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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009278847,0.019324516,0.010566130,0.191913241,0.000000000],[0.016298546,0.009098841,0.193539411,0.012663253,0.000000000],[0.010448787,0.264585590,0.001991650,0.025514464,0.000000000],[0.189457119,0.013143234,0.022364576,0.009811793,0.000000000],[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 [7] // Basepair G33 - C22 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.156208382,0.015747833,0.080665831,0.025131707,0.000000000],[0.231578224,0.026301300,0.027664507,0.021823405,0.000000000],[0.090678134,0.024729616,0.003730569,0.016550662,0.000000000],[0.029343356,0.021214564,0.214645878,0.013986030,0.000000000],[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 [2] | Right Index [6] // Basepair A34 - A21 cWW 
ClusterNode  | Deletion Probability [0.0000000123740933] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.249846784555315] // Cluster node 6DME|1|A|A|35:6DME|1|A|G|36 and 6DME|1|A|C|20:6DME|1|A|C|20
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.011623860,0.132376000,0.011552172,0.163328520,0.000000000],[0.015467301,0.010456880,0.133220571,0.012393501,0.000000000],[0.011421606,0.136002279,0.002450521,0.181919338,0.000000000],[0.122821200,0.013119015,0.018990684,0.022856552,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|G|36 - 6DME|1|A|C|20 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.105488956,0.098299466,0.093939886,0.053122947,0.000000000],[0.083214750,0.083846198,0.001719570,0.012338546,0.000000000],[0.013044424,0.001719570,0.117710338,0.080417647,0.000000000],[0.086228482,0.087736867,0.001719570,0.079452783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|A|35 - 6DME|1|A|G|36 cSH 
Insertion    | Location [1] | Length Distribution [0.708546015,0.147571638,0.142770506,0.001061303,0.000050538] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
InitialNode  | Left Length Distribution [0.992332775,0.007314709,0.000352516] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992332775,0.007314709,0.000352516] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster
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
