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 [14] // Initial node G200 - C221 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010195092,0.020769450,0.011804402,0.193474890,0.000000000],[0.017202006,0.008406578,0.208382157,0.013263440,0.000000000],[0.011655809,0.234558465,0.002149506,0.027571043,0.000000000],[0.192357660,0.013922753,0.023782986,0.010503762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [14] // Basepair G200 - C221 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.180898075,0.022979953,0.009978689,0.007794541,0.000000000],[0.223106457,0.018378246,0.010047856,0.008559157,0.000000000],[0.175423867,0.020184915,0.094841633,0.006698679,0.000000000],[0.184471354,0.020276628,0.009230277,0.007129673,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [2] | Right Index [13] // Basepair C201 - A220 cSW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.332826416872369] // Cluster node C202:A203 and C218:A219
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004434773,0.001207200,0.004843947,0.001207200,0.000000000],[0.039987114,0.864647803,0.038094142,0.008450400,0.000000000],[0.001207200,0.001207200,0.005505466,0.005368552,0.000000000],[0.010022668,0.001207200,0.005026705,0.007582431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - C218 tWH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.019854918,0.271099652,0.002514918,0.024980606,0.000000000],[0.002514918,0.011900540,0.002514918,0.002514918,0.000000000],[0.140902150,0.233169698,0.017178551,0.012038356,0.000000000],[0.002514918,0.002514918,0.025973821,0.227812200,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A203 - C218 tHW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.056651997,0.047332496,0.000584264,0.003719453,0.000000000],[0.428592377,0.286158103,0.004089845,0.004089845,0.000000000],[0.048923171,0.000584264,0.004054179,0.006806626,0.000000000],[0.054562714,0.052682138,0.000584264,0.000584264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C202 - A219 tSH 
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 [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009247054,0.007386523,0.036100978,0.006101933,0.000000000],[0.005030892,0.004674688,0.007451505,0.005316705,0.000000000],[0.001064501,0.001064501,0.764758390,0.001064501,0.000000000],[0.099309926,0.001064501,0.049298902,0.001064501,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [5] | Right Index [10] // Basepair G204 - G217 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.045558309,0.014099396,0.342018043,0.016229361,0.000000000],[0.014438420,0.005788124,0.019549681,0.043692861,0.000000000],[0.375595066,0.019303593,0.003559872,0.015694806,0.000000000],[0.016257062,0.041075014,0.016050017,0.011090375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [9] // Basepair G205 - A216 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010030806,0.017205487,0.011658168,0.192396585,0.000000000],[0.020773653,0.008567443,0.234601962,0.013925571,0.000000000],[0.011806790,0.208424324,0.002149941,0.023787799,0.000000000],[0.193514041,0.013266124,0.027576622,0.010314686,0.000000000],[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 [7] | Right Index [8] // Basepair C206 - G215 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
