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 [16] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 [16] // Basepair C30 - G52 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [2] | Right Index [15] // Fixed node on left for 8CRE|1|1|U|31
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [15] // Fixed node on right for 8CRE|1|1|A|50
InitialNode  | Left Length Distribution [1.000000000] | 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 [14] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[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 [14] // Basepair G32 - A50 tSH 
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.018593320,0.041379046,0.004114731,0.440599350,0.000000000],[0.004114731,0.331568716,0.009863283,0.004114731,0.000000000],[0.019312206,0.004114731,0.031292185,0.023873178,0.000000000],[0.004114731,0.004114731,0.018300908,0.040529420,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Left Index [4] | Right Index [13] // Basepair A33 - U49 tHW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.423555925,0.045267352,0.002701525,0.002756200,0.000000000],[0.347000771,0.000563471,0.048036311,0.005354151,0.000000000],[0.019665174,0.047422412,0.001406423,0.000563471,0.000000000],[0.026789942,0.027789929,0.000563471,0.000563471,0.000000000],[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 [5] | Right Index [12] // Basepair A34 - A47 tHH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.087494077,0.121692735,0.139732981,0.138877570,0.000000000],[0.130741883,0.171560190,0.001590790,0.152966086,0.000000000],[0.001590790,0.001590790,0.007372771,0.001590790,0.000000000],[0.006899277,0.001590790,0.033117691,0.001590790,0.000000000],[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 [6] | Right Index [11] // Basepair C35 - C46 tHS 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003879780,0.071159900,0.003463989,0.006050075,0.000000000],[0.004288078,0.004623609,0.005171369,0.003802660,0.000000000],[0.003391639,0.005268056,0.001069338,0.013660999,0.000000000],[0.036996003,0.028827946,0.030683553,0.777663006,0.000000000],[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 [7] | Right Index [10] // Basepair U36 - U45 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009177479,0.018274610,0.010201403,0.196065482,0.000000000],[0.020197122,0.009641546,0.197064662,0.011676789,0.000000000],[0.010173530,0.207057088,0.002039267,0.024050960,0.000000000],[0.219982557,0.011400443,0.042929120,0.010067941,0.000000000],[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 [8] | Right Index [9] // Basepair U37 - A44 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
