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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009514109,0.016973007,0.011119951,0.166196516,0.000000000],[0.063759997,0.012217332,0.200761073,0.013467537,0.000000000],[0.011189835,0.189541432,0.002205826,0.022228458,0.000000000],[0.174455388,0.013169422,0.082862780,0.010337335,0.000000000],[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 [8] // Basepair C1440 - G1461 cWW 
BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.075930122,0.074643662,0.001960966,0.109468622,0.000000000],[0.112392528,0.074591685,0.039982692,0.001960966,0.000000000],[0.141548695,0.001960966,0.130458031,0.075388892,0.000000000],[0.080638476,0.075151766,0.001960966,0.001960966,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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] // Basepair G1441 - A1460 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.062500000,0.562500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 4LFB|1|A|G|1442
InitialNode  | Left Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Left Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 4LFB|1|A|G|1443
InitialNode  | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009190185,0.019556070,0.010271277,0.213082011,0.000000000],[0.017097064,0.009222955,0.202911173,0.011925712,0.000000000],[0.010225608,0.224479173,0.001995078,0.033709602,0.000000000],[0.190792347,0.012301885,0.022962688,0.010277172,0.000000000],[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 G1447 - C1459 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
