| 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 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 5 5 | 11 5 I | 12 6 6 | 13 6 I | 14 7 7 | 15 7 I | 16 8 | 17 7 I | 18 7 8 | 19 6 I | 20 6 9 | 21 5 I | 22 5 10 | 23 4 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_34628.2_Instance_1 IL_34628.2_IL_3Q3Z_004_C16_G58 | C | A | A | U | G | A | U | G | U | U | G | A | G | |||||||||||||||||||
| IL_34628.2_Sequence_1 IL_34628.2_IL_3Q3Z_004_C16_G58 | C | A | A | U | G | A | U | G | * | U | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_34628.2_Instance_2 IL_34628.2_IL_3Q3Z_002_C16_G58 | C | A | A | U | G | A | U | G | U | U | G | A | G | |||||||||||||||||||
| IL_34628.2_Sequence_2 IL_34628.2_IL_3Q3Z_002_C16_G58 | C | A | A | U | G | A | U | G | * | U | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_34628.2_Instance_3 IL_34628.2_IL_3NVI_001_G15_C8 | G | C | G | U | G | A | U | G | C | U | G | A | C | |||||||||||||||||||
| IL_34628.2_Sequence_3 IL_34628.2_IL_3NVI_001_G15_C8 | G | C | G | U | G | A | U | G | * | C | U | G | A | C | true | 77 | 0 | 0 | 4.56 |
1 2 s35 1 12 cWW 2 11 tSS 2 12 s55 3 4 s35 3 11 s33 4 10 s33 4 11 tSH 5 6 s35 5 10 tHS 5 11 s55 5 12 perp 6 7 s35 6 9 cWW 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 6 5 7BPh 10 4 6BR 11 4 6BR 12 5 2BR 4 10 6BR 5 10 6BR 3 11 6BRJAR3D SCFG/MRF model for IL_34628.2:
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 [12] // Initial node C16 - G58 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006602025,0.012407655,0.022705391,0.125946391,0.000000000],[0.012381398,0.005539457,0.435066187,0.008871608,0.000000000],[0.007657263,0.147915900,0.004178169,0.016776766,0.000000000],[0.125938168,0.008876460,0.052341644,0.006795516,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C16 - G58 cWW ClusterNode | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.399377512311362] // Cluster node A17:G20 and A57:A57 Interaction | Interacting Bases [1,4] | Pair Probability [[0.470625919,0.082176614,0.075801341,0.076535297,0.000000000],[0.064281502,0.010914553,0.010914553,0.010914553,0.000000000],[0.067198556,0.013560294,0.013785616,0.015974780,0.000000000],[0.054572764,0.010914553,0.010914553,0.010914553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A17 - A57 tSS Interaction | Interacting Bases [3,4] | Pair Probability [[0.054325971,0.063323874,0.000654559,0.003116925,0.000000000],[0.054809310,0.057448150,0.000654559,0.000654559,0.000000000],[0.356405549,0.003272793,0.015855996,0.272230694,0.000000000],[0.059050408,0.056887536,0.000654559,0.000654559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G20 - A57 tSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.617647059,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.323529412,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A18 Insertion | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.054325971,0.054809310,0.356405549,0.059050408,0.000000000],[0.063323874,0.057448150,0.003272793,0.056887536,0.000000000],[0.000654559,0.000654559,0.015855996,0.000654559,0.000000000],[0.003116925,0.000654559,0.272230694,0.000654559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A21 - G56 tHS BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003621880,0.038167502,0.003486392,0.008394012,0.000000000],[0.004473969,0.004553906,0.005265058,0.003843820,0.000000000],[0.003418893,0.005362656,0.001097422,0.011174125,0.000000000],[0.049341309,0.029206938,0.031270362,0.797321755,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair U22 - U55 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.014258858,0.211706755,0.014176550,0.093357766,0.000000000],[0.015234759,0.010399964,0.094014042,0.014566320,0.000000000],[0.013899989,0.109909176,0.002989625,0.256526531,0.000000000],[0.088532666,0.015883070,0.017860543,0.026683387,0.000000000],[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 G23 - U54 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_34628.2:
> IL_34628.2 IL_3Q3Z_004 C 16 G 58 CAAUGAUG*UUGAG > IL_34628.2 IL_3Q3Z_002 C 16 G 58 CAAUGAUG*UUGAG > IL_34628.2 IL_3NVI_001 G 15 C 8 GCGUGAUG*CUGAC