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 [11] // Initial node A1430 - U1470 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011134496,0.019611426,0.012682293,0.136578475,0.000000000],[0.168530603,0.012682600,0.118742615,0.013871213,0.000000000],[0.012849956,0.116192085,0.002838101,0.021636967,0.000000000],[0.126193227,0.013057190,0.198002729,0.015396023,0.000000000],[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 [11] // Basepair A1430 - U1470 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.144252810,0.142028198,0.001480190,0.009479171,0.000000000],[0.132612935,0.091907177,0.001480190,0.001480190,0.000000000],[0.132253308,0.001480190,0.010148820,0.066697799,0.000000000],[0.133203331,0.128535313,0.001480190,0.001480190,0.000000000],[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 [10] // Basepair A1431 - C1469 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.111901106,0.130435065,0.001348266,0.006420269,0.000000000],[0.112896691,0.118332196,0.001348266,0.001348266,0.000000000],[0.154434405,0.001348266,0.006532064,0.112148628,0.000000000],[0.121632542,0.117177440,0.001348266,0.001348266,0.000000000],[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 [3] | Right Index [9] // Basepair G1432 - A1468 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.133737833,0.147730480,0.115492465,0.128805683,0.000000000],[0.111737375,0.195434870,0.001379266,0.124366223,0.000000000],[0.001379266,0.001379266,0.009570662,0.001379266,0.000000000],[0.008780478,0.001379266,0.016068337,0.001379266,0.000000000],[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 [4] | Right Index [8] // Basepair A1433 - C1467 tHS 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [7] | Norm Constant [0.272972264529784] // Cluster node A1434:G1435 and C1466:C1466
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.019031869,0.608075411,0.004993410,0.004993410,0.000000000],[0.021976200,0.257997875,0.004993410,0.004993410,0.000000000],[0.004993410,0.004993410,0.018938417,0.004993410,0.000000000],[0.004993410,0.004993410,0.024046127,0.004993410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1434 - C1466 bif 
Interaction  | Interacting Bases [2,3] | 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 G1435 - C1466 cWW 
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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
