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 [8] // Initial node C105 - G126 from junction 
BasepairNode | Deletion Probability [0.0000040113606825] | Pair Probability [[0.009303385,0.020606440,0.010352389,0.224394684,0.000000000],[0.019084521,0.008572365,0.213736718,0.011538453,0.000000000],[0.010368187,0.203786078,0.002067853,0.025420108,0.000000000],[0.192395003,0.011467640,0.024007914,0.012898260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.824969064,0.008249691,0.165337550,0.001374948,0.000068747] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | 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 [8] // Basepair C105 - G126 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [7] | Norm Constant [0.325985083110521] // Cluster node A106:A106 and G123:A125
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.090273333,0.187976707,0.013697566,0.032978943,0.000000000],[0.017577621,0.017891685,0.020685705,0.015101851,0.000000000],[0.013432372,0.021069153,0.004311624,0.043901633,0.000000000],[0.027693624,0.016392876,0.017551006,0.459464302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A106 - A125 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.094625064,0.099445771,0.005326262,0.004472504,0.000000000],[0.092560928,0.100307341,0.001118543,0.140439759,0.000000000],[0.083930061,0.005637867,0.010582824,0.124852072,0.000000000],[0.025988045,0.109101383,0.001118543,0.100493033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G123 - A125 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A124
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009579898,0.018858927,0.010968709,0.198510678,0.000000000],[0.018733316,0.008310552,0.229411558,0.012602551,0.000000000],[0.010989873,0.219102584,0.002068376,0.024744711,0.000000000],[0.187963655,0.012508405,0.024679279,0.010966928,0.000000000],[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 [3] | Right Index [4] // Basepair C107 - G122 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
