| 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 5 I | 10 5 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 | 17 8 I | 18 8 8 | 19 7 I | 20 7 9 | 21 6 I | 22 5 10 | 23 4 I | 24 4 11 | 25 3 I | 26 3 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_31754.1_Instance_1 IL_31754.1_IL_2QBG_101_C2652_G2668 | C | U | A | G | U | A | C | G | G | A | C | C | G | |||||||||||||||||||||
| IL_31754.1_Sequence_1 IL_31754.1_IL_2QBG_101_C_2652_G_2668 | C | U | A | G | U | A | C | * | G | G | A | C | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 3 s33 2 12 cSW 3 5 s55 3 10 s53 3 11 tHW 4 5 cSH 4 9 s33 5 6 s35 5 9 s33 5 10 tWH 6 7 s35 6 9 tHS 6 10 s55 7 8 cWW 7 9 s55 8 9 s35 10 11 s33 11 12 s55 12 13 s35 9 5 6BPh 7 6 7BPh 4 10 6BPh 3 11 6BPh 12 11 7BPh 5 4 7BR 9 4 6BR 6 9 6BRJAR3D SCFG/MRF model for IL_31754.1:
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 C2652 - G2668 from junction BasepairNode | Deletion Probability [0.0000224390099112] | 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C2652 - G2668 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.001791371,0.239209592,0.002204493,0.002376080,0.000000000],[0.003571518,0.240441448,0.001689592,0.002453572,0.000000000],[0.001915832,0.233023057,0.002967661,0.001700970,0.000000000],[0.002623970,0.260810191,0.001476768,0.001743884,0.000000000],[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 [2] | Right Index [12] // Basepair U2653 - C2667 cSW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.049616382,0.638365634,0.006284646,0.062425204,0.000000000],[0.000897807,0.004248402,0.000897807,0.000897807,0.000000000],[0.050300996,0.083239809,0.006132612,0.004297602,0.000000000],[0.000897807,0.000897807,0.009272457,0.081327223,0.000000000],[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 [3] | Right Index [11] // Basepair A2654 - C2666 tHW ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.565894006694928] // Cluster node G2655:U2656 and A2665:A2665 Interaction | Interacting Bases [2,3] | Pair Probability [[0.006980622,0.001464000,0.007181242,0.001464000,0.000000000],[0.014541871,0.012154730,0.009717806,0.001464000,0.000000000],[0.001464000,0.001464000,0.017133401,0.006829134,0.000000000],[0.741901139,0.007320001,0.090303495,0.078616557,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2656 - A2665 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2655 - U2656 cSH 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044149057,0.044541851,0.382258874,0.047988462,0.000000000],[0.051461378,0.046686356,0.003723579,0.046230763,0.000000000],[0.000531940,0.000531940,0.018039957,0.000531940,0.000000000],[0.002533030,0.000531940,0.309726994,0.000531940,0.000000000],[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 [6] | Right Index [9] // Basepair A2657 - G2664 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003925557,0.006733370,0.004562426,0.075294433,0.000000000],[0.056908405,0.023470090,0.598866861,0.038148420,0.000000000],[0.004620589,0.081566892,0.000841380,0.009309359,0.000000000],[0.075731750,0.005191700,0.010792115,0.004036654,0.000000000],[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 C2658 - G2663 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_31754.1:
> IL_31754.1 IL_2QBG_101 C 2652 G 2668 CUAGUAC*GGACCG