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 [18] // Initial node G20 - C45 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003952716,0.056367336,0.004576658,0.075011714,0.000000000],[0.006669351,0.022815069,0.080791377,0.005142338,0.000000000],[0.004519048,0.602973996,0.000833380,0.010689507,0.000000000],[0.074578555,0.037785716,0.009220848,0.004072390,0.000000000],[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 [18] // Basepair G20 - C45 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000152587890625000050000000] | Num Left Bases [3] | Num Right Bases [13] | Left Index [2] | Right Index [17] | Norm Constant [0.025236805498983] // Cluster node G21:G23 and C32:A44
Interaction  | Interacting Bases [3,4] | 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]] // Cluster Interaction G23 - C32 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.172411429,0.192167986,0.229920841,0.184388661,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.011541768,0.013321536,0.020537534,0.158885204,0.000000000],[0.002103130,0.002103130,0.002103130,0.002103130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A22 - G33 tSS 
Interaction  | Interacting Bases [1,16] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A44 tSH 
Interaction  | Interacting Bases [3,16] | Pair Probability [[0.027441087,0.006151523,0.007255111,0.006230281,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.680617569,0.117598954,0.118861917,0.014691247,0.000000000],[0.006610097,0.001322019,0.001322019,0.001322019,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G23 - A44 tSS 
Interaction  | Interacting Bases [10,14] | Pair Probability [[0.025971800,0.005446896,0.026718220,0.005446896,0.000000000],[0.054103855,0.045222361,0.036155648,0.005446896,0.000000000],[0.005446896,0.005446896,0.063745789,0.025408179,0.000000000],[0.564297448,0.005446896,0.067195854,0.058499471,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A42 tWH 
Interaction  | Interacting Bases [9,15] | Pair Probability [[0.042142294,0.004723046,0.206685502,0.004723046,0.000000000],[0.048779144,0.021003908,0.037384201,0.004723046,0.000000000],[0.004723046,0.004723046,0.032699768,0.491912438,0.000000000],[0.022031629,0.004723046,0.019996218,0.049026621,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - U43 tWH 
Interaction  | Interacting Bases [4,16] | Pair Probability [[0.137353716,0.027973270,0.027144157,0.027605601,0.000000000],[0.265454914,0.028129651,0.003444892,0.025860767,0.000000000],[0.146388091,0.029726665,0.026997642,0.029902458,0.000000000],[0.141951395,0.027674455,0.026559644,0.027832681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C32 - A44 cSS 
Interaction  | Interacting Bases [6,6] | 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]] // Right strand conserved insertion C34
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.906250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C35
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G36
Interaction  | Interacting Bases [11,11] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G39
Interaction  | Interacting Bases [12,12] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A40
Interaction  | Interacting Bases [13,13] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A41
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 [5] | Right Index [4] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
