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 [0.0000001233745871] | Pair Probability [[0.008763342,0.015714778,0.010074541,0.182671298,0.000000000],[0.018632366,0.008925211,0.291130597,0.012672481,0.000000000],[0.010187681,0.186607373,0.001920315,0.021563540,0.000000000],[0.185039448,0.012209691,0.024600607,0.009286731,0.000000000],[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 [0.004503490,0.990767845,0.004503490,0.000225175] | Right Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Left Index [1] | Right Index [8] // Basepair C40 - G29 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 7QQX|1|A|G|27
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 [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.884615385,0.038461538,0.038461538,0.038461538,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 7QQX|1|A|A|28
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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.038461538,0.884615385,0.038461538,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 7QQX|1|A|G|29
InitialNode  | Left Length Distribution [0.004503490,0.990767845,0.004503490,0.000225175] | Left Letter Distribution [0.038461538,0.038461538,0.038461538,0.884615385,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.038461538,0.038461538,0.884615385,0.038461538,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 7QQX|1|A|A|42
InitialNode  | Left Length Distribution [1.000000000] | 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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008301821,0.016122213,0.009106566,0.180403230,0.000000000],[0.020256605,0.009034512,0.181010196,0.010149368,0.000000000],[0.009124327,0.178693612,0.001878500,0.021178825,0.000000000],[0.286949092,0.009533382,0.048973372,0.009284379,0.000000000],[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 [5] | Right Index [6] // Basepair U45 - A26 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
