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 [[0.009966691,0.016017398,0.011961436,0.130841452,0.000000000],[0.128758310,0.016489380,0.156152284,0.014169946,0.000000000],[0.012106818,0.143449627,0.002502611,0.020019512,0.000000000],[0.150350483,0.013545569,0.162475729,0.011192755,0.000000000],[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 U4 - G21 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.066346764,0.034815187,0.000717135,0.003526002,0.000000000],[0.309426988,0.205155555,0.002849893,0.002849893,0.000000000],[0.134850329,0.001328628,0.007559591,0.086616417,0.000000000],[0.077108253,0.065415094,0.000717135,0.000717135,0.000000000],[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 C5 - A20 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.029111875,0.378210903,0.003401157,0.034203112,0.000000000],[0.036153770,0.024779621,0.011874409,0.003401157,0.000000000],[0.097296540,0.003401157,0.030585081,0.015291671,0.000000000],[0.003401157,0.003401157,0.031351173,0.294136064,0.000000000],[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 [3] | Right Index [10] // Basepair A6 - C19 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.022328159,0.033013448,0.060776904,0.038427415,0.000000000],[0.071653768,0.052532348,0.005685807,0.037933337,0.000000000],[0.001152463,0.001152463,0.559204546,0.001152463,0.000000000],[0.069845296,0.001152463,0.042836657,0.001152463,0.000000000],[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 G7 - G18 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018950070,0.013663575,0.250759906,0.052536113,0.000000000],[0.105032401,0.016930834,0.021914310,0.035835594,0.000000000],[0.289516627,0.020470187,0.003425600,0.014717903,0.000000000],[0.021680039,0.033784356,0.089204342,0.011578143,0.000000000],[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 G8 - A17 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009439388,0.016795352,0.010908234,0.161262394,0.000000000],[0.074605705,0.012992213,0.174340184,0.012667152,0.000000000],[0.010976477,0.172344453,0.002248601,0.021565418,0.000000000],[0.192963155,0.012143402,0.104225661,0.010522212,0.000000000],[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 U9 - A16 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
