| 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 5 4 | 9 6 I | 10 7 5 | 11 7 I | 12 8 | 13 7 I | 14 7 6 | 15 6 I | 16 5 7 | 17 5 I | 18 5 8 | 19 5 I | 20 5 9 | 21 4 I | 22 4 10 | 23 3 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_48918.3_Instance_1 IL_48918.3_IL_4B5R_002_G17_C38 | G | G | G | A | G | C | G | A | A | G | A | A | C | |||||||||||||||||||
| IL_48918.3_Sequence_1 IL_48918.3_IL_4B5R_002_G17_C38 | G | G | G | A | G | * | C | G | A | A | G | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_48918.3_Instance_2 IL_48918.3_IL_3UMY_004_G2155_C2136 | G | G | G | A | G | C | U | G | U | G | A | A | C | |||||||||||||||||||
| IL_48918.3_Sequence_2 IL_48918.3_IL_3UMY_004_G_2155_C_2136 | G | G | G | A | G | * | C | U | G | U | G | A | A | C | true | 96 | 0 | 0 | 0.64 | |||||||||||||
| IL_48918.3_Instance_3 IL_48918.3_IL_4BW0_001_G3_C23 | G | G | G | A | G | C | G | A | A | G | A | A | C | |||||||||||||||||||
| IL_48918.3_Sequence_3 IL_48918.3_IL_4BW0_001_G3_C23 | G | G | G | A | G | * | C | G | A | A | G | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_48918.3_Instance_4 IL_48918.3_IL_4IOA_052_U1426_A1605 | U | G | G | A | G | C | G | U | U | G | A | A | A | |||||||||||||||||||
| IL_48918.3_Sequence_4 IL_48918.3_IL_4IOA_052_U_1426_A_1605 | U | G | G | A | G | * | C | G | U | U | G | A | A | A | true | 96 | 0 | 0 | 0.65 |
1 2 s35 1 12 cWW 2 3 s35 2 10 s33 2 11 tSH 2 12 s55 3 9 s33 3 10 tSH 4 7 tSS 4 8 s33 4 9 tHS 4 10 s55 5 6 cWW 5 7 s55 5 10 perp 6 7 s35 8 9 s35 10 11 s35 11 12 s35 2 10 6BPh 11 2 6BR 3 9 6BR 4 9 6BR 5 10 2BRJAR3D SCFG/MRF model for IL_48918.3:
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 G17 - C38 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009734462,0.020214697,0.011090593,0.193143617,0.000000000],[0.018660673,0.008521127,0.200813940,0.012300663,0.000000000],[0.010985401,0.234217224,0.002109217,0.026079210,0.000000000],[0.203918224,0.012767771,0.024324928,0.011118254,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G17 - C38 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.059593935,0.069464361,0.000718031,0.003419172,0.000000000],[0.060124143,0.063018870,0.000718031,0.000718031,0.000000000],[0.342732568,0.003042710,0.014741292,0.253092402,0.000000000],[0.064776498,0.062403894,0.000718031,0.000718031,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G18 - A37 tSH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.067789995,0.079017918,0.000816783,0.003889416,0.000000000],[0.068393123,0.071685967,0.000816783,0.000816783,0.000000000],[0.314619289,0.002761578,0.013379263,0.229707799,0.000000000],[0.073685325,0.070986412,0.000816783,0.000816783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair G19 - A36 tSH ClusterNode | Deletion Probability [0.0000000000031049] | Num Left Bases [1] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.483768278986921] // Cluster node A20:A20 and G32:G35 Interaction | Interacting Bases [1,2] | Pair Probability [[0.199847682,0.220162527,0.263802060,0.230794523,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.004829830,0.005482656,0.008232375,0.059659296,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G32 tSS Interaction | Interacting Bases [1,4] | Pair Probability [[0.106208866,0.107153807,0.197447047,0.115445278,0.000000000],[0.123800031,0.112312816,0.001279681,0.111216801,0.000000000],[0.001279681,0.001279681,0.006199787,0.001279681,0.000000000],[0.006093680,0.001279681,0.106443797,0.001279681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G35 tHS Interaction | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A33 Insertion | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 8, position 3 in cluster node InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [[0.006165426,0.012560210,0.007138647,0.117002874,0.000000000],[0.010402818,0.005083832,0.126017962,0.008020992,0.000000000],[0.023812274,0.477595607,0.004391341,0.056326351,0.000000000],[0.116327236,0.008419708,0.014382630,0.006352092,0.000000000],[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 G21 - C31 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_48918.3:
> IL_48918.3 IL_4B5R_002 G 17 C 38 GGGAG*CGAAGAAC > IL_48918.3 IL_3UMY_004 G 2155 C 2136 GGGAG*CUGUGAAC > IL_48918.3 IL_4BW0_001 G 3 C 23 GGGAG*CGAAGAAC > IL_48918.3 IL_4IOA_052 U 1426 A 1605 UGGAG*CGUUGAAA