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 [10] // Initial node C1004 - G1151 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008817364,0.018381954,0.009785358,0.206269672,0.000000000],[0.020516944,0.008438985,0.223661289,0.010919998,0.000000000],[0.009843600,0.184652701,0.001994662,0.022747658,0.000000000],[0.226368298,0.010661853,0.024935691,0.012003973,0.000000000],[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 [10] // Basepair C1004 - G1151 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.375000000,0.541666667,0.041666667,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.541666667,0.375000000,0.041666667,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.708333333,0.208333333,0.041666667,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left
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 [5] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [5] | Right Index [9] | Norm Constant [0.999999999999999] // Cluster node C1008:G1011 and C1150:C1150
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009160501,0.019617847,0.010363923,0.212411613,0.000000000],[0.017414703,0.008074462,0.208142248,0.011590854,0.000000000],[0.010317943,0.237552545,0.001992866,0.024923795,0.000000000],[0.182586497,0.011794457,0.022702265,0.011353480,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1011 - C1150 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.108026987,0.108970689,0.008009132,0.006289163,0.000000000],[0.162368586,0.088700096,0.001351892,0.090898797,0.000000000],[0.006358471,0.028715989,0.034561486,0.088161796,0.000000000],[0.071026857,0.108115302,0.001351892,0.087092865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1008 - A1009 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1010
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 [9] | Right Index [8] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
