| 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 11 5 | 11 12 I | 12 13 6 | 13 13 I | 14 14 7 | 15 14 I | 16 15 | 17 14 I | 18 14 8 | 19 13 I | 20 13 9 | 21 12 I | 22 11 10 | 23 10 I | 24 9 11 | 25 8 I | 26 7 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_16458.4_Instance_1 IL_16458.4,IL_7A0S_094,C2631_G2647 | C | U | A | G | U | A | C | G | G | A | C | C | G | |||||||||||||||||||||
| IL_16458.4_Sequence_1 IL_16458.47A0S_C_2631_G_2647 | C | U | A | G | U | A | C | * | G | G | A | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_16458.4_Instance_2 IL_16458.4,IL_5J7L_346,C2652_G2668 | C | U | A | G | U | A | C | G | G | A | C | C | G | |||||||||||||||||||||
| IL_16458.4_Sequence_2 IL_16458.45J7L_C_2652_G_2668 | C | U | A | G | U | A | C | * | G | G | A | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_16458.4_Instance_3 IL_16458.4,IL_9DFE_102,C2652_G2668 | C | U | A | G | U | A | C | G | G | A | C | C | G | |||||||||||||||||||||
| IL_16458.4_Sequence_3 IL_16458.49DFE_C_2652_G_2668 | C | U | A | G | U | A | C | * | G | G | A | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_16458.4_Instance_4 IL_16458.4,IL_4WF9_100,U2679_G2695 | U | U | A | G | U | A | C | G | G | A | C | C | G | |||||||||||||||||||||
| IL_16458.4_Sequence_4 IL_16458.44WF9_U_2679_G_2695 | U | U | A | G | U | A | C | * | G | G | A | C | C | G | true | 96 | 0 | 0 | 0.79 | |||||||||||||||
| IL_16458.4_Instance_5 IL_16458.4,IL_4V9F_019,C585_G572 | C | C | A | G | U | A | A | U | G | A | C | C | G | |||||||||||||||||||||
| IL_16458.4_Sequence_5 IL_16458.44V9F_C585_G572 | C | C | A | G | U | A | A | * | U | G | A | C | C | G | true | 88 | 0 | 0 | 2.66 |
1 2 s35 1 13 cWW 2 3 s33 2 13 s55 3 5 s55 3 10 s53 4 5 cSH 4 9 s33 5 6 s35 5 9 s33 5 10 tWH 6 7 s35 6 9 tHS 6 10 s55 7 8 cWW 7 9 s55 8 9 s35 10 11 s35 11 12 s35 12 13 s35 9 5 6BPh 7 6 7BPh 4 10 6BPh 3 11 6BPh 12 11 7BPh 6 9 6BRJAR3D SCFG/MRF model for IL_16458.4:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009596250,0.016007098,0.011294117,0.161729647,0.000000000],[0.074536499,0.012978608,0.208727819,0.013832501,0.000000000],[0.011450528,0.165029434,0.002266375,0.021087156,0.000000000],[0.173236538,0.013177859,0.094562621,0.010486950,0.000000000],[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 [13] // Basepair C2631 - G2647 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 7A0S|1|X|U|2632 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 [3] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 7A0S|1|X|A|2633 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.013513514,0.959459459,0.013513514,0.013513514,0.000000000] | Position [2] | Left Index [4] | Right Index [12] // Fixed node on right for 7A0S|1|X|C|2646 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right for 7A0S|1|X|C|2645 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.279407267137871] // Cluster node 7A0S|1|X|G|2634:7A0S|1|X|U|2635 and 7A0S|1|X|A|2644:7A0S|1|X|A|2644 Interaction | Interacting Bases [2,3] | Pair Probability [[0.018239161,0.004036356,0.018944354,0.004036356,0.000000000],[0.040590873,0.325253122,0.004036356,0.004036356,0.000000000],[0.004036356,0.009675411,0.030696143,0.017952320,0.000000000],[0.451254601,0.004036356,0.023418451,0.039757431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|2635 - 7A0S|1|X|A|2644 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.029480255,0.030039027,0.001651639,0.029356727,0.000000000],[0.022008936,0.033167853,0.000365701,0.029418270,0.000000000],[0.180298720,0.002559906,0.219933704,0.326838453,0.000000000],[0.029937668,0.029757948,0.000365701,0.034819492,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|2634 - 7A0S|1|X|U|2635 cSH 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042449481,0.042764850,0.404323454,0.047384957,0.000000000],[0.044938497,0.044834438,0.003567044,0.044592391,0.000000000],[0.000509578,0.000509578,0.017438145,0.000509578,0.000000000],[0.002401641,0.000509578,0.302757213,0.000509578,0.000000000],[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 [6] | Right Index [9] // Basepair A2636 - G2643 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004713507,0.009494604,0.005271585,0.109838539,0.000000000],[0.046713143,0.022607327,0.522182511,0.031468857,0.000000000],[0.005305405,0.100177811,0.001034229,0.017499094,0.000000000],[0.099529028,0.006196980,0.012639932,0.005327448,0.000000000],[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 [7] | Right Index [8] // Basepair C2637 - G2642 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_16458.4:
> IL_16458.4 7A0S C 2631 G 2647 CUAGUAC*GGACCG > IL_16458.4 5J7L C 2652 G 2668 CUAGUAC*GGACCG > IL_16458.4 9DFE C 2652 G 2668 CUAGUAC*GGACCG > IL_16458.4 4WF9 U 2679 G 2695 UUAGUAC*GGACCG > IL_16458.4 4V9F C 585 G 572 CCAGUAA*UGACCG