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 [11] // Initial node C1018 - G1144 from junction 
BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.009389328,0.018311644,0.010532081,0.196004232,0.000000000],[0.022201629,0.008876226,0.219726245,0.011917651,0.000000000],[0.010613182,0.196724789,0.002110478,0.023262344,0.000000000],[0.219745044,0.011558533,0.027184577,0.011842020,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1018 - G1144 cWW 
ClusterNode  | Deletion Probability [0.000000000000056748929858366210000000000000000000000000000000] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [10] | Norm Constant [0.360205348511261] // Cluster node U1019:A1021 and U1141:A1142A
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.033115265,0.068984957,0.006945048,0.732966383,0.000000000],[0.002457439,0.020402667,0.002457439,0.002457439,0.000000000],[0.012054279,0.016312099,0.028759757,0.030316299,0.000000000],[0.002457439,0.002457439,0.011463236,0.026392811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - U1141 tHW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1019 - A1142A tWH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.633374642,0.055859126,0.005949131,0.028182839,0.000000000],[0.018190876,0.007495204,0.005886151,0.007392232,0.000000000],[0.001934929,0.005882949,0.182786709,0.010588182,0.000000000],[0.009168390,0.007392376,0.010598000,0.009318263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1021 - A1142A tWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.704545455,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.022727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1020
Insertion    | Location [4] | Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 4 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Cluster
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G1022:G1024 and C1140:C1140
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.004887557,0.009956935,0.005659065,0.092752426,0.000000000],[0.008246692,0.004030138,0.099899013,0.006358532,0.000000000],[0.027939145,0.553701311,0.005152398,0.066088192,0.000000000],[0.092216823,0.006674609,0.011401633,0.005035534,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1024 - C1140 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.106243868,0.109450239,0.005969057,0.004938655,0.000000000],[0.102770254,0.119376597,0.001269566,0.120308197,0.000000000],[0.010380152,0.005676417,0.011603300,0.165418103,0.000000000],[0.009141931,0.106461489,0.001269566,0.119722610,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1022 - U1023 cSH 
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 [8] | Right Index [7] // New Initial node after Cluster
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
