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
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214533025748902239021246] | Num Left Bases [6] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.002631750717555] // Cluster node 5J7L|1|DA|C|97:5J7L|1|DA|A|103 and 5J7L|1|DA|A|83:5J7L|1|DA|G|85
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.490885373,0.093275450,0.080135126,0.086621764,0.000000000],[0.056132539,0.038208747,0.000961969,0.086439173,0.000000000],[0.004809844,0.000961969,0.008356384,0.000961969,0.000000000],[0.029330166,0.000961969,0.020995590,0.000961969,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|103 - 5J7L|1|DA|A|83 tHS 
Interaction  | Interacting Bases [2,8] | Pair Probability [[0.021644907,0.017792930,0.020496934,0.013012017,0.000000000],[0.002614097,0.002614097,0.227437495,0.002614097,0.000000000],[0.271310703,0.002614097,0.254121285,0.153270951,0.000000000],[0.002614097,0.002614097,0.002614097,0.002614097,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|98 - 5J7L|1|DA|A|84 tSS 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.198669318,0.151650079,0.009050375,0.009233541,0.000000000],[0.166069526,0.001887683,0.160926363,0.017936931,0.000000000],[0.009411467,0.158869742,0.004711656,0.001887683,0.000000000],[0.012821277,0.093098993,0.001887683,0.001887683,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|101 - 5J7L|1|DA|A|84 tHH 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|97 - 5J7L|1|DA|G|85 cWW 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.191916759,0.191457524,0.206852541,0.181565662,0.000000000],[0.001969516,0.001969516,0.020408579,0.001969516,0.000000000],[0.015442820,0.001969516,0.016084729,0.160515261,0.000000000],[0.001969516,0.001969516,0.001969516,0.001969516,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|103 - 5J7L|1|DA|G|85 tSS 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.074958370,0.074522986,0.072592901,0.075257560,0.000000000],[0.093663030,0.076039825,0.003534873,0.067669678,0.000000000],[0.079480999,0.003480647,0.006829583,0.080842831,0.000000000],[0.075739436,0.073025027,0.072599406,0.069762848,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|97 - 5J7L|1|DA|A|103 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|U|99
Interaction  | Interacting Bases [4,4] | 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|U|100
Insertion    | Location [5] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 5, position 5 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.121583738,0.122053423,0.125556588,0.144924515,0.000000000],[0.111055049,0.114840499,0.001350235,0.124802948,0.000000000],[0.001350235,0.001350235,0.008345120,0.001350235,0.000000000],[0.006642085,0.001350235,0.112094623,0.001350235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A104 - U82 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [8] | Right Index [9] // Basepair C105 - G81 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
