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 [0.0000000884732057] | Pair Probability [[0.008274927,0.015650103,0.009351310,0.192217362,0.000000000],[0.017817497,0.008545554,0.274976677,0.011296358,0.000000000],[0.009426807,0.176441776,0.001824698,0.023834721,0.000000000],[0.202842690,0.010954954,0.027500026,0.009044539,0.000000000],[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 [0.064637602,0.808067083,0.126761520,0.000514383,0.000019411] | Right Letter Distribution [0.657894737,0.026315789,0.078947368,0.236842105,0.000000000] | Left Index [1] | Right Index [9] // Basepair C998 - G1157 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.016277056,0.003602139,0.016906387,0.003602139,0.000000000],[0.036224250,0.290263531,0.003602139,0.003602139,0.000000000],[0.003602139,0.008634564,0.027393960,0.016021072,0.000000000],[0.495595109,0.003602139,0.020899176,0.050172064,0.000000000],[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 [8] // Basepair U999 - A1155 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.027777778,0.083333333,0.138888889,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 5J7L|1|DA|A|1000
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 [4] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.047101768,0.047401697,0.418853588,0.069739221,0.000000000],[0.047827225,0.048182683,0.002935466,0.049142960,0.000000000],[0.000552821,0.000552821,0.014551714,0.000552821,0.000000000],[0.002637555,0.000552821,0.248862017,0.000552821,0.000000000],[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 [4] | Right Index [7] // Basepair A1001 - G1154 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008421689,0.017542337,0.009482111,0.193883303,0.000000000],[0.015798629,0.008437537,0.185832708,0.011140979,0.000000000],[0.009414466,0.275282328,0.001826912,0.025852040,0.000000000],[0.192468710,0.011417574,0.024041183,0.009157494,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G1002 - C1153 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
