| 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 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 9 I | 16 9 8 | 17 10 I | 18 11 | 19 10 I | 20 9 9 | 21 9 I | 22 9 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_77014.1_Instance_1 IL_77014.1_IL_3P59_003_G51_C112 | G | G | A | A | C | U | A | C | G | C | C | |||||||||||||||||||
| IL_77014.1_Sequence_1 IL_77014.1_IL_3P59_003_G51_C112 | G | G | A | A | C | U | A | C | * | G | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 3 s35 2 11 s55 3 4 s35 5 7 cSH 5 9 tWH 6 7 s35 7 8 s35 7 10 cWW 8 9 cWW 9 10 s35 11 9 7BPh 6 5 7BRJAR3D SCFG/MRF model for IL_77014.1:
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 [11] // Initial node G51 - C112 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003991852,0.056925429,0.004621971,0.075754404,0.000000000],[0.006735384,0.023040960,0.081591292,0.005193253,0.000000000],[0.004563791,0.599043046,0.000841632,0.010795344,0.000000000],[0.075316957,0.038159832,0.009312144,0.004112711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair G51 - C112 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [5] | Right Index [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000015625000000000003000000000000000000000000000000] | Num Left Bases [4] | Num Right Bases [2] | Left Index [5] | Right Index [10] | Norm Constant [0.016946694239089] // Cluster node C55:C58 and G110:C111 Interaction | Interacting Bases [1,5] | Pair Probability [[0.017042123,0.002977202,0.037605848,0.002977202,0.000000000],[0.276030134,0.013421133,0.307621142,0.002977202,0.000000000],[0.002977202,0.002977202,0.014455549,0.023565365,0.000000000],[0.019762200,0.002977202,0.013381459,0.259251838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C55 - G110 tWH Interaction | Interacting Bases [4,5] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C58 - G110 cWW Interaction | Interacting Bases [3,6] | Pair Probability [[0.014465575,0.343792072,0.013542226,0.037981708,0.000000000],[0.013601003,0.011560757,0.026720538,0.013366648,0.000000000],[0.013224246,0.032261987,0.003338911,0.299980183,0.000000000],[0.031215838,0.014829276,0.013994275,0.116124756,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A57 - C111 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.121142655,0.120842989,0.006476604,0.005755261,0.000000000],[0.144971527,0.110518240,0.001350705,0.112517076,0.000000000],[0.006512780,0.006422996,0.011124298,0.109338445,0.000000000],[0.016481658,0.116826263,0.001350705,0.108367796,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C55 - A57 cSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U56 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 [9] | Right Index [8] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_77014.1:
> IL_77014.1 IL_3P59_003 G 51 C 112 GGAACUAC*GCC