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 [14] // Initial node G24 - C516 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003849789,0.050954645,0.004205623,0.179999416,0.000000000],[0.006121463,0.014587489,0.063201629,0.013952603,0.000000000],[0.004152707,0.385104148,0.000824854,0.157082684,0.000000000],[0.060630465,0.023681555,0.007901793,0.023749136,0.000000000],[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 [14] // Basepair G24 - C516 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.944444444,0.018518519,0.018518519,0.018518519,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // 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 [3] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [12] // Basepair G26 - A514 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.042467188,0.049500945,0.000511675,0.002436533,0.000000000],[0.042845019,0.044907828,0.000511675,0.000511675,0.000000000],[0.405791869,0.003581728,0.017352721,0.297927871,0.000000000],[0.046160330,0.044469591,0.000511675,0.000511675,0.000000000],[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 [11] // Basepair G27 - A513 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.064373739,0.064946473,0.330650278,0.069971976,0.000000000],[0.075035834,0.068073375,0.002830312,0.067409074,0.000000000],[0.000775621,0.000775621,0.013712268,0.000775621,0.000000000],[0.003693410,0.000775621,0.235425154,0.000775621,0.000000000],[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 [10] // Basepair A28 - G512 tHS 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003391032,0.035734817,0.003264180,0.055013013,0.000000000],[0.004188811,0.004263654,0.004929479,0.025191782,0.000000000],[0.003200983,0.005020856,0.001027476,0.073233431,0.000000000],[0.006599491,0.003906482,0.004182469,0.766852045,0.000000000],[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 [6] | Right Index [9] // Basepair U29 - U511 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009662245,0.019360521,0.011052990,0.190423231,0.000000000],[0.018822386,0.008416510,0.210415236,0.012452350,0.000000000],[0.010998513,0.231797422,0.002089006,0.025286298,0.000000000],[0.201082692,0.012694357,0.024632354,0.010813889,0.000000000],[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 [7] | Right Index [8] // Basepair G30 - C510 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
