| 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 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_16845.5_Instance_1 HL_16845.5_HL_4WF9_048_C2236_G2242 | C | U | U | A | U | C | G | |||||||||
| HL_16845.5_Sequence_1 HL_16845.5_HL_4WF9_048_C_2236_G_2242 | C | U | U | A | U | C | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_16845.5_Instance_2 HL_16845.5_HL_5J7L_185_G2209_C2215 | G | U | A | A | U | C | C | |||||||||
| HL_16845.5_Sequence_2 HL_16845.5_HL_5J7L_185_G_2209_C_2215 | G | U | A | A | U | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s33 1 5 cWW 2 3 s53 2 4 tHH 3 4 s35 4 5 s35JAR3D SCFG/MRF model for HL_16845.5:
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 [5] // Initial node C2236 - G2242 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [5] // Basepair C2236 - G2242 cWW BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.130459369,0.015302404,0.012037839,0.011672714,0.000000000],[0.224490191,0.002645205,0.024226344,0.012342007,0.000000000],[0.028299430,0.020741958,0.007941767,0.002645205,0.000000000],[0.217776765,0.284128392,0.002645205,0.002645205,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair U2237 - C2241 tHH HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A2239:A2239 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 A2239Sequences of instances from HL_16845.5:
> HL_16845.5 HL_4WF9_048 C 2236 G 2242 CUUAUCG > HL_16845.5 HL_5J7L_185 G 2209 C 2215 GUAAUCC