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 [12] // Initial node C16 - G58 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006602025,0.012407655,0.022705391,0.125946391,0.000000000],[0.012381398,0.005539457,0.435066187,0.008871608,0.000000000],[0.007657263,0.147915900,0.004178169,0.016776766,0.000000000],[0.125938168,0.008876460,0.052341644,0.006795516,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C16 - G58 cWW 
ClusterNode  | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.399377512311362] // Cluster node A17:G20 and A57:A57
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.470625919,0.082176614,0.075801341,0.076535297,0.000000000],[0.064281502,0.010914553,0.010914553,0.010914553,0.000000000],[0.067198556,0.013560294,0.013785616,0.015974780,0.000000000],[0.054572764,0.010914553,0.010914553,0.010914553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A17 - A57 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.054325971,0.063323874,0.000654559,0.003116925,0.000000000],[0.054809310,0.057448150,0.000654559,0.000654559,0.000000000],[0.356405549,0.003272793,0.015855996,0.272230694,0.000000000],[0.059050408,0.056887536,0.000654559,0.000654559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G20 - A57 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.617647059,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.323529412,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A18
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.054325971,0.054809310,0.356405549,0.059050408,0.000000000],[0.063323874,0.057448150,0.003272793,0.056887536,0.000000000],[0.000654559,0.000654559,0.015855996,0.000654559,0.000000000],[0.003116925,0.000654559,0.272230694,0.000654559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair A21 - G56 tHS 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003621880,0.038167502,0.003486392,0.008394012,0.000000000],[0.004473969,0.004553906,0.005265058,0.003843820,0.000000000],[0.003418893,0.005362656,0.001097422,0.011174125,0.000000000],[0.049341309,0.029206938,0.031270362,0.797321755,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair U22 - U55 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.014258858,0.211706755,0.014176550,0.093357766,0.000000000],[0.015234759,0.010399964,0.094014042,0.014566320,0.000000000],[0.013899989,0.109909176,0.002989625,0.256526531,0.000000000],[0.088532666,0.015883070,0.017860543,0.026683387,0.000000000],[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 G23 - U54 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
