| 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 7 3 | 7 7 I | 8 8 4 | 9 9 I | 10 10 5 | 11 10 I | 12 11 6 | 13 11 I | 14 12 7 | 15 12 I | 16 13 8 | 17 13 I | 18 14 | 19 13 I | 20 13 9 | 21 12 I | 22 12 10 | 23 11 I | 24 11 11 | 25 10 I | 26 10 12 | 27 9 I | 28 8 13 | 29 8 I | 30 8 14 | 31 7 I | 32 7 15 | 33 6 I | 34 5 16 | 35 2 I | 36 2 17 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_17682.1_Instance_1 IL_17682.1_IL_4A1B_002_C29_G51 | C | U | G | A | A | C | U | U | A | U | C | A | G | U | A | A | G | |||||||||||||||||||||||||
| IL_17682.1_Sequence_1 IL_17682.1_IL_4A1B_002_C29_G51 | C | U | G | A | A | C | U | U | * | A | U | C | A | G | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 17 cWW 2 3 s35 2 17 s55 3 13 s33 3 14 s33 3 15 tSH 4 5 s35 4 14 tHW 4 15 s55 5 6 s35 5 12 tHH 6 7 s35 6 11 tHS 7 8 s35 7 10 cWW 8 9 cWW 8 10 s55 9 10 s35 10 11 s35 11 12 s33 12 14 s55 13 14 cSH 15 16 s35 16 17 s35 13 4 6BPh 7 6 7BPh 3 14 6BPh 15 3 6BR 14 13 7BRJAR3D SCFG/MRF model for IL_17682.1:
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 [17] // Initial node C29 - G51 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 [17] // Basepair C29 - G51 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [16] // 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 [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [16] // 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 [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224390099112] | 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]] | 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 [15] // Basepair G31 - A49 tSH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [4] | Right Index [14] | Norm Constant [0.565894006694928] // Cluster node A32:A32 and G47:U48 Interaction | Interacting Bases [1,3] | Pair Probability [[0.006980622,0.014541871,0.001464000,0.741901139,0.000000000],[0.001464000,0.012154730,0.001464000,0.007320001,0.000000000],[0.007181242,0.009717806,0.017133401,0.090303495,0.000000000],[0.001464000,0.001464000,0.006829134,0.078616557,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A32 - U48 tHW Interaction | Interacting Bases [2,3] | 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 G47 - U48 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 [5] | Right Index [12] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.214636672,0.041327996,0.010220578,0.010236110,0.000000000],[0.026440627,0.002047357,0.176007769,0.145427765,0.000000000],[0.012790266,0.169881869,0.005015775,0.002047357,0.000000000],[0.012581023,0.167244122,0.002047357,0.002047357,0.000000000],[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 [5] | Right Index [12] // Basepair A33 - A46 tHH BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.067529094,0.118956523,0.149216401,0.143517090,0.000000000],[0.149836953,0.179916717,0.001700157,0.147086012,0.000000000],[0.001700157,0.001700157,0.007466133,0.001700157,0.000000000],[0.007270178,0.001700157,0.019003954,0.001700157,0.000000000],[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 [11] // Basepair C34 - C45 tHS BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003693601,0.038923294,0.003555430,0.008560230,0.000000000],[0.004562562,0.004644083,0.005369317,0.003919935,0.000000000],[0.003486594,0.005468847,0.001119153,0.011395395,0.000000000],[0.050318365,0.029785294,0.031889577,0.793308324,0.000000000],[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 [7] | Right Index [10] // Basepair U35 - U44 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009206316,0.020335270,0.009916234,0.209350778,0.000000000],[0.024742834,0.009627484,0.195778801,0.010479833,0.000000000],[0.009933160,0.194648267,0.002175103,0.023883287,0.000000000],[0.227411257,0.010406240,0.028134421,0.013970716,0.000000000],[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 [8] | Right Index [9] // Basepair U36 - A43 cWW 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_17682.1:
> IL_17682.1 IL_4A1B_002 C 29 G 51 CUGAACUU*AUCAGUAAG