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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010720626,0.013330514,0.013610420,0.035532791,0.000000000],[0.288400856,0.026644634,0.040374951,0.015284874,0.000000000],[0.013908384,0.035390462,0.003151655,0.013986402,0.000000000],[0.082165115,0.013993207,0.380586042,0.012919067,0.000000000],[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 [10] // Basepair U3297 - G3336 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.179781315,0.038064550,0.000431631,0.002034278,0.000000000],[0.181116961,0.037976408,0.000431631,0.000431631,0.000000000],[0.281236045,0.000431631,0.002110107,0.036635205,0.000000000],[0.200683960,0.037771386,0.000431631,0.000431631,0.000000000],[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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.166666667,0.166666667,0.611111111,0.055555556,0.000000000] | Left Index [2] | Right Index [9] // Basepair G3298 - A3335 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.013513514,0.148648649,0.148648649,0.689189189,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 8CRE|1|1|U|3299
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.824324324,0.013513514,0.148648649,0.013513514,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 8CRE|1|1|A|3300
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004335521,0.020477235,0.149411656,0.420632776,0.000000000],[0.003516278,0.000713935,0.007760565,0.367252143,0.000000000],[0.003901095,0.004122716,0.001625204,0.004086278,0.000000000],[0.003234620,0.003218494,0.001625204,0.004086278,0.000000000],[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 [8] // Basepair A3301 - U3333 tHH 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013436561,0.207673960,0.012767884,0.112425448,0.000000000],[0.014000663,0.011308071,0.080103685,0.013426519,0.000000000],[0.012525502,0.103896437,0.002778175,0.274931976,0.000000000],[0.079037080,0.014469041,0.016193555,0.031025444,0.000000000],[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 [6] | Right Index [7] // Basepair G3302 - C3332 cWW 
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
