Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.066624459375454] // Cluster node 8CRE|1|CM|U|1363:8CRE|1|CM|C|1365 and 8CRE|1|CM|A|1333:8CRE|1|CM|A|1333
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|1363 - 8CRE|1|CM|A|1333 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.069668957,0.069985942,0.003916025,0.070855926,0.000000000],[0.069330701,0.079833341,0.000864144,0.071667035,0.000000000],[0.070563039,0.000864144,0.072678473,0.082277753,0.000000000],[0.071086215,0.070395388,0.000864144,0.195148774,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|1363 - 8CRE|1|CM|U|1364 cSH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.090686381,0.097185987,0.008449069,0.092553141,0.000000000],[0.092777259,0.094922194,0.001079314,0.012187904,0.000000000],[0.013636301,0.001079314,0.098454187,0.087826315,0.000000000],[0.092620430,0.127539205,0.001079314,0.087923686,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|CM|U|1363 - 8CRE|1|CM|C|1365 cSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003342868,0.006491880,0.003666912,0.072642400,0.000000000],[0.008156663,0.003637899,0.072886805,0.004086814,0.000000000],[0.003674064,0.071953993,0.000756410,0.008528011,0.000000000],[0.549094592,0.026871438,0.138039672,0.026169580,0.000000000],[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 [4] | Right Index [5] // Basepair U1366 - A1330 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
