| 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 11 4 | 9 11 I | 10 12 5 | 11 12 I | 12 12 6 | 13 12 I | 14 12 7 | 15 11 I | 16 11 8 | 17 10 I | 18 9 9 | 19 8 I | 20 7 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_07432.1_Instance_1 HL_07432.1_HL_4GCW_001_C11_G24 | C | U | C | A | G | CAG | G | U | A | G | A | G | ||||||||||||||||
| HL_07432.1_Sequence_1 HL_07432.1_HL_4GCW_001_C11_G24 | C | U | C | A | G | CAG | G | U | A | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_07432.1_Instance_2 HL_07432.1_HL_4GCW_003_C11_G24 | C | U | C | A | G | CAG | G | U | A | G | A | G | ||||||||||||||||
| HL_07432.1_Sequence_2 HL_07432.1_HL_4GCW_003_C11_G24 | C | U | C | A | G | CAG | G | U | A | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 11 cWW 2 3 s35 4 5 s35 4 8 cWS 4 9 s55 6 7 cSH 9 10 s35 10 11 s35JAR3D SCFG/MRF model for HL_07432.1:
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 [11] // Initial node C11 - G24 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 [11] // Basepair C11 - G24 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // 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 [10] // 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 [10] // 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 [10] // 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 [4] | Right Index [10] // 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 [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // 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 [4] | Right Index [8] // New Initial node after Fixed node 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 [4] | Right Index [8] // Basepair A14 - A21 cWS HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G15:U20 Interaction | Interacting Bases [2,3] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G19 - U20 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 G15 Insertion | Location [1] | Length Distribution [0.000000000,0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.312500000,0.312500000,0.312500000,0.062500000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 1Sequences of instances from HL_07432.1:
> HL_07432.1 HL_4GCW_001 C 11 G 24 CUCAGCAGGUAGAG > HL_07432.1 HL_4GCW_003 C 11 G 24 CUCAGCAGGUAGAG