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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000001177014991] | Pair Probability [[0.009106890,0.016989933,0.010236072,0.193756118,0.000000000],[0.020753249,0.009584275,0.218305904,0.012178967,0.000000000],[0.010305927,0.194944276,0.002027252,0.022809627,0.000000000],[0.218224654,0.011603275,0.039263037,0.009910544,0.000000000],[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 [0.250611247,0.495110024,0.250764059,0.003361858,0.000152812] | Right Letter Distribution [0.250000000,0.250000000,0.083333333,0.416666667,0.000000000] | Left Index [1] | Right Index [8] // Basepair U117 - A234 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 1L9A|1|B|A|118
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.416666667,0.250000000,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 1L9A|1|B|G|232
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.325937747,0.020728829,0.219818448,0.021852677,0.000000000],[0.016073860,0.009828018,0.022584562,0.033685971,0.000000000],[0.187974472,0.022967102,0.004685027,0.022045688,0.000000000],[0.021460655,0.036490627,0.017553975,0.016312343,0.000000000],[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 [3] | Right Index [6] // Basepair A119 - A231 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009326698,0.018435943,0.010553497,0.195602659,0.000000000],[0.018760973,0.009472791,0.208714091,0.012603753,0.000000000],[0.010528061,0.219157994,0.002038177,0.024530043,0.000000000],[0.206573441,0.012562820,0.031136373,0.010002685,0.000000000],[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 G120 - C230 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
