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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G1651 - C2006 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5J7L|1|DA|A|1652
InitialNode  | Left Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.642857143,0.071428571,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 5J7L|1|DA|G|1653
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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 5J7L|1|DA|A|1654
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 [5] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.197486077,0.155378232,0.150349437,0.148252769,0.000000000],[0.039234368,0.077744071,0.001637813,0.146550779,0.000000000],[0.001637813,0.001637813,0.013228560,0.001637813,0.000000000],[0.009623119,0.001637813,0.052325709,0.001637813,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1655 - A2005 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003637459,0.006522837,0.004181706,0.075822585,0.000000000],[0.054137016,0.025932524,0.605573545,0.036820353,0.000000000],[0.004228668,0.077456358,0.000797078,0.008950521,0.000000000],[0.076805549,0.005067957,0.010211137,0.003854705,0.000000000],[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 C1656 - G2004 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
