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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C1914 - G1930 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1915 - A1929 tSH 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.044295562,0.040459734,0.000491920,0.002419854,0.000000000],[0.044466678,0.041838855,0.000491920,0.000491920,0.000000000],[0.045742956,0.000491920,0.003040306,0.040838473,0.000000000],[0.409764308,0.318278721,0.003443437,0.003443437,0.000000000],[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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.055555556,0.611111111,0.277777778,0.000000000] | Left Index [3] | Right Index [10] // Basepair U1916 - A1928 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.726985591,0.075925561,0.004531187,0.004622891,0.000000000],[0.124046326,0.000201430,0.017172088,0.001914009,0.000000000],[0.007029934,0.016952631,0.000502770,0.000201430,0.000000000],[0.009576906,0.009934383,0.000201430,0.000201430,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A1917 - A1926 tHH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.113379207,0.104112383,0.182922785,0.129742854,0.000000000],[0.120606222,0.115065551,0.001434268,0.119892387,0.000000000],[0.001434268,0.001434268,0.007766243,0.001434268,0.000000000],[0.006940992,0.001434268,0.090965772,0.001434268,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1918 - G1925 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003569469,0.006400915,0.004103544,0.074405341,0.000000000],[0.053125109,0.025447804,0.612946003,0.036132122,0.000000000],[0.004149628,0.076008576,0.000782179,0.008783222,0.000000000],[0.075369931,0.004973229,0.010020275,0.003782654,0.000000000],[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 [6] | Right Index [7] // Basepair C1919 - G1924 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
