| 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 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 | 17 8 I | 18 8 8 | 19 7 I | 20 7 9 | 21 6 I | 22 6 10 | 23 5 I | 24 4 11 | 25 4 I | 26 4 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_97833.1_Instance_1 IL_97833.1_IL_1LNG_003_G200_C221 | G | C | C | A | G | G | C | G | A | G | C | A | A | C | ||||||||||||||||||||||
| IL_97833.1_Sequence_1 IL_97833.1_IL_1LNG_003_G200_C221 | G | C | C | A | G | G | C | * | G | A | G | C | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_97833.1_Instance_2 IL_97833.1_IL_3KTW_004_G201_C222 | G | C | C | A | G | G | C | G | A | G | C | A | A | C | ||||||||||||||||||||||
| IL_97833.1_Sequence_2 IL_97833.1_IL_3KTW_004_G201_C222 | G | C | C | A | G | G | C | * | G | A | G | C | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 3 s35 2 13 cSW 3 10 s33 3 11 tWH 3 12 tSH 4 5 s35 4 11 tHW 4 12 s55 5 6 s35 5 10 tHS 6 7 s35 6 9 cWW 6 10 s55 7 8 cWW 8 9 s35 9 10 s35 10 11 s35 11 12 s35 12 13 s35 13 14 s35 10 4 6BPh 3 11 6BPh 12 3 6BRJAR3D SCFG/MRF model for IL_97833.1:
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 [14] // Initial node G200 - C221 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[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 [14] // Basepair G200 - C221 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.180898075,0.022979953,0.009978689,0.007794541,0.000000000],[0.223106457,0.018378246,0.010047856,0.008559157,0.000000000],[0.175423867,0.020184915,0.094841633,0.006698679,0.000000000],[0.184471354,0.020276628,0.009230277,0.007129673,0.000000000],[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 [13] // Basepair C201 - A220 cSW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.332826416872369] // Cluster node C202:A203 and C218:A219 Interaction | Interacting Bases [1,3] | Pair Probability [[0.004434773,0.001207200,0.004843947,0.001207200,0.000000000],[0.039987114,0.864647803,0.038094142,0.008450400,0.000000000],[0.001207200,0.001207200,0.005505466,0.005368552,0.000000000],[0.010022668,0.001207200,0.005026705,0.007582431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - C218 tWH Interaction | Interacting Bases [2,3] | Pair Probability [[0.019854918,0.271099652,0.002514918,0.024980606,0.000000000],[0.002514918,0.011900540,0.002514918,0.002514918,0.000000000],[0.140902150,0.233169698,0.017178551,0.012038356,0.000000000],[0.002514918,0.002514918,0.025973821,0.227812200,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A203 - C218 tHW Interaction | Interacting Bases [1,4] | Pair Probability [[0.056651997,0.047332496,0.000584264,0.003719453,0.000000000],[0.428592377,0.286158103,0.004089845,0.004089845,0.000000000],[0.048923171,0.000584264,0.004054179,0.006806626,0.000000000],[0.054562714,0.052682138,0.000584264,0.000584264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - A219 tSH 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 [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009247054,0.007386523,0.036100978,0.006101933,0.000000000],[0.005030892,0.004674688,0.007451505,0.005316705,0.000000000],[0.001064501,0.001064501,0.764758390,0.001064501,0.000000000],[0.099309926,0.001064501,0.049298902,0.001064501,0.000000000],[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 [10] // Basepair G204 - G217 tHS BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045558309,0.014099396,0.342018043,0.016229361,0.000000000],[0.014438420,0.005788124,0.019549681,0.043692861,0.000000000],[0.375595066,0.019303593,0.003559872,0.015694806,0.000000000],[0.016257062,0.041075014,0.016050017,0.011090375,0.000000000],[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 [6] | Right Index [9] // Basepair G205 - A216 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 C206 - G215 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_97833.1:
> IL_97833.1 IL_1LNG_003 G 200 C 221 GCCAGGC*GAGCAAC > IL_97833.1 IL_3KTW_004 G 201 C 222 GCCAGGC*GAGCAAC