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 [6] // Initial node G37 - C15 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008668452,0.016988087,0.009924636,0.188219101,0.000000000],[0.017131643,0.007544544,0.250353907,0.011380325,0.000000000],[0.009939034,0.232642761,0.001874181,0.022305022,0.000000000],[0.179374627,0.011316366,0.022479125,0.009858189,0.000000000],[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 [6] // Basepair G37 - C15 cWW 
ClusterNode  | Deletion Probability [0.0000000001763743] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.094752302846867] // Cluster node U38:U38 and A12:A14
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008590864,0.016331836,0.009816266,0.171008313,0.000000000],[0.018142150,0.007634138,0.258662220,0.011276526,0.000000000],[0.009857818,0.214012712,0.001875006,0.021485688,0.000000000],[0.207140253,0.011092461,0.023320816,0.009752934,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A12 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.148845005,0.016642779,0.008840780,0.006304384,0.000000000],[0.259403036,0.012911978,0.009864416,0.006983616,0.000000000],[0.184512997,0.013990132,0.108087970,0.005348851,0.000000000],[0.190360302,0.014390467,0.007769248,0.005744039,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A14 cSW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.213394359,0.097711652,0.029298823,0.008073800,0.000000000],[0.081617278,0.055476529,0.001516816,0.058595049,0.000000000],[0.006792689,0.077315958,0.022342735,0.056169929,0.000000000],[0.131754900,0.103459442,0.001516816,0.054963226,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A13 - A14 cSH 
Insertion    | Location [3] | Length Distribution [0.879505504,0.061208480,0.000474150,0.058630827,0.000172418,0.000008621] | Letter Distribution [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000]// Insertion after nucleotide 4, position 3 in cluster node
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 [3] | Right Index [2] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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
