| 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 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 6 I | 16 6 8 | 17 6 I | 18 6 9 | 19 5 I | 20 5 10 | 21 4 I | 22 4 11 | 23 3 I | 24 3 12 | 25 2 I | 26 2 13 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_12571.1_Instance_1 HL_12571.1_HL_1WZ2_005_C912_G926 | C | G | A | G | C | C | U | G | G | U | C | A | A | A | G | |||||||||||||||||
| HL_12571.1_Sequence_1 HL_12571.1_HL_1WZ2_005_C912_G926 | C | G | A | G | C | C | U | G | G | U | C | A | A | A | G | true | 100 | 0 | 0 | 0.02 | ||||||||||||
| HL_12571.1_Instance_2 HL_12571.1_HL_2ZZM_001_C12_G23 | C | A | A | G | C | C | U | G | G | C | C | A | A | A | G | |||||||||||||||||
| HL_12571.1_Sequence_2 HL_12571.1_HL_2ZZM_001_C12_G23 | C | A | A | G | C | C | U | G | G | C | C | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 3 s35 2 12 tSH 2 13 s55 3 4 s35 3 11 cWS 3 12 s55 4 5 s35 4 10 tSW 6 7 s33 8 9 perp 12 13 s35 6 5 7BPh 12 2 6BRJAR3D SCFG/MRF model for HL_12571.1:
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 [13] // Initial node C912 - G926 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [13] // Basepair C912 - G926 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.154632842,0.070001426,0.001561279,0.008583379,0.000000000],[0.142561388,0.094674247,0.001561279,0.001561279,0.000000000],[0.151162568,0.001561279,0.010992220,0.076743448,0.000000000],[0.142578616,0.138702190,0.001561279,0.001561279,0.000000000],[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 [12] // Basepair G913 - A925 tSH BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.239509115,0.202271002,0.213757220,0.206617428,0.000000000],[0.016161407,0.013181506,0.002199013,0.013377455,0.000000000],[0.021852929,0.002199013,0.028008345,0.010460203,0.000000000],[0.007850573,0.008281367,0.006553550,0.007719875,0.000000000],[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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [3] | Right Index [11] // Basepair A914 - A924 cWS BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.135802279,0.007408683,0.000000000],[0.007408683,0.760476157,0.007408683,0.007408683,0.000000000],[0.007408683,0.007408683,0.007408683,0.007408683,0.000000000],[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 [4] | Right Index [10] // Basepair G915 - C922 tSW HairpinNode | Num Bases [5] | Left Index [5] | Right Index [9] | Norm Constant [1.000000000000000] // Hairpin node C916:U921 Interaction | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C916 Interaction | Interacting Bases [2,2] | 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 C917 Interaction | Interacting Bases [3,3] | 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 U918 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 G920 Interaction | Interacting Bases [5,5] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U921 Insertion | Location [3] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 7, position 3Sequences of instances from HL_12571.1:
> HL_12571.1 HL_1WZ2_005 C 912 G 926 CGAGCCUGGUCAAAG > HL_12571.1 HL_2ZZM_001 C 12 G 23 CAAGCCUGGCCAAAG