| 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 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 10 7 | 15 9 I | 16 9 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_76406.3_Instance_1 HL_76406.3_HL_4V9F_057_G2338_C2346 | G | A | C | A | G | A | G | A | C | |||||||||||||||
| HL_76406.3_Sequence_1 HL_76406.3_HL_4V9F_057_G_2338_C_2346 | G | A | C | A | G | A | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_76406.3_Instance_2 HL_76406.3_HL_5TBW_056_A2673_U2681 | A | A | C | A | G | A | A | A | U | |||||||||||||||
| HL_76406.3_Sequence_2 HL_76406.3_HL_5TBW_056_A_2673_U_2681 | A | A | C | A | G | A | A | A | U | true | 100 | 0 | 0 | 0.06 |
1 9 cWW 2 3 s35 3 4 s33 4 5 s53 4 8 s53 5 7 s55 5 8 cWH 6 7 s35 9 8 7BPhJAR3D SCFG/MRF model for HL_76406.3:
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 G2338 - C2346 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003625340,0.031935851,0.004007138,0.313070369,0.000000000],[0.006591797,0.014892244,0.075717760,0.015993196,0.000000000],[0.003979397,0.333377958,0.000787133,0.074010905,0.000000000],[0.075219462,0.020993034,0.008855864,0.016942552,0.000000000],[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 G2338 - C2346 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 [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | 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 [4] | 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 [1] | Left Index [4] | 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.002839261,0.002839261,0.245743704,0.235280129,0.000000000],[0.002839261,0.019473421,0.002839261,0.010750004,0.000000000],[0.303533980,0.002839261,0.118056128,0.002839261,0.000000000],[0.010460384,0.002839261,0.009699227,0.027128194,0.000000000],[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 [5] | Right Index [8] // Basepair G2342 - A2345 cWH HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2343:G2344 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 A2343 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 G2344Sequences of instances from HL_76406.3:
> HL_76406.3 HL_4V9F_057 G 2338 C 2346 GACAGAGAC > HL_76406.3 HL_5TBW_056 A 2673 U 2681 AACAGAAAU