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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair U6 - A67 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 6ORD|1|QY|A|7
InitialNode  | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [14] // Fixed node on left for 6ORD|1|QY|U|8
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [14] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [4] | Right Index [14] // Fixed node on right for 6ORD|1|QY|C|48
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [13] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [4] | Right Index [13] // Junction node G10 - U65 ID J8173
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[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 [4] | Right Index [5] // Basepair G10 - C25 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
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 [6] | Right Index [13] // Initial node 6ORD|1|QY|G|26 - 6ORD|1|QY|U|65 from node 
JunctionNode | Branches [2]  | Left Index [6] | Right Index [13] // Junction node G26 - U65 ID J8686
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair G26 - A44 cWW 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [7] | Right Index [8] // Basepair C27 - G43 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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 [10] | Right Index [13] // Initial node 6ORD|1|QY|G|45 - 6ORD|1|QY|U|65 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [10] | Right Index [13] // Fixed node on left for 6ORD|1|QY|A|44
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [11] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [1] | Left Index [11] | Right Index [13] // Fixed node on left for 6ORD|1|QY|G|45
InitialNode  | Left Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [13] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[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 [12] | Right Index [13] // Basepair A49 - U65 cWW 
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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
