Interaction | Interacting Bases [1,1] | 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]] // Hairpin conserved non-basepairing position A14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16Sequences of instances from HL_86843.1:
> HL_86843.1 HL_1U0B_001 A 12 U 23 AAAGCGGUUAU > HL_86843.1 HL_5X6B_001 C 12 G 22 CUAGGGGCUAG