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 [5] // Initial node G2391 - C2972 from junction 
ClusterNode  | Deletion Probability [0.0000000034550030] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.305651423960523] // Cluster node G2391:G2391 and A2970:C2972
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004733746,0.037240585,0.005339211,0.240859165,0.000000000],[0.008690836,0.014981024,0.097250365,0.012347507,0.000000000],[0.005288794,0.395468482,0.001029139,0.030717388,0.000000000],[0.094380619,0.024015626,0.011358393,0.016299118,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2391 - C2972 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.101253721,0.135894093,0.006054057,0.060998411,0.000000000],[0.104207646,0.097420758,0.001164766,0.100868758,0.000000000],[0.005756469,0.006285621,0.013783047,0.100415395,0.000000000],[0.058267301,0.110073967,0.001164766,0.096391223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2970 - C2972 cSH 
Insertion    | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
InitialNode  | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009472747,0.022988174,0.010372983,0.225098889,0.000000000],[0.018936855,0.008916940,0.195696316,0.011163054,0.000000000],[0.010312898,0.208310389,0.002127705,0.027444663,0.000000000],[0.199992661,0.011428674,0.023422512,0.014314540,0.000000000],[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 [2] | Right Index [3] // Basepair A2393 - U2969 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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
