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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003460721,0.008205641,0.003696126,0.542567125,0.000000000],[0.006530862,0.003571569,0.072386052,0.027032792,0.000000000],[0.003688931,0.073324465,0.000760952,0.138868552,0.000000000],[0.073078592,0.004111354,0.008579218,0.030137047,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [9] // Basepair A844 - U934 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000381350679448848525461538405014458471171802] | Num Left Bases [4] | Num Right Bases [3] | Left Index [2] | Right Index [8] | Norm Constant [0.251730496825129] // Cluster node 5J7L|1|DA|A|845||A:5J7L|1|DA|C|848 and 5J7L|1|DA|G|930:5J7L|1|DA|A|933
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|848 - 5J7L|1|DA|G|930 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.017376847,0.042940161,0.003635060,0.373406976,0.000000000],[0.017064104,0.039159201,0.015138258,0.041984236,0.000000000],[0.003635060,0.018018508,0.017398138,0.291185254,0.000000000],[0.041525169,0.034858775,0.017919960,0.024754293,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|845||A - 5J7L|1|DA|U|932 tWW 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.022793898,0.008853192,0.005000689,0.099064837,0.000000000],[0.055617554,0.004961122,0.099398140,0.005573323,0.000000000],[0.025052211,0.098126034,0.001031541,0.011629929,0.000000000],[0.525671381,0.005235067,0.026892751,0.005098331,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|847||A - 5J7L|1|DA|A|933 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.091584266,0.098148224,0.008532723,0.093469509,0.000000000],[0.093695846,0.095862018,0.001090000,0.012308576,0.000000000],[0.013771314,0.001090000,0.099428981,0.088695882,0.000000000],[0.093537464,0.118900979,0.001090000,0.088794218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|846||A - 5J7L|1|DA|C|848 cSH 
Insertion    | Location [5] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 6, position 5 in cluster node
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | 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
