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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008037250,0.015279466,0.009105722,0.185990786,0.000000000],[0.016955645,0.008245457,0.282668808,0.011037195,0.000000000],[0.009164108,0.188135037,0.001766318,0.022701851,0.000000000],[0.195874422,0.010773166,0.025536418,0.008728351,0.000000000],[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 [6] // Basepair C8 - G16 cWW 
BasepairNode | Deletion Probability [0.0000038223279522] | Pair Probability [[0.137412152,0.047100721,0.032983169,0.033122936,0.000000000],[0.016244876,0.015224507,0.015868271,0.015489890,0.000000000],[0.036866039,0.149296629,0.019009083,0.382912081,0.000000000],[0.013474369,0.013157189,0.010776463,0.061061624,0.000000000],[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 [0.648604883,0.350398605,0.000952915,0.000043597] | Right Letter Distribution [0.166666667,0.055555556,0.722222222,0.055555556,0.000000000] | Left Index [2] | Right Index [5] // Basepair A9 - A15 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007980787,0.016182142,0.008912632,0.186111802,0.000000000],[0.016520630,0.008227927,0.186936517,0.010324532,0.000000000],[0.008886176,0.237798079,0.001756527,0.023454123,0.000000000],[0.237522360,0.010281895,0.030328475,0.008775394,0.000000000],[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 [3] | Right Index [4] // Basepair G10 - C14 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
