Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [12] // Initial node G21 - C59 from junction 
BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.003952716,0.056367336,0.004576658,0.075011714,0.000000000],[0.006669351,0.022815069,0.080791377,0.005142338,0.000000000],[0.004519048,0.602973996,0.000833380,0.010689507,0.000000000],[0.074578555,0.037785716,0.009220848,0.004072390,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G21 - C59 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [11] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000008487548749722519800000000000000000000] | Num Left Bases [5] | Num Right Bases [4] | Left Index [2] | Right Index [10] | Norm Constant [0.024808460704894] // Cluster node G22:U28 and A54:A57
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.015164621,0.014596964,0.003316707,0.003316707,0.000000000],[0.341474666,0.012192158,0.003316707,0.102247189,0.000000000],[0.003316707,0.003316707,0.204081524,0.003316707,0.000000000],[0.003316707,0.003316707,0.280392512,0.003316707,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C27 - A54 bif 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009183469,0.022285751,0.009814417,0.220857782,0.000000000],[0.022291510,0.009418174,0.193045342,0.010327057,0.000000000],[0.009814439,0.193043865,0.002150936,0.025717104,0.000000000],[0.220868443,0.010326961,0.025722659,0.015132092,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U28 - A54 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.018651682,0.015154458,0.043678332,0.018110765,0.000000000],[0.016812716,0.009974951,0.024519362,0.398157400,0.000000000],[0.046462097,0.023358245,0.003785496,0.016914760,0.000000000],[0.018238846,0.314182292,0.018739559,0.013259038,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C27 - U55 cWW 
Interaction  | Interacting Bases [5,9] | Pair Probability [[0.343551684,0.013009703,0.002770506,0.012447068,0.000000000],[0.018196343,0.186036580,0.013571899,0.012534088,0.000000000],[0.016782196,0.026237419,0.002770506,0.009403153,0.000000000],[0.286854562,0.033075011,0.013375361,0.009383920,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U28 - A57 tSW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.182627929,0.026212171,0.101178320,0.072488382,0.000000000],[0.052618857,0.023706576,0.024051089,0.016245789,0.000000000],[0.061258760,0.234587796,0.002247839,0.009558020,0.000000000],[0.021287620,0.013586802,0.148929228,0.009414824,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G22 - C26 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G25
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A56
Insertion    | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | 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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
