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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.010314056,0.063361168,0.011165057,0.174595639,0.000000000],[0.016420899,0.009731951,0.179035235,0.013043747,0.000000000],[0.011056644,0.210999173,0.002195769,0.082400211,0.000000000],[0.165657257,0.013499233,0.021652982,0.014870977,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [9] // Basepair G943 - C929 cWW 
BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.154836587,0.153392826,0.019758913,0.097087008,0.000000000],[0.014845222,0.011427970,0.063031146,0.015276731,0.000000000],[0.016940995,0.075070742,0.035394807,0.087596551,0.000000000],[0.062228923,0.016707513,0.016892981,0.159511085,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [8] // Basepair G944 - C928 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.013655430,0.014484361,0.099903376,0.134962891,0.000000000],[0.082274911,0.013104784,0.116470566,0.019079598,0.000000000],[0.087339607,0.103957221,0.002528776,0.017655349,0.000000000],[0.126148077,0.019049935,0.138980106,0.010405012,0.000000000],[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 [7] // Basepair A945 - G927 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.312500000,0.312500000,0.312500000,0.000000000] | Position [1] | Left Index [4] | Right Index [6] // Fixed node on left for 1J2B|1|C|C|929
InitialNode  | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [[0.010219218,0.061835778,0.011107030,0.173377702,0.000000000],[0.017950372,0.009812717,0.210199288,0.013287507,0.000000000],[0.011117080,0.179880118,0.002195997,0.080812972,0.000000000],[0.166918894,0.013258429,0.023245708,0.014781190,0.000000000],[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 G947 - C926 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
