| 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 5 2 | 5 5 I | 6 5 3 | 7 6 I | 8 7 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 | 13 8 I | 14 8 6 | 15 7 I | 16 7 7 | 17 6 I | 18 5 8 | 19 5 I | 20 5 9 | 21 5 I | 22 5 10 | 23 5 I | 24 5 11 | 25 4 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_80652.1_Instance_1 IL_80652.1_IL_2QBG_100_C2636_G2782 | C | U | G | A | G | C | G | A | G | A | U | G | A | G | ||||||||||||||||||||
| IL_80652.1_Sequence_1 IL_80652.1_IL_2QBG_100_C_2636_G_2782 | C | U | G | A | G | * | C | G | A | G | A | U | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 3 s35 2 8 tWH 2 13 s55 3 4 s35 3 7 s33 3 10 tSH 4 5 s35 4 7 tHS 4 10 s55 5 6 cWW 5 7 s55 6 7 s35 8 10 s53 8 13 s35 9 11 cSH 11 12 s55 3 8 6BPh 7 3 6BR 4 7 6BRJAR3D SCFG/MRF model for IL_80652.1:
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 C2636 - G2782 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 C2636 - G2782 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [2] | Right Index [12] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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 [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [2] | Right Index [11] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000015625000000000003000000000000000000000000000000] | Num Left Bases [2] | Num Right Bases [4] | Left Index [2] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node U2637:G2638 and A2776:U2779 Interaction | Interacting Bases [1,3] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2776 tWH Interaction | Interacting Bases [2,5] | Pair Probability [[0.044149057,0.051461378,0.000531940,0.002533030,0.000000000],[0.044541851,0.046686356,0.000531940,0.000531940,0.000000000],[0.382258874,0.003723579,0.018039957,0.309726994,0.000000000],[0.047988462,0.046230763,0.000531940,0.000531940,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2638 - A2778 tSH Interaction | Interacting Bases [4,6] | Pair Probability [[0.109399626,0.112701236,0.006146356,0.005085348,0.000000000],[0.105822836,0.122922437,0.001307276,0.123881708,0.000000000],[0.010688473,0.005845023,0.011947953,0.140628542,0.000000000],[0.009413474,0.109623711,0.001307276,0.123278727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2777 - U2779 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 [4] | Right Index [7] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.055401733,0.055894643,0.343661105,0.060219723,0.000000000],[0.064577812,0.058585737,0.003337601,0.058014022,0.000000000],[0.000667520,0.000667520,0.016169976,0.000667520,0.000000000],[0.003178646,0.000667520,0.277621400,0.000667520,0.000000000],[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 [4] | Right Index [7] // Basepair A2639 - G2775 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 G2640 - C2774 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_80652.1:
> IL_80652.1 IL_2QBG_100 C 2636 G 2782 CUGAG*CGAGAUGAG