Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005563209,0.008262228,0.018091094,0.099692097,0.000000000],[0.015272512,0.004772643,0.505034903,0.006314058,0.000000000],[0.006362373,0.101223902,0.003490307,0.011908173,0.000000000],[0.133310474,0.006127283,0.069732920,0.004841823,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C3 - G17 cWW 
ClusterNode  | Deletion Probability [0.0000000000031219] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.470662777498451] // Cluster node 5G4T|1|A|G|4:5G4T|1|A|G|7 and 5G4T|1|B|A|16:5G4T|1|B|A|16
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.082176660,0.014316284,0.015160030,0.012850929,0.000000000],[0.029418362,0.005971669,0.068285341,0.005971669,0.000000000],[0.542438928,0.005971669,0.075555523,0.051013339,0.000000000],[0.072954587,0.005971669,0.005971669,0.005971669,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5G4T|1|A|G|4 - 5G4T|1|B|A|16 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.052965220,0.056070824,0.000635812,0.002996585,0.000000000],[0.053358714,0.055940987,0.000635812,0.000635812,0.000000000],[0.450482841,0.002316352,0.011323909,0.196603197,0.000000000],[0.059123331,0.055638979,0.000635812,0.000635812,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5G4T|1|A|G|7 - 5G4T|1|B|A|16 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.741379310,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.017241379,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.120689655,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.120689655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5G4T|1|A|A|5
Insertion    | Location [2] | Length Distribution [0.001844848,0.996218061,0.001844848,0.000092242] | Letter Distribution [0.465517241,0.189655172,0.051724138,0.293103448,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.0000244705618206] | Pair Probability [[0.057192438,0.037336519,0.491973135,0.040842178,0.000000000],[0.037912459,0.037263122,0.002815064,0.038590543,0.000000000],[0.000561611,0.000440177,0.013877256,0.000440177,0.000000000],[0.002857096,0.000440177,0.237017871,0.000440177,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A8 - G15 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.066028364,0.075214628,0.402100985,0.068377018,0.000000000],[0.049792264,0.064504005,0.002302054,0.062709036,0.000000000],[0.000752428,0.000752428,0.011821040,0.000752428,0.000000000],[0.003722356,0.000752428,0.189666110,0.000752428,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A9 - G14 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009532599,0.097201109,0.009775427,0.133793126,0.000000000],[0.014158910,0.008707036,0.234005991,0.011141529,0.000000000],[0.009734887,0.122912757,0.002020387,0.188098296,0.000000000],[0.112472120,0.011347231,0.017610445,0.017488151,0.000000000],[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 C10 - G13 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
