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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009252003,0.018892763,0.010549706,0.191568511,0.000000000],[0.016731454,0.009121701,0.203695325,0.012732248,0.000000000],[0.010465893,0.254442413,0.001991715,0.025065205,0.000000000],[0.189814218,0.013075076,0.022815388,0.009786380,0.000000000],[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 [10] // Basepair G4 - C53 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.027927600,0.013680095,0.393365084,0.016383004,0.000000000],[0.038025646,0.009098313,0.017695249,0.039762803,0.000000000],[0.324054816,0.017893971,0.003372903,0.014884762,0.000000000],[0.016351114,0.042012656,0.014565881,0.010926104,0.000000000],[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 [2] | Right Index [9] // Basepair A5 - G52 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.242329585,0.019554064,0.024112449,0.119259274,0.000000000],[0.045263942,0.009132029,0.152932728,0.017221854,0.000000000],[0.019925147,0.121857365,0.030651698,0.023568003,0.000000000],[0.120395959,0.018162068,0.022152059,0.013481776,0.000000000],[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 [3] | Right Index [8] // Basepair C6 - G51 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.055555556,0.722222222,0.055555556,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 8K85|1|A|G|7
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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 8K85|1|A|G|8
InitialNode  | Left Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Left Letter Distribution [0.312500000,0.062500000,0.062500000,0.562500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009117787,0.016733999,0.010467584,0.189844861,0.000000000],[0.018895995,0.009236003,0.254474892,0.013077223,0.000000000],[0.010551423,0.203726527,0.001992038,0.022818912,0.000000000],[0.191599712,0.012734286,0.025069445,0.009659312,0.000000000],[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 C10 - G50 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
