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 truncation
