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 [0.0000239574126029] | Pair Probability [[0.009375029,0.019213306,0.010583069,0.196223339,0.000000000],[0.017981530,0.009431632,0.197640103,0.012479529,0.000000000],[0.010497262,0.230209052,0.002038061,0.025338924,0.000000000],[0.205930492,0.012685537,0.030324695,0.010048441,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G46 - C74 cWW 
BasepairNode | Deletion Probability [0.0000000308662435] | Pair Probability [[0.020766168,0.014915127,0.270921994,0.061032507,0.000000000],[0.016103478,0.009769780,0.062350217,0.035233605,0.000000000],[0.284052038,0.061679391,0.003159712,0.017215100,0.000000000],[0.072643346,0.034472605,0.024715997,0.010968936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.250000000,0.250000000,0.083333333,0.416666667,0.000000000] | Left Index [2] | Right Index [7] // Basepair G47 - A73 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.223092516,0.188623178,0.003385883,0.028087646,0.000000000],[0.080527913,0.013832044,0.010438729,0.013892665,0.000000000],[0.003385883,0.011656744,0.188983927,0.163604702,0.000000000],[0.016581701,0.013673680,0.022538464,0.017694326,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair G48 - G71 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009401513,0.017549866,0.010782207,0.195587161,0.000000000],[0.019107025,0.009484786,0.232344244,0.013401212,0.000000000],[0.010842591,0.210218542,0.002049451,0.023823814,0.000000000],[0.196851077,0.013154215,0.025444740,0.009957556,0.000000000],[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 [4] | Right Index [5] // Basepair C49 - G70 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
