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 C926 - G947 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009685694,0.019182219,0.010986155,0.195803621,0.000000000],[0.020623118,0.008749922,0.213456437,0.012400460,0.000000000],[0.010991697,0.213086471,0.002130191,0.024759915,0.000000000],[0.208179451,0.012376361,0.026149698,0.011438589,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair C926 - G947 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [2] | Left Index [4] | 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 [0.993970181,0.005999820,0.000029999] | 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
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [7] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010041880,0.019391351,0.011641525,0.191240548,0.000000000],[0.018213986,0.008378062,0.218250356,0.013353236,0.000000000],[0.011592485,0.230126887,0.002128781,0.026054525,0.000000000],[0.190871828,0.013570829,0.024804352,0.010339370,0.000000000],[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 C929 - G943 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
