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 U1009 - A957 from junction 
ClusterNode  | Deletion Probability [0.0000000250261143] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.026353112417028] // Cluster node U1009:C1010 and A957:A957
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.007087812,0.013604265,0.008008610,0.153195201,0.000000000],[0.035070638,0.006885220,0.232591707,0.008978534,0.000000000],[0.008055311,0.175121578,0.001625852,0.016955527,0.000000000],[0.246453501,0.008762438,0.068720802,0.008883005,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1009 - A957 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.095591915,0.106824167,0.178277454,0.088940395,0.000000000],[0.177764611,0.079495179,0.019247943,0.088356483,0.000000000],[0.001148396,0.001148396,0.028598932,0.001148396,0.000000000],[0.028336673,0.010198169,0.093774496,0.001148396,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1010 - A957 tHS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.071009696,0.093309902,0.007442406,0.005625961,0.000000000],[0.146912668,0.074881625,0.001218629,0.076253838,0.000000000],[0.062794928,0.037675486,0.014189529,0.069006930,0.000000000],[0.088994680,0.163818414,0.010445824,0.076419484,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1009 - C1010 cSH 
Insertion    | Location [1] | Length Distribution [0.743300802,0.209903027,0.046727319,0.000066152,0.000002700] | Letter Distribution [0.766666667,0.166666667,0.033333333,0.033333333,0.000000000]// Insertion after nucleotide 1, position 1 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 [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006974620,0.013674620,0.007915035,0.148008959,0.000000000],[0.014958019,0.006302134,0.273084914,0.008986373,0.000000000],[0.007935635,0.223147879,0.001534242,0.017694250,0.000000000],[0.233663470,0.008895267,0.018972439,0.008252145,0.000000000],[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 C1011 - G956 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
