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 [10] // Initial node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.241220344742765] // Cluster node 5NWQ|1|A|G|29:5NWQ|1|A|A|32 and 5NWQ|1|A|C|20:5NWQ|1|A|C|20
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.003861747,0.056298454,0.004397499,0.079872036,0.000000000],[0.006783263,0.026507815,0.080548829,0.005270297,0.000000000],[0.004348662,0.590132004,0.000828901,0.010618820,0.000000000],[0.078849827,0.038290418,0.009307874,0.004083553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|29 - 5NWQ|1|A|C|20 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.166586913,0.165788799,0.002070551,0.010011986,0.000000000],[0.193757756,0.009129710,0.002070551,0.008278035,0.000000000],[0.216956090,0.002070551,0.002070551,0.006790033,0.000000000],[0.179185112,0.008998530,0.016291903,0.009942930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|29 - 5NWQ|1|A|A|32 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5NWQ|1|A|A|30
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5NWQ|1|A|C|31
InitialNode  | 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 [5] | Right Index [9] // Initial node 5NWQ|1|A|A|33 - 5NWQ|1|A|A|19 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [5] | Right Index [9] // Fixed node on left for 5NWQ|1|A|A|30
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [6] | Right Index [9] | Norm Constant [0.064907758104499] // Cluster node 5NWQ|1|A|G|34:5NWQ|1|A|A|35 and 5NWQ|1|A|U|18:5NWQ|1|A|A|19
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.053818499,0.067941945,0.002465838,0.014965233,0.000000000],[0.031217389,0.030696053,0.002465838,0.002465838,0.000000000],[0.209290967,0.002465838,0.017668093,0.256484744,0.000000000],[0.204710348,0.098411704,0.002465838,0.002465838,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|34 - 5NWQ|1|A|U|18 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|A|35 - 5NWQ|1|A|U|18 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.218661090,0.014620617,0.019969329,0.007807710,0.000000000],[0.206663216,0.011999471,0.002249461,0.008266368,0.000000000],[0.234847085,0.002249461,0.027362667,0.006356246,0.000000000],[0.208475927,0.012213416,0.010584145,0.007673792,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5NWQ|1|A|G|34 - 5NWQ|1|A|A|19 cSW 
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 [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
