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 [0.0000234451146992] | Pair Probability [[0.010572638,0.014877250,0.013044997,0.090228256,0.000000000],[0.206427106,0.021659062,0.106652866,0.015137891,0.000000000],[0.013291996,0.091543616,0.002872521,0.017432502,0.000000000],[0.123374477,0.014077094,0.246524532,0.012283196,0.000000000],[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 U3 - G8 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.146217981,0.053512369,0.001570915,0.007696513,0.000000000],[0.169325908,0.117962426,0.001570915,0.001570915,0.000000000],[0.148726299,0.001570915,0.009984515,0.052151474,0.000000000],[0.143160694,0.141836332,0.001570915,0.001570915,0.000000000],[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 [2] | Right Index [11] // Basepair C4 - A7 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.149343631,0.266558828,0.003562807,0.029219295,0.000000000],[0.003562807,0.022326558,0.011228334,0.003562807,0.000000000],[0.173069960,0.003562807,0.065177633,0.016372916,0.000000000],[0.003562807,0.003562807,0.034614727,0.210711273,0.000000000],[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 [10] // Basepair A5 - C6 tHW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.149343631,0.003562807,0.173069960,0.003562807,0.000000000],[0.266558828,0.022326558,0.003562807,0.003562807,0.000000000],[0.003562807,0.011228334,0.065177633,0.034614727,0.000000000],[0.029219295,0.003562807,0.016372916,0.210711273,0.000000000],[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 [9] // Basepair C6 - A5 tWH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.146217981,0.169325908,0.148726299,0.143160694,0.000000000],[0.053512369,0.117962426,0.001570915,0.141836332,0.000000000],[0.001570915,0.001570915,0.009984515,0.001570915,0.000000000],[0.007696513,0.001570915,0.052151474,0.001570915,0.000000000],[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 [8] // Basepair A7 - C4 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013670424,0.202694703,0.013111240,0.122296464,0.000000000],[0.014703520,0.011594218,0.091070574,0.013895076,0.000000000],[0.012868105,0.106114901,0.002831594,0.242445403,0.000000000],[0.089753694,0.014939126,0.017249809,0.030761150,0.000000000],[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 G8 - U3 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
