Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [9] // Initial node U172 - G194 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010119758,0.015381041,0.011773713,0.112831708,0.000000000],[0.142681571,0.011045710,0.145037150,0.013259572,0.000000000],[0.011944510,0.123602112,0.002515582,0.018248559,0.000000000],[0.144091318,0.012444267,0.213280671,0.011742757,0.000000000],[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 [9] // Basepair U172 - G194 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.033333333,0.100000000,0.033333333,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000105840881771] | Pair Probability [[0.172671224,0.085919845,0.001808419,0.104872879,0.000000000],[0.114691441,0.055711829,0.001808419,0.001808419,0.000000000],[0.106569534,0.001808419,0.128790389,0.037772399,0.000000000],[0.093027893,0.089122053,0.001808419,0.001808419,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G173 - A192 tSH 
BasepairNode | Deletion Probability [0.0000160934329480] | Pair Probability [[0.177077827,0.121481100,0.141533733,0.119606275,0.000000000],[0.111119146,0.107057298,0.001305849,0.133418568,0.000000000],[0.019569829,0.001305849,0.009851328,0.001305849,0.000000000],[0.009110720,0.001305849,0.043644933,0.001305849,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A174 - A191 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009506456,0.037620190,0.010717425,0.174190618,0.000000000],[0.017026146,0.007935753,0.231011961,0.012191369,0.000000000],[0.010702666,0.222205897,0.002030899,0.054241435,0.000000000],[0.164390525,0.012266178,0.022436068,0.011526414,0.000000000],[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 G175 - C190 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
