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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000001233454509] | Pair Probability [[0.008814246,0.017062051,0.009982750,0.203736191,0.000000000],[0.017995454,0.008966216,0.254115499,0.012104262,0.000000000],[0.010047675,0.196752680,0.001928715,0.027582299,0.000000000],[0.185487620,0.011948183,0.023820232,0.009655928,0.000000000],[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 [0.004949270,0.989853997,0.004949270,0.000247463] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C1407 - G1494 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.041666667,0.541666667,0.291666667,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 2OE8|1|A|G|1408
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 [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000017103020118] | Pair Probability [[0.015590537,0.044858556,0.013802746,0.018917469,0.000000000],[0.254112179,0.219102600,0.002204035,0.210550557,0.000000000],[0.023578619,0.002204035,0.050111604,0.009256143,0.000000000],[0.039746633,0.021507816,0.010262894,0.064193577,0.000000000],[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 [0.498635574,0.498635574,0.002604813,0.000124039] | Right Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000] | Left Index [3] | Right Index [6] // Basepair C1409 - A1492 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008706313,0.017653246,0.009722871,0.193940148,0.000000000],[0.018022506,0.008975920,0.194839837,0.011263126,0.000000000],[0.009694011,0.223052450,0.001916212,0.025586316,0.000000000],[0.222751666,0.011216613,0.033085609,0.009573157,0.000000000],[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 U1410 - A1490 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
