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 [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[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 [8] // Basepair G12 - C23 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [7] | Norm Constant [0.285362311623589] // Cluster node 3ZGZ|1|B|G|13:3ZGZ|1|B|G|13 and 3ZGZ|1|B|G|21:3ZGZ|1|B|A|22
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.104754894,0.110429214,0.092008273,0.210537532,0.000000000],[0.025184133,0.022941046,0.002489079,0.022167953,0.000000000],[0.151236163,0.002489079,0.204982108,0.011956389,0.000000000],[0.010024486,0.010464037,0.008480656,0.009854957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3ZGZ|1|B|G|13 - 3ZGZ|1|B|G|21 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.104355937,0.045189764,0.001019127,0.005611930,0.000000000],[0.093142996,0.061480989,0.001019127,0.001019127,0.000000000],[0.285637838,0.002759710,0.015709346,0.197413341,0.000000000],[0.093049013,0.090553501,0.001019127,0.001019127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3ZGZ|1|B|G|13 - 3ZGZ|1|B|A|22 tSH 
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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000000000000001] | Pair Probability [[0.246892522,0.200307206,0.211681907,0.204611433,0.000000000],[0.016004500,0.013053530,0.002177663,0.013247577,0.000000000],[0.021640765,0.002177663,0.027736420,0.010358648,0.000000000],[0.007774354,0.008200965,0.006489923,0.007644924,0.000000000],[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 [0.000000000,0.000000000,0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.029411765,0.147058824,0.441176471,0.382352941,0.000000000] | Left Index [3] | Right Index [5] // Basepair A14 - A20A cWS 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A15:A15
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A15
