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 [0.0000234451146992] | Pair Probability [[0.011136961,0.013848204,0.014138980,0.036912705,0.000000000],[0.299600889,0.027679377,0.041942910,0.015878461,0.000000000],[0.014448515,0.036764849,0.003274049,0.014529563,0.000000000],[0.085355993,0.014536633,0.356531131,0.013420778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair U1257 - G1424 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 8CRE|1|CM|G|1258
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | 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 [0.0000234451146992] | Pair Probability [[0.177014145,0.169762925,0.174600796,0.217520950,0.000000000],[0.016824339,0.013609444,0.001883947,0.013791422,0.000000000],[0.024400012,0.001883947,0.152081736,0.009268302,0.000000000],[0.007067753,0.007412749,0.005925146,0.006952386,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1260 - U1423 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008946623,0.017374423,0.009813872,0.194415132,0.000000000],[0.021829934,0.009736222,0.195069241,0.010937668,0.000000000],[0.009833013,0.192572728,0.002024403,0.022823782,0.000000000],[0.231566497,0.010273839,0.052777129,0.010005495,0.000000000],[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 U1261 - A1422 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
