| 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 5 5 | 11 5 I | 12 5 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_19398.1_Instance_1 HL_19398.1_HL_1QTQ_001_C912_G923 | C | A | A | G | CG | G | U | A | A | G | ||||||||||||||
| HL_19398.1_Sequence_1 HL_19398.1_HL_1QTQ_001_C912_G923 | C | A | A | G | CG | G | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_19398.1_Instance_2 HL_19398.1_HL_4JXZ_001_C912_G923 | C | A | A | G | CG | G | U | A | A | G | ||||||||||||||
| HL_19398.1_Sequence_2 HL_19398.1_HL_4JXZ_001_C912_G923 | C | A | A | G | CG | G | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 8 tSH 3 4 s35 3 7 cWS 3 8 s55 5 6 cSH 8 9 s35 8 2 6BRJAR3D SCFG/MRF model for HL_19398.1:
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 [9] // Initial node C912 - G923 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 [9] // Basepair C912 - G923 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.196519904,0.020646249,0.001769121,0.010788001,0.000000000],[0.171539375,0.070268271,0.001769121,0.001769121,0.000000000],[0.147373499,0.001769121,0.015367912,0.038612201,0.000000000],[0.159302830,0.158967034,0.001769121,0.001769121,0.000000000],[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 [8] // Basepair A913 - A922 tSH BasepairNode | Deletion Probability [0.0000229437914523] | 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair A914 - A921 cWS HairpinNode | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G915:U920 Interaction | Interacting Bases [2,3] | Pair Probability [[0.072088071,0.073454437,0.004038753,0.071786009,0.000000000],[0.053818455,0.081105356,0.000894248,0.071936499,0.000000000],[0.062983498,0.000894248,0.076829131,0.198159239,0.000000000],[0.073206585,0.072767115,0.000894248,0.085144108,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G919 - U920 cSH 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],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[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 G915 Insertion | Location [1] | Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.083333333,0.416666667,0.416666667,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 4, position 1Sequences of instances from HL_19398.1:
> HL_19398.1 HL_1QTQ_001 C 912 G 923 CAAGCGGUAAG > HL_19398.1 HL_4JXZ_001 C 912 G 923 CAAGCGGUAAG