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 [0.000000000000000000381350679448848525461538405014458471171802] | Num Left Bases [1] | Num Right Bases [3] | Left Index [1] | Right Index [6] | Norm Constant [0.252874089601252] // Cluster node 6XJQ|1|A|G|26:6XJQ|1|A|G|26 and 6XJQ|1|A|C|29:6XJQ|1|A|C|35
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6XJQ|1|A|G|26 - 6XJQ|1|A|C|35 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.002803848,0.003708984,0.002495174,0.003379005,0.000000000],[0.308045541,0.337328559,0.003274276,0.315256992,0.000000000],[0.004112495,0.000467754,0.004931670,0.001873112,0.000000000],[0.002874091,0.004645558,0.002188090,0.002614851,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6XJQ|1|A|C|29 - 6XJQ|1|A|C|35 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6XJQ|1|A|G|30
Insertion    | Location [3] | Length Distribution [0.000000000,0.000000000,0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 5, position 3 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C27:C28
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C28
