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 C2507 - G2582 from junction 
ClusterNode  | Deletion Probability [0.0000000083323644] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.287606645399910] // Cluster node C2507:C2507 and G2581:G2582
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.010463773,0.016250536,0.012173131,0.138240069,0.000000000],[0.115596488,0.010802910,0.177348529,0.013966399,0.000000000],[0.012360245,0.143711858,0.002511480,0.020205985,0.000000000],[0.151719213,0.013091915,0.149769567,0.011787900,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2507 - G2582 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.005352624,0.005352624,0.005352624,0.005352624,0.000000000],[0.037248401,0.005352624,0.208153515,0.005352624,0.000000000],[0.005352624,0.288273431,0.370197384,0.005352624,0.000000000],[0.005352624,0.005352624,0.037248401,0.005352624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2581 - G2582 cHH 
Insertion    | Location [2] | Length Distribution [0.824969064,0.006874742,0.001718686,0.164993813,0.001374948,0.000068747] | Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
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 [2] | Right Index [3] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015877772,0.298579733,0.014983514,0.042986372,0.000000000],[0.013928943,0.011113763,0.036770561,0.014849632,0.000000000],[0.014651906,0.042627226,0.003323323,0.388936094,0.000000000],[0.036491097,0.016451640,0.014589827,0.033838598,0.000000000],[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 G2508 - U2580 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
