Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [10] // Initial node G863 - C905 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009655575,0.020452677,0.010811709,0.200386604,0.000000000],[0.020851131,0.008969837,0.201120779,0.011820265,0.000000000],[0.010745793,0.213649208,0.002151642,0.025610090,0.000000000],[0.213671659,0.012113485,0.025820790,0.012168755,0.000000000],[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 [10] // Basepair G863 - C905 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.010610815,0.017566445,0.012200287,0.120859047,0.000000000],[0.206134582,0.013915363,0.114716350,0.013364208,0.000000000],[0.012383976,0.111101518,0.002917694,0.019539880,0.000000000],[0.138432870,0.012521397,0.179314102,0.014421465,0.000000000],[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 [9] // Basepair U864 - A904 cWW 
ClusterNode  | Deletion Probability [0.0000000000396545] | Num Left Bases [2] | Num Right Bases [2] | Left Index [3] | Right Index [8] | Norm Constant [0.181109043621461] // Cluster node A865:U866 and G902:G903
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.007750136,0.007750136,0.883747966,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.007750136,0.007750136,0.007750136,0.007750136,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G902 wat 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.101728279,0.102633356,0.132373524,0.110575038,0.000000000],[0.118577332,0.107574724,0.001225696,0.106524945,0.000000000],[0.001225696,0.001225696,0.005938240,0.001225696,0.000000000],[0.005836608,0.001225696,0.200883780,0.001225696,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U866 - G902 tHS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.177190689,0.109960849,0.281763742,0.012419737,0.000000000],[0.010771367,0.004154329,0.014747163,0.031379647,0.000000000],[0.261287932,0.014935165,0.002719598,0.012261563,0.000000000],[0.012398575,0.033379576,0.011990196,0.008639871,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A865 - G903 cWW 
Insertion    | Location [3] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 7, position 3 in cluster node
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 [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009183469,0.022285751,0.009814417,0.220857782,0.000000000],[0.022291510,0.009418174,0.193045342,0.010327057,0.000000000],[0.009814439,0.193043865,0.002150936,0.025717104,0.000000000],[0.220868443,0.010326961,0.025722659,0.015132092,0.000000000],[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 U867 - A901 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
