| 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 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_12566.4_Instance_1 IL_12566.4,IL_5J7L_304,G1651_C2006 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_12566.4_Sequence_1 IL_12566.45J7L_G_1651_C_2006 | G | A | G | A | A | C | * | G | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_12566.4_Instance_2 IL_12566.4,IL_7A0S_059,G1668_C1989 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_12566.4_Sequence_2 IL_12566.47A0S_G_1668_C_1989 | G | A | G | A | A | C | * | G | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_12566.4_Instance_3 IL_12566.4,IL_9DFE_063,G1651_C2006 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_12566.4_Sequence_3 IL_12566.49DFE_G_1651_C_2006 | G | A | G | A | A | C | * | G | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_12566.4_Instance_4 IL_12566.4,IL_4WF9_062,G1695_C2033 | G | C | G | A | A | C | G | A | C | |||||||||||||||||
| IL_12566.4_Sequence_4 IL_12566.44WF9_G_1695_C_2033 | G | C | G | A | A | C | * | G | A | C | true | 92 | 0 | 0 | 1.10 | |||||||||||
| IL_12566.4_Instance_5 IL_12566.4,IL_4V9F_059,G1728_C2047 | G | A | G | C | A | A | C | G | G | C | ||||||||||||||||
| IL_12566.4_Sequence_5 IL_12566.44V9F_G_1728_C_2047 | G | A | G | C | A | A | C | * | G | G | C | true | 76 | 0 | 0 | 3.41 |
1 2 s35 1 9 cWW 2 3 s35 4 5 s35 5 6 s35 5 8 tHS 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 6 5 7BPh 9 8 7BPh 5 8 6BR 4 9 7BRJAR3D SCFG/MRF model for IL_12566.4:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G1651 - C2006 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5J7L|1|DA|A|1652 InitialNode | Left Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | 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 [0.071428571,0.214285714,0.642857143,0.071428571,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 5J7L|1|DA|G|1653 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 5J7L|1|DA|A|1654 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.0000244705618206] | Pair Probability [[0.197486077,0.155378232,0.150349437,0.148252769,0.000000000],[0.039234368,0.077744071,0.001637813,0.146550779,0.000000000],[0.001637813,0.001637813,0.013228560,0.001637813,0.000000000],[0.009623119,0.001637813,0.052325709,0.001637813,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1655 - A2005 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003637459,0.006522837,0.004181706,0.075822585,0.000000000],[0.054137016,0.025932524,0.605573545,0.036820353,0.000000000],[0.004228668,0.077456358,0.000797078,0.008950521,0.000000000],[0.076805549,0.005067957,0.010211137,0.003854705,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair C1656 - G2004 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_12566.4:
> IL_12566.4 5J7L G 1651 C 2006 GAGAAC*GAC > IL_12566.4 7A0S G 1668 C 1989 GAGAAC*GAC > IL_12566.4 9DFE G 1651 C 2006 GAGAAC*GAC > IL_12566.4 4WF9 G 1695 C 2033 GCGAAC*GAC > IL_12566.4 4V9F G 1728 C 2047 GAGCAAC*GGC