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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.071428571,0.500000000,0.071428571,0.357142857,0.000000000] | Left Index [1] | Right Index [13] // Basepair C1934 - G1964 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.002824859,0.398305085,0.596045198,0.002824859,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 5J7L|1|DA|G|1935
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.013513514,0.581081081,0.391891892,0.013513514,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right for 5J7L|1|DA|G|1945
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [11] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000048323728403170814589206297593745167] | Num Left Bases [8] | Num Right Bases [1] | Left Index [3] | Right Index [11] | Norm Constant [0.248855558641365] // Cluster node 5J7L|1|DA|A|1936:5J7L|1|DA|G|1945 and 5J7L|1|DA|C|1961:5J7L|1|DA|C|1961
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1945 - 5J7L|1|DA|C|1961 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.078978008,0.083597937,0.020523612,0.080304904,0.000000000],[0.080464208,0.081988830,0.015285180,0.023181182,0.000000000],[0.024210704,0.057561603,0.084499376,0.076945069,0.000000000],[0.080352733,0.119807193,0.015285180,0.077014281,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1940 - 5J7L|1|DA|C|1941 cSH 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.002600388,0.013803359,0.000950158,0.003911621,0.000000000],[0.002113814,0.203551233,0.011680332,0.004865762,0.000000000],[0.002057656,0.454778136,0.000950158,0.002074797,0.000000000],[0.002133219,0.287831381,0.002211871,0.004486114,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1940 - 5J7L|1|DA|C|1942 tSW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.002980614,0.002980614,0.010981155,0.345680455,0.000000000],[0.002980614,0.014333499,0.002980614,0.002980614,0.000000000],[0.012844532,0.002980614,0.010301669,0.275793290,0.000000000],[0.012904793,0.282314310,0.002980614,0.013981998,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1936 - 5J7L|1|DA|U|1943 cHW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|1937
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|5MU|1939
Insertion    | Location [2] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node
Insertion    | Location [7] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.357142857,0.071428571,0.500000000,0.000000000]// Insertion after nucleotide 9, position 7 in cluster node
InitialNode  | 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 [11] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
