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 G53 - C61 from junction 
BasepairNode | Deletion Probability [0.0000193016245614] | Pair Probability [[0.002139153,0.026158058,0.002204275,0.047218748,0.000000000],[0.004000509,0.012342162,0.040663371,0.002729041,0.000000000],[0.002398413,0.760163179,0.000418822,0.005891760,0.000000000],[0.068505960,0.017757462,0.005226568,0.002182518,0.000000000],[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 [0.953241325,0.046714116,0.000043488,0.000001071] | Right Letter Distribution [0.357142857,0.500000000,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [9] // Basepair G53 - C61 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.019129288,0.093007916,0.037598945,0.850263852,0.000000000] | 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
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.413636364,0.059090909,0.231818182,0.295454545,0.000000000] | Position [2] | Left Index [2] | 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.019766468,0.002022751,0.010047874,0.002022751,0.000000000],[0.029511360,0.159194382,0.002022751,0.002022751,0.000000000],[0.002022751,0.004894405,0.015362920,0.009262413,0.000000000],[0.693989898,0.002022751,0.011649979,0.034183797,0.000000000],[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 [6] // Basepair U54 - A58 tWH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U55:G57
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000659631,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000659631,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.231530343,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.767150396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U55
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.186363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.004545455,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.059090909,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C56
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.386363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.004545455,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.604545455,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.004545455,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G57
