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 [8] // Initial node U59 - A80 from junction 
BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair U59 - A80 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.004508284,0.004508284,0.045685474,0.026411789,0.000000000],[0.004508284,0.042422116,0.209928331,0.023825784,0.000000000],[0.034825799,0.004508284,0.479674580,0.004508284,0.000000000],[0.058674243,0.004508284,0.013869760,0.037632420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G60 - G78 cWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left
InitialNode  | Left Length Distribution [0.009140559,0.731244716,0.009140559,0.000457028,0.000007617,0.000007617,0.000007617,0.003046853,0.243748239,0.003046853,0.000152343] | Left Letter Distribution [0.346153846,0.115384615,0.192307692,0.346153846,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.583333333,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 [4] | Right Index [5] // Basepair C63 - G76 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
