| 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 2 2 | 5 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 2 I | 12 2 6 | 13 2 I | 14 2 7 | 15 2 I | 16 2 8 | 17 2 I | 18 2 9 | 19 2 I | 20 2 10 | 21 2 I | 22 2 11 | 23 2 I | 24 2 12 | 25 3 I | 26 4 13 | 27 4 I | 28 5 | 29 4 I | 30 4 14 | 31 3 I | 32 2 15 | 33 2 I | 34 2 16 | 35 2 I | 36 2 17 | 37 2 I | 38 2 18 | 39 2 I | 40 2 19 | 41 2 I | 42 2 20 | 43 2 I | 44 2 21 | 45 2 I | 46 2 22 | 47 2 I | 48 2 23 | 49 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_90057.1_Instance_1 IL_90057.1_IL_1NBS_003_C184_G226 | C | A | C | A | G | U | G | A | C | G | A | A | G | U | A | G | U | G | G | A | A | C | G | C | G | |||||||||||||||||||||||||||||
| IL_90057.1_Sequence_1 IL_90057.1_IL_1NBS_003_C184_G226 | C | A | C | A | G | U | G | A | C | G | A | A | G | U | * | A | G | U | G | G | A | A | C | G | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||
| IL_90057.1_Instance_2 IL_90057.1_IL_1NBS_010_C184_G226 | C | A | C | A | G | U | G | A | C | G | A | A | G | U | A | G | U | G | G | A | A | C | G | C | G | |||||||||||||||||||||||||||||
| IL_90057.1_Sequence_2 IL_90057.1_IL_1NBS_010_C184_G226 | C | A | C | A | G | U | G | A | C | G | A | A | G | U | * | A | G | U | G | G | A | A | C | G | C | G | true | 100 | 0 | 0 | 0.00 |
1 19 tSS 1 23 cWW 2 3 s35 2 18 tHH 3 4 s35 4 5 s35 4 8 tWH 4 16 cSS 4 20 tWW 5 20 tSW 6 7 s35 6 12 cWS 6 13 s55 7 11 cSS 7 12 s55 7 15 cHW 7 20 s33 8 9 cSH 8 17 tWS 8 19 s33 8 20 s55 9 21 s55 9 22 cWH 9 23 s35 10 11 s35 10 21 cHW 11 12 s35 11 21 s53 12 13 s35 13 14 cWW 14 15 s35 15 16 s35 16 17 s35 16 20 tWH 17 20 s55 18 19 s35 20 21 cSH 4 2 7BPh 5 8 6BPh 10 8 6BPh 1 9 7BPh 17 20 6BPh 19 1 6BR 10 7 6BR 9 8 7BR 21 20 7BRJAR3D SCFG/MRF model for IL_90057.1:
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 [23] // Initial node C184 - G226 from junction ClusterNode | Deletion Probability [0.000000000000000000000000000000000000000000000000000011624274] | Num Left Bases [12] | Num Right Bases [9] | Left Index [1] | Right Index [23] | Norm Constant [0.000050680706613] // Cluster node C184:G196 and G217:G226 Interaction | Interacting Bases [7,13] | Pair Probability [[0.004749905,0.004749905,0.036692280,0.019008418,0.000000000],[0.004749905,0.044695720,0.004749905,0.004749905,0.000000000],[0.048133976,0.221179392,0.494598316,0.014613106,0.000000000],[0.027827322,0.025102721,0.004749905,0.039649321,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G190 - G217 cHW Interaction | Interacting Bases [4,14] | Pair Probability [[0.181988495,0.181795261,0.173934281,0.209629097,0.000000000],[0.023908124,0.022702883,0.001969550,0.024591260,0.000000000],[0.024882546,0.023911658,0.021881535,0.024573721,0.000000000],[0.025123882,0.011025252,0.022013973,0.026068482,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - U218 cSS Interaction | Interacting Bases [8,15] | Pair Probability [[0.008947363,0.079325473,0.616028953,0.005161128,0.000000000],[0.075466431,0.003967145,0.162538428,0.003586090,0.000000000],[0.000852030,0.003849229,0.005964211,0.004747888,0.000000000],[0.004064644,0.003498027,0.019386766,0.002616194,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A191 - G219 tWS Interaction | Interacting Bases [2,16] | Pair Probability [[0.020789531,0.016955835,0.436057743,0.349753317,0.000000000],[0.017600079,0.004164499,0.017933588,0.044394026,0.000000000],[0.017216889,0.021322694,0.004164499,0.004164499,0.000000000],[0.017579165,0.019574638,0.004164499,0.004164499,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A185 - G220 tHH Interaction | Interacting Bases [1,17] | Pair Probability [[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.191176471,0.171568627,0.171568627,0.171568627,0.000000000],[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.024509804,0.024509804,0.024509804,0.024509804,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C184 - A221 tSS Interaction | Interacting Bases [4,18] | Pair Probability [[0.742873018,0.067910692,0.007232652,0.034263267,0.000000000],[0.009713775,0.004002376,0.003143155,0.003947390,0.000000000],[0.001033236,0.003141446,0.097606567,0.005654000,0.000000000],[0.004895843,0.003947466,0.005659243,0.004975874,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - A222 tWW Interaction | Interacting Bases [5,18] | Pair