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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008819696,0.016095325,0.010040343,0.185509802,0.000000000],[0.019341809,0.009113711,0.257281078,0.012334023,0.000000000],[0.010133974,0.188240480,0.001946087,0.021872140,0.000000000],[0.207419317,0.011828074,0.030567544,0.009456597,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [5] // Basepair C2540 - G2523 cWW 
ClusterNode  | Deletion Probability [0.0000000006231837] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.291215390086696] // Cluster node 5J7L|1|DA|A|2541:5J7L|1|DA|G|2543 and 5J7L|1|DA|U|2522:5J7L|1|DA|U|2522
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.023039055,0.037604626,0.003778167,0.442036856,0.000000000],[0.018790543,0.015723906,0.003778167,0.003778167,0.000000000],[0.017806511,0.003778167,0.341001612,0.022929794,0.000000000],[0.018585580,0.039812517,0.003778167,0.003778167,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|2541 - 5J7L|1|DA|U|2522 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.013552813,0.220298406,0.012725731,0.103426658,0.000000000],[0.013543262,0.011293356,0.068735729,0.013246761,0.000000000],[0.012476886,0.092046155,0.002795829,0.305922153,0.000000000],[0.067951837,0.014319241,0.015357955,0.032307228,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|2543 - 5J7L|1|DA|U|2522 cWW 
Insertion    | Location [1] | Length Distribution [0.005492996,0.988739357,0.005492996,0.000274650] | Letter Distribution [0.863636364,0.045454545,0.045454545,0.045454545,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | Left Length Distribution [0.992346266,0.007389813,0.000263922] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992346266,0.007389813,0.000263922] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [3] // New Initial node after Cluster
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
