| 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 5 I | 8 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 5 I | 16 5 8 | 17 5 I | 18 5 9 | 19 6 I | 20 7 10 | 21 7 I | 22 8 | 23 7 I | 24 7 11 | 25 6 I | 26 5 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_98655.1_Instance_1 IL_98655.1_IL_3U5H_095_C2277_G2307 | C | C | A | A | A | U | G | C | C | U | C | G | C | G | C | G | ||||||||||||||||||
| IL_98655.1_Sequence_1 IL_98655.1_IL_3U5H_095_C_2277_G_2307 | C | C | A | A | A | U | G | C | C | U | C | G | * | C | G | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 12 s35 2 13 s55 3 6 s33 3 9 cHW 3 10 s55 4 5 s33 6 8 tSW 6 12 tHH 7 8 s35 8 9 s33 10 11 cWW 11 12 s33 11 3 7BPh 8 7 7BPh 12 11 6BPh 12 12 2BPh 7 6 7BR 8 6 7BR 2 12 6BRJAR3D SCFG/MRF model for IL_98655.1:
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 [13] // Initial node C2277 - G2307 from junction BasepairNode | Deletion Probability [0.0000001156129129] | 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]] | 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 [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [13] // Basepair C2277 - G2307 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // 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 [12] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000001906753397244242900000000000000000000000] | Num Left Bases [7] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.604403241390279] // Cluster node A2279:U2286 and G2305:G2305 Interaction | Interacting Bases [4,8] | Pair Probability [[0.000468052,0.000643520,0.009361507,0.000191051,0.000000000],[0.000541351,0.000191051,0.030994316,0.000191051,0.000000000],[0.000449454,0.000345270,0.946051705,0.000191051,0.000000000],[0.000370728,0.000457334,0.009361507,0.000191051,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2283 - G2305 tHH Interaction | Interacting Bases [4,6] | Pair Probability [[0.068988777,0.069312616,0.000849134,0.027382914,0.000000000],[0.019877084,0.062687093,0.009085441,0.006136942,0.000000000],[0.023140858,0.604295026,0.000849134,0.003610598,0.000000000],[0.008041524,0.035927461,0.056258894,0.003556505,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2283 - C2285 tSW Interaction | Interacting Bases [1,7] | Pair Probability [[0.003495037,0.003495037,0.015332069,0.359404723,0.000000000],[0.003495037,0.037384026,0.003495037,0.003495037,0.000000000],[0.017334262,0.017149526,0.013986624,0.280049403,0.000000000],[0.012470772,0.190754110,0.003495037,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2279 - U2286 cHW Interaction | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A2280 Interaction | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U2282 Interaction | Interacting Bases [5,5] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.785714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C2284 Insertion | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node InitialNode | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [11] // Basepair G2288 - C2304 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_98655.1:
> IL_98655.1 IL_3U5H_095 C 2277 G 2307 CCAAAUGCCUCG*CGCG