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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009144557,0.019838405,0.010084783,0.214730832,0.000000000],[0.017733483,0.009341630,0.192608427,0.011332799,0.000000000],[0.010033209,0.214437463,0.002002136,0.035555344,0.000000000],[0.202636174,0.011658290,0.028412642,0.010449825,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | 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 [12] // Basepair G7 - C66 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [11] // Fixed node on left for 2CSX|1|C|U|8
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 [11] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [3] | Right Index [11] // Junction node G10 - C65 ID J9502
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009368009,0.020030415,0.010540131,0.205635456,0.000000000],[0.016690726,0.009279029,0.195504376,0.012336141,0.000000000],[0.010440720,0.238674882,0.002020236,0.031139040,0.000000000],[0.192537250,0.012857479,0.022703477,0.010242632,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Basepair G10 - C25 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [5] | Right Index [11] // Initial node 2CSX|1|C|G|26 - 2CSX|1|C|C|65 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.642857143,0.071428571,0.214285714,0.071428571,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left for 2CSX|1|C|C|25
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 [6] | Right Index [11] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [6] | Right Index [11] // Junction node G27 - C65 ID J344
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010565328,0.072203042,0.011348759,0.171904585,0.000000000],[0.017188563,0.009967747,0.186218041,0.013319109,0.000000000],[0.011289177,0.187214431,0.002254192,0.092076175,0.000000000],[0.162578230,0.013577401,0.022316085,0.015979133,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair G27 - C43 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] | Right Index [11] // Initial node 2CSX|1|C|A|44 - 2CSX|1|C|C|65 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.214285714,0.357142857,0.357142857,0.071428571,0.000000000] | Position [1] | Left Index [8] | Right Index [11] // Fixed node on left for 2CSX|1|C|C|43
InitialNode  | Left Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Left Letter Distribution [0.083333333,0.083333333,0.250000000,0.583333333,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.357142857,0.071428571,0.500000000,0.071428571,0.000000000] | Position [1] | Left Index [9] | Right Index [11] // Fixed node on left for 2CSX|1|C|A|44
InitialNode  | Left Length Distribution [0.001959824,0.201861832,0.591866732,0.201959824,0.002253797,0.000097991] | Left Letter Distribution [0.041666667,0.375000000,0.125000000,0.458333333,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009243119,0.017930843,0.010492436,0.193613753,0.000000000],[0.018805252,0.009393104,0.217410587,0.012666299,0.000000000],[0.010496202,0.216920274,0.002021022,0.023996287,0.000000000],[0.204712248,0.012536017,0.029873140,0.009889417,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Basepair G49 - C65 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
