| 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 8 3 | 7 8 I | 8 9 4 | 9 9 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 8 I | 16 8 8 | 17 7 I | 18 6 9 | 19 5 I | 20 4 10 | 21 3 I | 22 3 11 | 23 2 I | 24 2 12 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_98870.1_Instance_1 HL_98870.1_HL_6DU4_001_C7_G23 | C | G | U | AGGC | U | A | C | A | G | A | G | A | A | G | ||||||||||||||||
| HL_98870.1_Sequence_1 HL_98870.1_HL_6DU4_001_C7_G23 | C | G | U | AGGC | U | A | C | A | G | A | G | A | A | G | true | 82 | 0 | 0 | 3.68 | |||||||||||
| HL_98870.1_Instance_2 HL_98870.1_HL_6DU5_001_U7_G21 | U | G | U | GG | U | A | C | A | G | A | G | A | A | G | ||||||||||||||||
| HL_98870.1_Sequence_2 HL_98870.1_HL_6DU5_001_U7_G21 | U | G | U | GG | U | A | C | A | G | A | G | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 12 cWW 2 9 s33 2 10 s33 2 11 tSH 2 12 s55 3 7 s35 3 8 tWW 3 9 s55 3 10 s55 4 5 perp 5 6 s35 7 8 s53 8 10 s55 10 11 s35 11 12 s35 6 5 7BPh 2 10 6BPh 11 2 6BR 8 9 2BRJAR3D SCFG/MRF model for HL_98870.1:
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 [12] // Initial node C7 - G23 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010391363,0.015542673,0.012620534,0.118031974,0.000000000],[0.161407275,0.018831736,0.135468706,0.014912387,0.000000000],[0.012838381,0.120099009,0.002697951,0.019069108,0.000000000],[0.143779637,0.013983083,0.188496931,0.011829251,0.000000000],[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 [12] // Basepair C7 - G23 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043697995,0.046260217,0.000524565,0.002472278,0.000000000],[0.044022640,0.046153098,0.000524565,0.000524565,0.000000000],[0.386803555,0.003671957,0.017951032,0.311661837,0.000000000],[0.048778633,0.045903932,0.000524565,0.000524565,0.000000000],[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 [2] | Right Index [11] // Basepair G8 - A22 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [10] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000000000029562] | Pair Probability [[0.031445336,0.006183253,0.001317180,0.015046827,0.000000000],[0.077797779,0.013377093,0.006529086,0.012631230,0.000000000],[0.006585900,0.005485414,0.006717406,0.006493376,0.000000000],[0.678197797,0.015213172,0.105512256,0.011466893,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.011890606,0.475624257,0.023781213,0.476218787,0.011890606,0.000594530] | Left Letter Distribution [0.187500000,0.187500000,0.562500000,0.062500000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair U9 - A19 tWW HairpinNode | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U14:G18 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U14 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]] // Hairpin conserved non-basepairing position A15 Interaction | Interacting Bases [3,3] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16 Interaction | Interacting Bases [4,4] | 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 G18 Insertion | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 3Sequences of instances from HL_98870.1:
> HL_98870.1 HL_6DU4_001 C 7 G 23 CGUAGGCUACAGAGAAG > HL_98870.1 HL_6DU5_001 U 7 G 21 UGUGGUACAGAGAAG