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 [0.0000001231336240] | Pair Probability [[0.009271545,0.017981432,0.010607783,0.192505806,0.000000000],[0.017981779,0.009265445,0.226529308,0.013026479,0.000000000],[0.010607796,0.226528663,0.002010668,0.024167927,0.000000000],[0.192506087,0.013026424,0.024168288,0.009814571,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G14 - C35 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 7Q80|1|B|A|15
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.687500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 7Q80|1|B|C|16
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 [4] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 7Q80|1|C|A|33
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 [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.687500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 7Q80|1|C|C|32
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 [4] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010235899,0.013402768,0.044927279,0.028238513,0.000000000],[0.398656227,0.037567338,0.031924485,0.014551830,0.000000000],[0.013344848,0.026925523,0.003290246,0.013916712,0.000000000],[0.035480019,0.013261304,0.301083025,0.013193984,0.000000000],[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 [7] // Basepair C17 - A31 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008996772,0.016133374,0.010342897,0.187537126,0.000000000],[0.019128677,0.009162952,0.244316465,0.013010038,0.000000000],[0.010459051,0.191578047,0.001971467,0.050069857,0.000000000],[0.189968357,0.012534922,0.025255896,0.009534102,0.000000000],[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 [5] | Right Index [6] // Basepair C18 - G30 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
