| 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 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 9 I | 16 9 8 | 17 10 I | 18 11 | 19 10 I | 20 9 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_41203.4_Instance_1 IL_41203.4,IL_9DFE_036,C1004_G1151 | C | C | C | C | C | A | A | G | C | G | ||||||||||||||||||
| IL_41203.4_Sequence_1 IL_41203.49DFE_C_1004_G_1151 | C | C | C | C | C | A | A | G | * | C | G | true | 99 | 0 | 0 | 0.13 | ||||||||||||
| IL_41203.4_Instance_2 IL_41203.4,IL_4V9F_038,U1101_A1255 | U | C | C | C | C | A | A | G | C | A | ||||||||||||||||||
| IL_41203.4_Sequence_2 IL_41203.44V9F_U_1101_A_1255 | U | C | C | C | C | A | A | G | * | C | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_41203.4_Instance_3 IL_41203.4,IL_5J7L_278,U1004_A1151 | U | C | C | C | A | A | A | G | C | A | ||||||||||||||||||
| IL_41203.4_Sequence_3 IL_41203.45J7L_U_1004_A_1151 | U | C | C | C | A | A | A | G | * | C | A | true | 98 | 0 | 0 | 0.22 | ||||||||||||
| IL_41203.4_Instance_4 IL_41203.4,IL_8CRE_052,U1169_A1322 | U | G | C | C | G | G | A | A | U | A | ||||||||||||||||||
| IL_41203.4_Sequence_4 IL_41203.48CRE_U_1169_A_1322 | U | G | C | C | G | G | A | A | * | U | A | true | 100 | 0 | 0 | 0.05 | ||||||||||||
| IL_41203.4_Instance_5 IL_41203.4,IL_8P9A_277,U1173_A1326 | U | G | C | C | G | G | A | A | U | A | ||||||||||||||||||
| IL_41203.4_Sequence_5 IL_41203.48P9A_U_1173_A_1326 | U | G | C | C | G | G | A | A | * | U | A | true | 100 | 0 | 0 | 0.05 | ||||||||||||
| IL_41203.4_Instance_6 IL_41203.4,IL_4WF9_037,U1048_A1195 | U | C | C | C | A | A | A | A | U | A | ||||||||||||||||||
| IL_41203.4_Sequence_6 IL_41203.44WF9_U_1048_A_1195 | U | C | C | C | A | A | A | A | * | U | A | true | 98 | 0 | 0 | 0.27 | ||||||||||||
| IL_41203.4_Instance_7 IL_41203.4,IL_7A0S_034,U1015_A1162 | U | C | C | C | U | A | A | A | U | A | ||||||||||||||||||
| IL_41203.4_Sequence_7 IL_41203.47A0S_U_1015_A_1162 | U | C | C | C | U | A | A | A | * | U | A | true | 98 | 0 | 0 | 0.26 | ||||||||||||
| IL_41203.4_Instance_8 IL_41203.4,IL_5J7L_024,C504_G541 | C | G | G | C | U | A | A | C | G | G | ||||||||||||||||||
| IL_41203.4_Sequence_8 IL_41203.45J7L_C504_G541 | C | G | G | C | U | A | A | C | * | G | G | true | 94 | 0 | 0 | 0.82 | ||||||||||||
| IL_41203.4_Instance_9 IL_41203.4,IL_8CRE_421,A548_U586 | A | G | G | G | C | A | A | G | C | U | ||||||||||||||||||
| IL_41203.4_Sequence_9 IL_41203.48CRE_A548_U586 | A | G | G | G | C | A | A | G | * | C | U | true | 87 | 0 | 0 | 1.86 | ||||||||||||
| IL_41203.4_Instance_10 IL_41203.4,IL_8P9A_402,A550_U588 | A | G | G | G | C | A | A | G | C | U | ||||||||||||||||||
| IL_41203.4_Sequence_10 IL_41203.48P9A_A550_U588 | A | G | G | G | C | A | A | G | * | C | U | true | 87 | 0 | 0 | 1.86 | ||||||||||||
| IL_41203.4_Instance_11 IL_41203.4,IL_4LFB_020,C504_G541 | C | G | G | C | C | A | A | C | G | G | ||||||||||||||||||
| IL_41203.4_Sequence_11 IL_41203.44LFB_C504_G541 | C | G | G | C | C | A | A | C | * | G | G | true | 96 | 0 | 0 | 0.61 |
1 8 s35 1 10 cWW 2 3 s35 3 4 s35 4 5 s33 5 6 cSH 6 7 s35 8 9 cWW 8 10 s55 9 10 s35JAR3D SCFG/MRF model for IL_41203.4:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008469224,0.016757220,0.009371274,0.200342005,0.000000000],[0.019057480,0.008962697,0.210572595,0.010722865,0.000000000],[0.009408594,0.181223228,0.001889386,0.026323806,0.000000000],[0.239733866,0.010372485,0.037266864,0.009526410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair C1004 - G1151 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.423076923,0.500000000,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1005 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.576923077,0.346153846,0.038461538,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1006 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.730769231,0.192307692,0.038461538,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 9DFE|1|1A|C|1007 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [9] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [5] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|C|1008:9DFE|1|1A|G|1011 and 9DFE|1|1A|C|1150:9DFE|1|1A|C|1150 Interaction | Interacting Bases [4,5] | Pair Probability [[0.008760916,0.018679442,0.009774356,0.221544309,0.000000000],[0.016382900,0.008810829,0.202616130,0.011314118,0.000000000],[0.009737063,0.231963022,0.001903876,0.032881708,0.000000000],[0.182158848,0.011663940,0.021961941,0.009846602,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1011 - 9DFE|1|1A|C|1150 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.118712360,0.094803052,0.004990382,0.024169785,0.000000000],[0.148107514,0.092360640,0.001063811,0.008632871,0.000000000],[0.008920351,0.001063811,0.125394814,0.073914129,0.000000000],[0.119934972,0.090951714,0.001063811,0.085915982,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|C|1008 - 9DFE|1|1A|A|1009 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.884615385,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 9DFE|1|1A|A|1010 InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [8] // New Initial node after Cluster 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_41203.4:
> IL_41203.4 9DFE C 1004 G 1151 CCCCCAAG*CG > IL_41203.4 4V9F U 1101 A 1255 UCCCCAAG*CA > IL_41203.4 5J7L U 1004 A 1151 UCCCAAAG*CA > IL_41203.4 8CRE U 1169 A 1322 UGCCGGAA*UA > IL_41203.4 8P9A U 1173 A 1326 UGCCGGAA*UA > IL_41203.4 4WF9 U 1048 A 1195 UCCCAAAA*UA > IL_41203.4 7A0S U 1015 A 1162 UCCCUAAA*UA > IL_41203.4 5J7L C 504 G 541 CGGCUAAC*GG > IL_41203.4 8CRE A 548 U 586 AGGGCAAG*CU > IL_41203.4 8P9A A 550 U 588 AGGGCAAG*CU > IL_41203.4 4LFB C 504 G 541 CGGCCAAC*GG