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 [0.0000189382091011] | Pair Probability [[0.002069682,0.021893024,0.001976302,0.047225891,0.000000000],[0.003937879,0.010325520,0.036415643,0.002494338,0.000000000],[0.002317546,0.771568221,0.000375046,0.005542748,0.000000000],[0.072409136,0.014862413,0.004579921,0.002006692,0.000000000],[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 [0.949644782,0.050319517,0.000034808,0.000000893] | Right Letter Distribution [0.388888889,0.500000000,0.055555556,0.055555556,0.000000000] | Left Index [1] | Right Index [9] // Basepair G53 - C61 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.029022403,0.078920570,0.029022403,0.863034623,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right for 4RDX|1|C|U|60
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 [0.419014085,0.080985915,0.320422535,0.179577465,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // Fixed node on right for 4RDX|1|C|G|59
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 [[0.020686121,0.000945860,0.004668472,0.000945860,0.000000000],[0.038099791,0.075515875,0.000945860,0.000945860,0.000000000],[0.002531456,0.002277773,0.007206479,0.004252567,0.000000000],[0.810925671,0.000945860,0.010002044,0.019104452,0.000000000],[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:A57
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000509165,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000509165,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.121690428,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.877291242,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U55
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.095070423,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.848591549,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.003521127,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.052816901,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C56
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.390845070,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.003521127,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.602112676,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.003521127,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A57
