| 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 4 I | 6 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 9 5 | 11 8 I | 12 8 6 | 13 7 I | 14 7 7 | 15 6 I | 16 5 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_06048.1_Instance_1 HL_06048.1_HL_5W1H_001_C-19_G-10 | C | A | A | G | A | A | A | G | A | G | ||||||||||||||
| HL_06048.1_Sequence_1 HL_06048.1_HL_5W1H_001_C-19_G-10 | C | A | A | G | A | A | A | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_06048.1_Instance_2 HL_06048.1_HL_5WLH_001_C-19_G-10 | C | A | A | G | A | A | A | G | A | G | ||||||||||||||
| HL_06048.1_Sequence_2 HL_06048.1_HL_5WLH_001_C-19_G-10 | C | A | A | G | A | A | A | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s35 3 7 cSS 4 6 cSS 5 6 s55 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_06048.1:
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 C-19 - G-10 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 C-19 - G-10 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left InitialNode | 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 [1.000000000] | 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 FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.082257101,0.085474491,0.108530030,0.083901141,0.000000000],[0.077064975,0.084007429,0.003447499,0.077365799,0.000000000],[0.078895708,0.003373101,0.007643728,0.077979839,0.000000000],[0.072852721,0.011490248,0.061320564,0.084395624,0.000000000],[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 A-17 - G-12 cSS BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.082257101,0.077064975,0.078895708,0.072852721,0.000000000],[0.085474491,0.084007429,0.003373101,0.011490248,0.000000000],[0.108530030,0.003447499,0.007643728,0.061320564,0.000000000],[0.083901141,0.077365799,0.077979839,0.084395624,0.000000000],[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 [4] | Right Index [6] // Basepair G-16 - A-13 cSS HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A-15:A-15 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 A-15Sequences of instances from HL_06048.1:
> HL_06048.1 HL_5W1H_001 C -19 G -10 CAAGAAAGAG > HL_06048.1 HL_5WLH_001 C -19 G -10 CAAGAAAGAG