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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 [14] // Basepair G143 - C172 cWW 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.018125141,0.015263839,0.233048493,0.076399111,0.000000000],[0.016976775,0.009949786,0.077711139,0.033435759,0.000000000],[0.261857232,0.076738061,0.003066422,0.017936141,0.000000000],[0.088805512,0.031619181,0.028146699,0.010920710,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair U144 - A171 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.387192728,0.003580665,0.315879003,0.003580665,0.000000000],[0.030648361,0.015195078,0.003580665,0.003580665,0.000000000],[0.003580665,0.008869795,0.131616019,0.038326316,0.000000000],[0.016180024,0.003580665,0.017162126,0.017446559,0.000000000],[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 [3] | Right Index [12] // Basepair A145 - A169 tWH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.017707924,0.003918792,0.018392577,0.003918792,0.000000000],[0.039408615,0.315779730,0.003918792,0.003918792,0.000000000],[0.003918792,0.009393603,0.029802081,0.017429436,0.000000000],[0.467237476,0.003918792,0.022736360,0.038599448,0.000000000],[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 [4] | Right Index [11] // Basepair U146 - A168 tWH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.018593320,0.041379046,0.004114731,0.440599350,0.000000000],[0.004114731,0.331568716,0.009863283,0.004114731,0.000000000],[0.019312206,0.004114731,0.031292185,0.023873178,0.000000000],[0.004114731,0.004114731,0.018300908,0.040529420,0.000000000],[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 A147 - U167 tHW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.028970555,0.413822916,0.003384646,0.034037077,0.000000000],[0.003384646,0.024659331,0.011816766,0.003384646,0.000000000],[0.096824226,0.003384646,0.030436609,0.015217440,0.000000000],[0.003384646,0.003384646,0.031198983,0.292708219,0.000000000],[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 A148 - C166 tHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003708089,0.006649494,0.004262905,0.077294868,0.000000000],[0.055188220,0.026436068,0.597914779,0.037535311,0.000000000],[0.004310778,0.078960365,0.000812555,0.009124318,0.000000000],[0.078296919,0.005166364,0.010409412,0.003929554,0.000000000],[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 C149 - G165 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
