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 G76 - C64 from junction 
BasepairNode | Deletion Probability [0.0000052393233623] | Pair Probability [[0.009696313,0.019313569,0.011232880,0.184287162,0.000000000],[0.016884566,0.008035654,0.208890895,0.012733823,0.000000000],[0.011131706,0.260092205,0.002049121,0.025767468,0.000000000],[0.183526462,0.013182737,0.023188255,0.009987184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | 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 G76 - C64 cWW 
ClusterNode  | Deletion Probability [0.0000000001323925] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.062935737109612] // Cluster node U77:U77 and A61:A63
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009104522,0.019068653,0.010130221,0.202038967,0.000000000],[0.020744927,0.008639905,0.211004470,0.011238095,0.000000000],[0.010155036,0.200458510,0.002050733,0.023679133,0.000000000],[0.223086224,0.011128398,0.025343219,0.012128987,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A61 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.126758533,0.055585452,0.014037661,0.008663852,0.000000000],[0.168755935,0.040188393,0.013939587,0.009789708,0.000000000],[0.117302516,0.039733096,0.144249774,0.007108942,0.000000000],[0.194184319,0.042380809,0.009741284,0.007580138,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A63 cSW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.119225934,0.088672012,0.046358530,0.009822107,0.000000000],[0.098358845,0.084485776,0.002105316,0.085313352,0.000000000],[0.092777380,0.010484959,0.066131830,0.084785516,0.000000000],[0.029200906,0.097227503,0.002105316,0.082944717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A61 - A62 cSH 
Insertion    | Location [2] | Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 2 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
