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 [0.0000239574126029] | Pair Probability [[0.009277126,0.019957246,0.010267742,0.217429628,0.000000000],[0.017754432,0.009419825,0.205851134,0.011718309,0.000000000],[0.010258285,0.207085186,0.002025617,0.038411566,0.000000000],[0.194231032,0.012046506,0.023601563,0.010664802,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G51 - C61 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.250000000,0.416666667,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 4V7M|1|AY|G|52
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 4V7M|1|AY|A|58
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 4V7M|1|AY|A|57
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 4V7M|1|AY|G|56
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000000006078908] | Pair Probability [[0.017820521,0.003943710,0.018509527,0.044576464,0.000000000],[0.039659197,0.317787634,0.003943710,0.003943710,0.000000000],[0.003943710,0.009453333,0.029991579,0.017540263,0.000000000],[0.423217119,0.003943710,0.022880930,0.038844885,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.250000000,0.250000000,0.150000000,0.350000000,0.000000000] | Left Index [3] | Right Index [5] // Basepair U53 - A57 tWH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U54:U54
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U54
