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 [9] // Initial node G963 - C994 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.005920700,0.042892868,0.006869810,0.113031849,0.000000000],[0.011260389,0.017890463,0.134015667,0.007991732,0.000000000],[0.006880836,0.473352674,0.001259882,0.014909433,0.000000000],[0.113114749,0.029325018,0.015190513,0.006093416,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G963 - C994 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G964:U967 and U993:U993
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.013748369,0.119816711,0.013578679,0.093317534,0.000000000],[0.021353163,0.016649569,0.079603771,0.014822702,0.000000000],[0.013384072,0.079523629,0.003964907,0.040938747,0.000000000],[0.101704498,0.015772974,0.022441654,0.349379021,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U967 - U993 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.056782158,0.057669685,0.019735388,0.016478813,0.000000000],[0.071586160,0.068179769,0.004118188,0.059337231,0.000000000],[0.389215811,0.015449748,0.031090124,0.065799650,0.000000000],[0.021391896,0.055519563,0.004118188,0.063527626,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G964 - A966 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion G965
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009933419,0.017038443,0.011544982,0.190528657,0.000000000],[0.020571967,0.008484264,0.242033011,0.013790371,0.000000000],[0.011692161,0.206400787,0.002129068,0.023556849,0.000000000],[0.191635263,0.013137326,0.027308888,0.010214543,0.000000000],[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 [6] | Right Index [7] // Basepair C968 - G992 cWW 
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
