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 [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [9] // Basepair C8 - G5 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [8] | Norm Constant [0.259819701056345] // Cluster node 5VCI|1|A|U|9:5VCI|1|A|A|11 and 5VCI|1|B|A|3:5VCI|1|B|U|4
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.017898242,0.003960910,0.018590254,0.003960910,0.000000000],[0.039832166,0.319173624,0.003960910,0.003960910,0.000000000],[0.003960910,0.009494562,0.030122383,0.017616762,0.000000000],[0.461511524,0.003960910,0.022980723,0.039014302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|U|9 - 5VCI|1|B|A|3 tWH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.008849144,0.020982013,0.009451078,0.259997638,0.000000000],[0.016699564,0.009132583,0.185092798,0.009874781,0.000000000],[0.009432681,0.187492341,0.001945771,0.050727154,0.000000000],[0.186863639,0.010512826,0.021937258,0.011008732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|11 - 5VCI|1|B|U|4 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.352852925,0.261010701,0.013075308,0.032881623,0.000000000],[0.050465493,0.047159357,0.000549112,0.003878037,0.000000000],[0.003890669,0.000549112,0.045624754,0.044265555,0.000000000],[0.052840181,0.046137608,0.000549112,0.044270456,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|A|A|11 cSH 
InitialNode  | 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 [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015099647,0.283013738,0.013648585,0.080630330,0.000000000],[0.013081510,0.012191763,0.034729394,0.013731825,0.000000000],[0.013356188,0.039620776,0.003092784,0.374698981,0.000000000],[0.034869064,0.014999364,0.013725146,0.039510904,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G12 - U2 cWW 
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
