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 [8] // Initial node
BasepairNode | Deletion Probability [0.0000001233745871] | Pair Probability [[0.008763342,0.015714778,0.010074541,0.182671298,0.000000000],[0.018632366,0.008925211,0.291130597,0.012672481,0.000000000],[0.010187681,0.186607373,0.001920315,0.021563540,0.000000000],[0.185039448,0.012209691,0.024600607,0.009286731,0.000000000],[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 [0.004503490,0.990767845,0.004503490,0.000225175] | Right Letter Distribution [0.038461538,0.038461538,0.038461538,0.884615385,0.000000000] | Left Index [1] | Right Index [8] // Basepair C19 - G37 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017253261,0.003818174,0.017920335,0.003818174,0.000000000],[0.038396772,0.307671872,0.003818174,0.003818174,0.000000000],[0.003818174,0.009152416,0.029036892,0.016981924,0.000000000],[0.480916514,0.003818174,0.022152588,0.037608381,0.000000000],[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 [7] // Basepair U20 - A35 tWH 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Cluster node 5BTM|1|A|A|21:5BTM|1|A|G|23 and 5BTM|1|A|U|34:5BTM|1|A|U|34
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.014555516,0.272815045,0.013156744,0.077724733,0.000000000],[0.012610104,0.011752420,0.033477885,0.013236984,0.000000000],[0.012874883,0.038193001,0.002981333,0.397232351,0.000000000],[0.033612521,0.014458846,0.013230546,0.038087087,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5BTM|1|A|G|23 - 5BTM|1|A|U|34 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.372580984,0.269968494,0.013045101,0.039359223,0.000000000],[0.045047905,0.042264576,0.000491836,0.003511848,0.000000000],[0.003543956,0.000491836,0.041145174,0.039703616,0.000000000],[0.047144785,0.041542776,0.000491836,0.039666054,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5BTM|1|A|A|21 - 5BTM|1|A|A|22 cSH 
InitialNode  | Left Length Distribution [0.995173718,0.004600491,0.000225791] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995173718,0.004600491,0.000225791] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
