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 [[0.009117787,0.016733999,0.010467584,0.189844861,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | 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 C1874 - G1867 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.143645405,0.086894129,0.001403410,0.007281600,0.000000000],[0.124060837,0.100221149,0.001403410,0.001403410,0.000000000],[0.179024738,0.001403410,0.008690899,0.088735625,0.000000000],[0.129083474,0.123941684,0.001403410,0.001403410,0.000000000],[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 [8] // Basepair G1875 - A1866 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.107987991,0.096183028,0.135018428,0.138788209,0.000000000],[0.059244635,0.071098115,0.001879416,0.093517091,0.000000000],[0.001879416,0.001879416,0.136208906,0.001879416,0.000000000],[0.085661198,0.001879416,0.065015903,0.001879416,0.000000000],[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 [7] // Basepair A1876 - U1865 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 5J7L|1|DA|G|1867
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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012482246,0.170477642,0.012008947,0.147775691,0.000000000],[0.014574816,0.010875866,0.100377512,0.012477159,0.000000000],[0.011819843,0.114007625,0.002607761,0.232252099,0.000000000],[0.100380093,0.013452335,0.017305668,0.027124696,0.000000000],[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 G1878 - U1864 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
