| 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 5 I | 14 5 7 | 15 4 I | 16 4 8 | 17 3 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_49992.1_Instance_1 HL_49992.1_HL_5J7L_029_G1356_C1366 | G | A | U | C | A | G | A | A | U | G | C | |||||||||||||||
| HL_49992.1_Sequence_1 HL_49992.1_HL_5J7L_029_G_1356_C_1366 | G | A | U | C | A | G | A | A | U | G | C | true | 94 | 0 | 0 | 0.92 | ||||||||||
| HL_49992.1_Instance_2 HL_49992.1_HL_6DME_003_G78_C88 | G | G | A | U | A | A | A | A | G | A | C | |||||||||||||||
| HL_49992.1_Sequence_2 HL_49992.1_HL_6DME_003_G78_C88 | G | G | A | U | A | A | A | A | G | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 3 s35 2 9 cWW 3 4 s35 3 8 tWH 4 6 s33 4 7 tWH 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_49992.1:
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 [10] // Initial node G1356 - C1366 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [10] // Basepair G1356 - C1366 cWW BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.026360983,0.014468857,0.363686975,0.017517064,0.000000000],[0.014470066,0.009929271,0.019045359,0.043765025,0.000000000],[0.363736790,0.019044611,0.003609907,0.015759427,0.000000000],[0.017517184,0.043756557,0.015760627,0.011571297,0.000000000],[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 [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair A1357 - G1365 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.199980210,0.003885421,0.169238699,0.003885421,0.000000000],[0.036366779,0.175081720,0.003885421,0.003885421,0.000000000],[0.003885421,0.009458368,0.082252671,0.028591197,0.000000000],[0.225726841,0.003885421,0.020718805,0.029272186,0.000000000],[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 [8] // Basepair U1358 - A1363 tWH BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.017068734,0.003777338,0.017728674,0.003777338,0.000000000],[0.136916593,0.304381264,0.003777338,0.003777338,0.000000000],[0.003777338,0.009054529,0.028726337,0.016800299,0.000000000],[0.387537728,0.003777338,0.021915662,0.037206152,0.000000000],[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 [7] // Basepair C1359 - A1362 tWH HairpinNode | Num Bases [2] | Left Index [5] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A1360:G1361 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 A1360 Interaction | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1361Sequences of instances from HL_49992.1:
> HL_49992.1 HL_5J7L_029 G 1356 C 1366 GAUCAGAAUGC > HL_49992.1 HL_6DME_003 G 78 C 88 GGAUAAAAGAC