| 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 7 4 | 9 7 I | 10 7 5 | 11 7 I | 12 7 6 | 13 7 I | 14 7 7 | 15 7 I | 16 7 8 | 17 7 I | 18 7 9 | 19 8 I | 20 9 | 21 8 I | 22 7 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_94403.5_Instance_1 IL_94403.5_IL_3V2F_082_G2110_C2179 | G | C | G | U | A | G | G | A | U | A | G | C | C | |||||||||||||||||
| IL_94403.5_Sequence_1 IL_94403.5_IL_3V2F_082_G_2110_C_2179 | G | C | G | U | A | G | G | A | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_94403.5_Instance_2 IL_94403.5_IL_1MZP_002_G6_C50 | G | C | G | U | A | G | G | A | U | A | G | C | C | |||||||||||||||||
| IL_94403.5_Sequence_2 IL_94403.5_IL_1MZP_002_G6_C50 | G | C | G | U | A | G | G | A | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_94403.5_Instance_3 IL_94403.5_IL_3UMY_002_G2110_C2179 | G | C | G | U | A | G | G | A | U | A | G | C | C | |||||||||||||||||
| IL_94403.5_Sequence_3 IL_94403.5_IL_3UMY_002_G_2110_C_2179 | G | C | G | U | A | G | G | A | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_94403.5_Instance_4 IL_94403.5_IL_4JRC_004_C37_G69 | C | C | G | A | A | G | C | G | A | G | U | G | ||||||||||||||||||
| IL_94403.5_Sequence_4 IL_94403.5_IL_4JRC_004_C37_G69 | C | C | G | A | A | G | C | G | A | G | * | U | G | true | 80 | 0 | 0 | 3.90 |
1 9 s35 1 11 cWW 2 3 s35 3 4 s35 4 5 s35 4 8 tWH 5 7 s33 6 7 s35 9 10 cWW 9 11 s55 10 11 s35 5 8 6BPhJAR3D SCFG/MRF model for IL_94403.5:
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 [11] // Initial node G2110 - C2179 from junction BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009958751,0.019496181,0.011541539,0.189489827,0.000000000],[0.017746938,0.008284356,0.215611394,0.013170723,0.000000000],[0.011468679,0.238062912,0.002108276,0.026113208,0.000000000],[0.188942010,0.013494008,0.024255791,0.010255407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | 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 [11] // Basepair G2110 - C2179 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left 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 [1.000000000] | 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 [0.000000000000000001418723246459155300000000000000000000000000] | Num Left Bases [6] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node A2114:G2120 and C2178:C2178 Interaction | Interacting Bases [6,7] | Pair Probability [[0.011545053,0.091357941,0.012500960,0.153268922,0.000000000],[0.016202600,0.009015557,0.162650528,0.013540081,0.000000000],[0.012307163,0.197820616,0.002427935,0.114576839,0.000000000],[0.150792068,0.014433261,0.021211816,0.016348660,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2120 - C2178 cWW Interaction | Interacting Bases [1,5] | Pair Probability [[0.429334136,0.003908726,0.335179201,0.003908726,0.000000000],[0.030858831,0.014359107,0.022374364,0.003908726,0.000000000],[0.003908726,0.003908726,0.048417298,0.034876366,0.000000000],[0.018637522,0.003908726,0.023139890,0.019370929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2114 - A2119 tWH Interaction | Interacting Bases [2,2] | Pair Probability [[0.016666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.016666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.950000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.016666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2115 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G2116 Interaction | Interacting Bases [4,4] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2117 Insertion | Location [4] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 7, position 4 in cluster node 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 [10] | Right Index [9] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_94403.5:
> IL_94403.5 IL_3V2F_082 G 2110 C 2179 GCGUAGGAUAG*CC > IL_94403.5 IL_1MZP_002 G 6 C 50 GCGUAGGAUAG*CC > IL_94403.5 IL_3UMY_002 G 2110 C 2179 GCGUAGGAUAG*CC > IL_94403.5 IL_4JRC_004 C 37 G 69 CCGAAGCGAG*UG