Probability [[0.008947363,0.075466431,0.000852030,0.004064644,0.000000000],[0.079325473,0.003967145,0.003849229,0.003498027,0.000000000],[0.616028953,0.162538428,0.005964211,0.019386766,0.000000000],[0.005161128,0.003586090,0.004747888,0.002616194,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G188 - A222 tSW Interaction | Interacting Bases [10,19] | Pair Probability [[0.000194944,0.000974721,0.002275854,0.000956556,0.000000000],[0.000194944,0.081105411,0.000194944,0.000194944,0.000000000],[0.112944347,0.701912479,0.063543053,0.005338350,0.000000000],[0.001071393,0.012289112,0.000194944,0.016614002,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G193 - C223 cHW Interaction | Interacting Bases [9,20] | Pair Probability [[0.000797307,0.000797307,0.065990589,0.004381919,0.000000000],[0.003986537,0.331715203,0.418261570,0.050261569,0.000000000],[0.009308076,0.000797307,0.037126635,0.000797307,0.000000000],[0.003912246,0.000797307,0.003119066,0.067950053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C192 - G224 cWH Interaction | Interacting Bases [1,21] | Pair Probability [[0.003887072,0.006667356,0.004517696,0.074556253,0.000000000],[0.056350480,0.023239991,0.602799539,0.037774416,0.000000000],[0.004575289,0.080767216,0.000833131,0.009218090,0.000000000],[0.074989282,0.005140801,0.010686310,0.003997079,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C184 - G226 cWW Interaction | Interacting Bases [4,8] | Pair Probability [[0.519623131,0.005000153,0.428770720,0.005000153,0.000000000],[0.005639356,0.002624082,0.004088846,0.000714308,0.000000000],[0.000714308,0.000714308,0.008848111,0.006373548,0.000000000],[0.003405949,0.000714308,0.004228743,0.003539977,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A187 - A191 tWH Interaction | Interacting Bases [8,9] | Pair Probability [[0.107358724,0.143107315,0.006419081,0.005362531,0.000000000],[0.110490754,0.103294657,0.001234995,0.106950551,0.000000000],[0.006103550,0.006664607,0.014614084,0.106469853,0.000000000],[0.061780476,0.116710780,0.001234995,0.102203046,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A191 - C192 cSH Interaction | Interacting Bases [7,11] | Pair Probability [[0.072106438,0.068212864,0.069372989,0.069940665,0.000000000],[0.074749653,0.068873836,0.070120860,0.017346033,0.000000000],[0.098375108,0.008401879,0.032027853,0.066558883,0.000000000],[0.072098922,0.070130398,0.070288073,0.071395548,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G190 - A195 cSS Interaction | Interacting Bases [6,12] | Pair Probability [[0.008423477,0.009919438,0.008066461,0.009502076,0.000000000],[0.014035600,0.014368927,0.013928497,0.014300052,0.000000000],[0.012447882,0.010476921,0.010369283,0.008576553,0.000000000],[0.250441890,0.022833380,0.320949650,0.271359911,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U189 - G196 cWS Interaction | Interacting Bases [14,18] | Pair Probability [[0.023610727,0.004951724,0.024289290,0.004951724,0.000000000],[0.049185322,0.041111237,0.032868771,0.004951724,0.000000000],[0.004951724,0.004951724,0.057950718,0.023098344,0.000000000],[0.603906771,0.004951724,0.061087140,0.053181337,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U218 - A222 tWH Interaction | Interacting Bases [18,19] | Pair Probability [[0.107358724,0.143107315,0.006419081,0.005362531,0.000000000],[0.110490754,0.103294657,0.001234995,0.106950551,0.000000000],[0.006103550,0.006664607,0.014614084,0.106469853,0.000000000],[0.061780476,0.116710780,0.001234995,0.102203046,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A222 - C223 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.625000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C186 Insertion | Location [10] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 10, position 10 in cluster node Insertion | Location [20] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 22, position 20 in cluster node InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[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 [13] | Right Index [14] // Basepair U197 - A216 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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_90057.1:
> IL_90057.1 IL_1NBS_003 C 184 G 226 CACAGUGACGAAGU*AGUGGAACGCG > IL_90057.1 IL_1NBS_010 C 184 G 226 CACAGUGACGAAGU*AGUGGAACGCG