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 [0.0000244705618206] | Pair Probability [[0.008549811,0.018833463,0.009436267,0.235637538,0.000000000],[0.015951852,0.008650378,0.179151811,0.010616745,0.000000000],[0.009378286,0.235581363,0.001862721,0.034920332,0.000000000],[0.187508016,0.011058813,0.023061826,0.009800778,0.000000000],[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 [1] | Right Index [9] // Basepair G59 - C67 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.033333333,0.900000000,0.033333333,0.033333333,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5SWD|1|B|C|60
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 [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.900000000,0.033333333,0.033333333,0.033333333,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 5SWD|1|B|A|66
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 [3] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.175120870,0.016977452,0.016576027,0.006903952,0.000000000],[0.293785413,0.014961987,0.001900552,0.007360351,0.000000000],[0.174731717,0.001900552,0.055641936,0.005865017,0.000000000],[0.198376040,0.014627322,0.008485558,0.006785253,0.000000000],[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 C61 - A65 cSW 
HairpinNode  | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U62:A64
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.070934828,0.081279033,0.003963804,0.066646368,0.000000000],[0.063987010,0.079149636,0.000868314,0.081125505,0.000000000],[0.060667246,0.000868314,0.074217992,0.118394426,0.000000000],[0.072115706,0.071492142,0.000868314,0.153421361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - U63 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.983870968,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.005376344,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.005376344,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.005376344,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A64
