| 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 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 8 I | 12 8 6 | 13 8 I | 14 8 7 | 15 8 I | 16 8 8 | 17 8 I | 18 8 9 | 19 8 I | 20 8 10 | 21 8 I | 22 8 11 | 23 8 I | 24 8 | 25 9 I | 26 10 12 | 27 9 I | 28 8 13 | 29 8 I | 30 8 14 | 31 8 I | 32 8 15 | 33 8 I | 34 8 16 | 35 8 I | 36 8 17 | 37 8 I | 38 8 18 | 39 8 I | 40 8 19 | 41 8 I | 42 8 20 | 43 3 I | 44 3 21 | 45 2 I | 46 2 22 | 47 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_79564.1_Instance_1 HL_79564.1_HL_6C63_001_C6_G31 | C | G | A | A | G | G | A | G | A | G | G | A | G | A | G | G | A | A | G | A | G | G | A | G | A | G | ||||||||||||||||||||||||||
| HL_79564.1_Sequence_1 HL_79564.1_HL_6C63_001_C6_G31 | C | G | A | A | G | G | A | G | A | G | G | A | G | A | G | G | A | A | G | A | G | G | A | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 22 cWW 2 4 s33 2 21 tSH 3 4 s35 4 21 s35 5 6 s35 5 8 tSH 5 9 cWH 5 17 cHW 5 18 s35 6 7 s33 6 9 s53 6 10 cWH 6 18 cHW 7 11 cHW 7 20 cWH 9 10 s35 9 12 cWH 10 11 s33 10 12 s53 10 13 cWH 11 15 cHW 12 13 s35 12 16 tSH 12 17 cWH 13 15 s33 13 17 s53 13 18 cWH 14 19 s33 15 20 cHW 17 18 s35 18 20 s33 21 22 s35 2 5 6BPh 20 19 2BPh 8 5 6BRJAR3D SCFG/MRF model for HL_79564.1:
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 [22] // Initial node C6 - G31 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [22] // Basepair C6 - G31 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.046718239,0.000529759,0.002496756,0.000000000],[0.044458508,0.046610059,0.000529759,0.000529759,0.000000000],[0.380732303,0.003708313,0.018128765,0.314747597,0.000000000],[0.049261589,0.046358426,0.000529759,0.000529759,0.000000000],[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 [21] // Basepair G7 - A30 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [20] // 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 [4] | Right Index [20] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [20] // 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 [5] | Right Index [20] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000000000000000000000000086627951752960] | Num Left Bases [8] | Num Right Bases [8] | Left Index [5] | Right Index [20] | Norm Constant [0.000066561677031] // Cluster node G10:G20 and G21:G29 Interaction | Interacting Bases [6,9] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G16 - G21 cWH Interaction | Interacting Bases [7,11] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G18 - G24 cHW Interaction | Interacting Bases [8,12] | Pair Probability [[0.113862076,0.120538352,0.001366838,0.006441913,0.000000000],[0.114707989,0.120259235,0.001366838,0.001366838,0.000000000],[0.146584821,0.001366838,0.006682038,0.116012068,0.000000000],[0.127100484,0.119609993,0.001366838,0.001366838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G20 - A25 tSH Interaction | Interacting Bases [1,13] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G26 cHW Interaction | Interacting Bases [8,13] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G20 - G26 cWH Interaction | Interacting Bases [2,14] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G27 cHW Interaction | Interacting Bases [3,16] | Pair Probability [[0.001117702,0.001117702,0.080464698,0.009468992,0.000000000],[0.001117702,0.011847185,0.007823915,0.004031144,0.000000000],[0.046473914,0.001117702,0.792292506,0.001117702,0.000000000],[0.003863029,0.001117702,0.024475008,0.012553396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - G29 cWH Interaction | Interacting Bases [1,4] | Pair Probability [[0.113862076,0.120538352,0.001366838,0.006441913,0.000000000],[0.114707989,0.120259235,0.001366838,0.001366838,0.000000000],[0.146584821,0.001366838,0.006682038,0.116012068,0.000000000],[0.127100484,0.119609993,0.001366838,0.001366838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - A14 tSH Interaction | Interacting Bases [1,5] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - G15 cWH Interaction | Interacting Bases [2,6] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G11 - G16 cWH Interaction | Interacting Bases [3,7] | Pair Probability [[0.004966430,0.004966430,0.206503547,0.017165095,0.000000000],[0.004966430,0.052642128,0.004966430,0.004966430,0.000000000],[0.051077026,0.004966430,0.506544030,0.015536138,0.000000000],[0.042074794,0.017912101,0.004966430,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G13 - G18 cHW Interaction | Interacting Bases [5,8] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G15 - G20 cWH Interaction | Interacting Bases [9,14] | Pair Probability [[0.004966430,0.004966430,0.051077026,0.042074794,0.000000000],[0.004966430,0.052642128,0.004966430,0.017912101,0.000000000],[0.206503547,0.004966430,0.506544030,0.004966430,0.000000000],[0.017165095,0.004966430,0.015536138,0.055780127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - G27 cWH Interaction | Interacting Bases [11,16] | Pair Probability [[0.000933318,0.000933318,0.271650781,0.003225757,0.000000000],[0.000933318,0.009892791,0.006533228,0.000933318,0.000000000],[0.009598669,0.000933318,0.663223761,0.002919634,0.000000000],[0.007906921,0.003366138,0.006533228,0.010482501,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G24 - G29 cHW Interaction | Interacting Bases [10,10] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A23 Interaction | Interacting Bases [15,15] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A28 Insertion | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 6, position 2 in cluster node Insertion | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 10, position 6 in cluster node Insertion | Location [7] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 11, position 7 in cluster node Insertion | Location [9] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 13, position 9 in cluster node 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 [13] | Right Index [12] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [12] | Right Index [12] | Norm Constant [1.000000000000000] // Hairpin node G20:G20 Interaction | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G20Sequences of instances from HL_79564.1:
> HL_79564.1 HL_6C63_001 C 6 G 31 CGAAGGAGAGGAGAGGAAGAGGAGAG