| 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 4 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 | 13 6 I | 14 6 6 | 15 5 I | 16 4 7 | 17 4 I | 18 4 8 | 19 3 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_97509.1_Instance_1 IL_97509.1_IL_4BPP_046_G863_C905 | G | U | A | U | U | A | G | G | A | C | ||||||||||||||||||
| IL_97509.1_Sequence_1 IL_97509.1_IL_4BPP_046_G863_C905 | G | U | A | U | U | * | A | G | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_97509.1_Instance_2 IL_97509.1_IL_3U5F_003_U37_A471 | U | C | A | A | A | U | G | A | C | A | A | |||||||||||||||||
| IL_97509.1_Sequence_2 IL_97509.1_IL_3U5F_003_U37_A471 | U | C | A | A | A | * | U | G | A | C | A | A | true | 88 | 0 | 0 | 1.65 |
1 2 s35 1 10 cWW 2 3 s35 2 9 cWW 2 10 s55 3 4 s35 3 7 wat 3 8 cWW 4 5 s35 4 7 tHS 4 8 s55 5 6 cWW 5 7 s55 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for IL_97509.1:
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 G863 - C905 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009655575,0.020452677,0.010811709,0.200386604,0.000000000],[0.020851131,0.008969837,0.201120779,0.011820265,0.000000000],[0.010745793,0.213649208,0.002151642,0.025610090,0.000000000],[0.213671659,0.012113485,0.025820790,0.012168755,0.000000000],[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 G863 - C905 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010610815,0.017566445,0.012200287,0.120859047,0.000000000],[0.206134582,0.013915363,0.114716350,0.013364208,0.000000000],[0.012383976,0.111101518,0.002917694,0.019539880,0.000000000],[0.138432870,0.012521397,0.179314102,0.014421465,0.000000000],[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 [2] | Right Index [9] // Basepair U864 - A904 cWW ClusterNode | Deletion Probability [0.0000000000396545] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [8] | Norm Constant [0.181109043621461] // Cluster node A865:U866 and G902:G903 Interaction | Interacting Bases [1,3] | Pair Probability [[0.007750136,0.007750136,0.883747966,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G902 wat Interaction | Interacting Bases [2,3] | Pair Probability [[0.101728279,0.102633356,0.132373524,0.110575038,0.000000000],[0.118577332,0.107574724,0.001225696,0.106524945,0.000000000],[0.001225696,0.001225696,0.005938240,0.001225696,0.000000000],[0.005836608,0.001225696,0.200883780,0.001225696,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U866 - G902 tHS Interaction | Interacting Bases [1,4] | Pair Probability [[0.177190689,0.109960849,0.281763742,0.012419737,0.000000000],[0.010771367,0.004154329,0.014747163,0.031379647,0.000000000],[0.261287932,0.014935165,0.002719598,0.012261563,0.000000000],[0.012398575,0.033379576,0.011990196,0.008639871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G903 cWW Insertion | Location [3] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 7, position 3 in cluster node 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009183469,0.022285751,0.009814417,0.220857782,0.000000000],[0.022291510,0.009418174,0.193045342,0.010327057,0.000000000],[0.009814439,0.193043865,0.002150936,0.025717104,0.000000000],[0.220868443,0.010326961,0.025722659,0.015132092,0.000000000],[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 [5] | Right Index [6] // Basepair U867 - A901 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_97509.1:
> IL_97509.1 IL_4BPP_046 G 863 C 905 GUAUU*AGGAC > IL_97509.1 IL_3U5F_003 U 37 A 471 UCAAA*UGACAA