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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G201 - C222 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010153793,0.013295259,0.012926971,0.028012001,0.000000000],[0.435119769,0.037265996,0.031668407,0.014435104,0.000000000],[0.013237803,0.026709543,0.003263854,0.013805080,0.000000000],[0.035195420,0.013154930,0.298667921,0.013088150,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair C202 - A221 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [12] | Norm Constant [0.257276798587684] // Cluster node 3KTW|1|C|C|203:3KTW|1|C|A|204 and 3KTW|1|C|C|219:3KTW|1|C|A|220
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.004692036,0.001105661,0.005021001,0.001105661,0.000000000],[0.056388190,0.793570728,0.007739629,0.007739629,0.000000000],[0.001105661,0.001610391,0.006784273,0.005207273,0.000000000],[0.089095169,0.001105661,0.004826812,0.012902223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|C|203 - 3KTW|1|C|C|219 tWH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.030717309,0.378479886,0.003588720,0.036089313,0.000000000],[0.003588720,0.026146144,0.012529247,0.003588720,0.000000000],[0.102662158,0.003588720,0.032271758,0.016134962,0.000000000],[0.003588720,0.003588720,0.033080098,0.310356803,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|A|204 - 3KTW|1|C|C|219 tHW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.059133653,0.007656442,0.000609857,0.003033099,0.000000000],[0.446508052,0.298693334,0.004269002,0.004269002,0.000000000],[0.051180538,0.000609857,0.004231774,0.007720767,0.000000000],[0.055127570,0.055737339,0.000609857,0.000609857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3KTW|1|C|C|203 - 3KTW|1|C|A|220 tSH 
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009233717,0.007375870,0.036375504,0.006569651,0.000000000],[0.004568870,0.004667945,0.007440758,0.005516210,0.000000000],[0.001062965,0.001062965,0.763683665,0.001062965,0.000000000],[0.095938841,0.001062965,0.053314141,0.001062965,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Basepair G205 - G218 tHS 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.022937090,0.014347847,0.348044880,0.017561601,0.000000000],[0.014692845,0.010155161,0.019218678,0.045122890,0.000000000],[0.381868061,0.019005244,0.003622602,0.015644206,0.000000000],[0.017595852,0.042706478,0.015986694,0.011489870,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair G206 - A217 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[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 [7] | Right Index [8] // Basepair C207 - G216 cWW 
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
