| 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 6 I | 10 7 5 | 11 8 I | 12 13 6 | 13 13 I | 14 13 7 | 15 13 I | 16 13 8 | 17 13 I | 18 13 9 | 19 13 I | 20 13 10 | 21 13 I | 22 13 11 | 23 13 I | 24 13 12 | 25 13 I | 26 13 13 | 27 14 I | 28 15 14 | 29 15 I | 30 16 | 31 15 I | 32 15 15 | 33 14 I | 34 13 16 | 35 12 I | 36 11 17 | 37 10 I | 38 9 18 | 39 4 I | 40 4 19 | 41 3 I | 42 3 20 | 43 2 I | 44 2 21 | 45 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_50715.3_Instance_1 IL_50715.3,IL_4WF9_040,C1168_G1074 | C | G | A | A | A | A | U | G | U | A | C | C | G | G | G | G | C | G | G | A | A | A | A | G | ||||||||||||||||||||||||||
| IL_50715.3_Sequence_1 IL_50715.34WF9_C_1168_G_1074 | C | G | A | A | A | A | U | G | U | A | C | C | G | G | G | G | C | * | G | G | A | A | A | A | G | true | 92 | 0 | 0 | 2.00 | ||||||||||||||||||||
| IL_50715.3_Instance_2 IL_50715.3,IL_5J7L_281,G1124_C1030 | G | G | A | A | G | A | U | G | U | A | A | C | G | G | G | G | C | G | G | G | A | A | A | C | ||||||||||||||||||||||||||
| IL_50715.3_Sequence_2 IL_50715.35J7L_G_1124_C_1030 | G | G | A | A | G | A | U | G | U | A | A | C | G | G | G | G | C | * | G | G | G | A | A | A | C | true | 88 | 0 | 0 | 2.95 | ||||||||||||||||||||
| IL_50715.3_Instance_3 IL_50715.3,IL_7A0S_037,C1135_G1041 | C | G | A | A | A | A | U | G | A | U | C | G | G | G | G | C | G | G | U | U | A | A | G | |||||||||||||||||||||||||||
| IL_50715.3_Sequence_3 IL_50715.37A0S_C_1135_G_1041 | C | G | A | A | A | A | U | G | A | U | C | G | G | G | G | C | * | G | G | U | U | A | A | G | true | 97 | 0 | 0 | 0.85 | |||||||||||||||||||||
| IL_50715.3_Instance_4 IL_50715.3,IL_9DFE_039,C1124_G1030 | C | G | A | A | A | A | U | G | A | U | C | G | G | G | G | C | G | G | U | A | A | A | G | |||||||||||||||||||||||||||
| IL_50715.3_Sequence_4 IL_50715.39DFE_C_1124_G_1030 | C | G | A | A | A | A | U | G | A | U | C | G | G | G | G | C | * | G | G | U | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 21 cWW 2 3 s33 2 19 s33 2 20 tSH 2 21 s55 3 18 s53 3 19 tHH 4 5 s35 6 7 cSH 7 8 s35 9 11 s33 9 12 tWH 9 13 s55 9 16 s55 10 11 s35 11 12 s35 12 13 s35 13 14 s35 13 16 tWW 14 15 cWW 15 16 s33 17 18 s35 18 19 s35 19 20 s35 20 21 s35 19 3 6BPh 9 12 7BPh 3 19 6BPh 2 20 6BPh 20 2 6BRJAR3D SCFG/MRF model for IL_50715.3:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [21] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009401513,0.017549866,0.010782207,0.195587161,0.000000000],[0.019107025,0.009484786,0.232344244,0.013401212,0.000000000],[0.010842591,0.210218542,0.002049451,0.023823814,0.000000000],[0.196851077,0.013154215,0.025444740,0.009957556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [21] // Basepair C1168 - G1074 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.042857649,0.045370598,0.000514478,0.002424734,0.000000000],[0.043176051,0.045265538,0.000514478,0.000514478,0.000000000],[0.398595795,0.003601343,0.017605820,0.305668340,0.000000000],[0.047840582,0.045021164,0.000514478,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [20] // Basepair G1169 - A1073 tSH BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.767445428,0.083662994,0.004992951,0.005094001,0.000000000],[0.091617979,0.000148772,0.012682939,0.001413647,0.000000000],[0.005192160,0.012520853,0.000371335,0.000148772,0.000000000],[0.007073299,0.007337324,0.000148772,0.000148772,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [19] // Basepair A1170 - A1072 tHH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [18] // Fixed node on left for 4WF9|1|X|A|1071 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [18] // Fixed node on left for 4WF9|1|X|A|1072 InitialNode | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Position [2] | Left Index [6] | Right Index [18] // Fixed node on right for 4WF9|1|X|C|1178 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [17] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.250000000,0.416666667,0.000000000] | Position [2] | Left Index [6] | Right Index [17] // Fixed node on right for 4WF9|1|X|A|1177 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [16] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000008744450558789937820511531234700380977] | Num Left Bases [8] | Num Right Bases [1] | Left Index [6] | Right Index [16] | Norm Constant [1.000000000000000] // Cluster node 4WF9|1|X|G|1175:4WF9|1|X|G|1183 and 4WF9|1|X|G|1069:4WF9|1|X|G|1069 Interaction | Interacting Bases [8,9] | Pair Probability [[0.344802048,0.021791490,0.003728686,0.017846250,0.000000000],[0.043205333,0.014077990,0.012049275,0.014040701,0.000000000],[0.003728686,0.011140973,0.411330104,0.018428277,0.000000000],[0.019015698,0.014180515,0.032771384,0.017862592,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1183 - 4WF9|1|X|G|1069 tWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.070701762,0.072041852,0.003961084,0.070405509,0.000000000],[0.052783485,0.079545637,0.000877051,0.070553105,0.000000000],[0.061772277,0.000877051,0.075351648,0.106935897,0.000000000],[0.178442123,0.071367748,0.000877051,0.083506721,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1175 - 4WF9|1|X|U|1176 cSH Interaction | Interacting Bases [4,7] | Pair Probability [[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.168269231,0.168269231,0.206730769,0.168269231,0.000000000],[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.024038462,0.024038462,0.024038462,0.024038462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|1179 - 4WF9|1|X|G|1182 tWH Interaction | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|A|1177 Interaction | Interacting Bases [5,5] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|G|1180 Interaction | Interacting Bases [6,6] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|G|1181 Insertion | Location [1] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 6, position 1 in cluster node Insertion | Location [3] | Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 8, position 3 in cluster node InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [15] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [14] | Right Index [15] // Basepair C1184 - G1068 cWW HairpinNode | Num Bases [1] | Left Index [15] | Right Index [15] | 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_50715.3:
> IL_50715.3 4WF9 C 1168 G 1074 CGAAAAUGUACCGGGGC*GGAAAAG > IL_50715.3 5J7L G 1124 C 1030 GGAAGAUGUAACGGGGC*GGGAAAC > IL_50715.3 7A0S C 1135 G 1041 CGAAAAUGAUCGGGGC*GGUUAAG > IL_50715.3 9DFE C 1124 G 1030 CGAAAAUGAUCGGGGC*GGUAAAG