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 [10] // 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 [10] // Basepair G1910 - C1920 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.029411765,0.029411765,0.029411765,0.911764706,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 9DFE|1|1A|PSU|1911
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 [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [3] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|A|1912:9DFE|1|1A|A|1912 and 9DFE|1|1A|PSU|1917:9DFE|1|1A|A|1919
Interaction  | Interacting Bases [1,2] | 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]] // Cluster Interaction 9DFE|1|1A|A|1912 - 9DFE|1|1A|PSU|1917 tHW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.239970025,0.200720039,0.010906733,0.041939827,0.000000000],[0.030483930,0.041095973,0.000506089,0.020412171,0.000000000],[0.147004449,0.001663893,0.042884793,0.120378914,0.000000000],[0.031778319,0.028747204,0.000506089,0.041001552,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|1918 - 9DFE|1|1A|A|1919 cSH 
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node C1914:A1916
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1914
Interaction  | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1915
Interaction  | Interacting Bases [3,3] | 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 A1916
