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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000189657778974] | Pair Probability [[0.007254050,0.012212825,0.008573343,0.116976024,0.000000000],[0.074083044,0.010870955,0.241924012,0.010182756,0.000000000],[0.008664105,0.161567920,0.001765957,0.016023730,0.000000000],[0.142304215,0.009774436,0.169733779,0.008088849,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.950006015,0.049873682,0.000117332,0.000002970] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | 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 [5] // Basepair C2496 - G2455 cWW 
ClusterNode  | Deletion Probability [0.0000001090702450] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.269997599475133] // Cluster node 9DFE|1|1A|A|2497:9DFE|1|1A|C|2498 and 9DFE|1|1A|G|2454:9DFE|1|1A|G|2454
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.006859043,0.013695562,0.007712596,0.241305589,0.000000000],[0.018854797,0.007295180,0.299757026,0.009097647,0.000000000],[0.007755563,0.172384196,0.001517610,0.024466163,0.000000000],[0.141737052,0.009069619,0.030763239,0.007729117,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|C|2498 - 9DFE|1|1A|G|2454 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.123752841,0.145749012,0.062196495,0.032831430,0.000000000],[0.079017867,0.092714775,0.004566895,0.016458179,0.000000000],[0.034873827,0.034831999,0.071248893,0.067003407,0.000000000],[0.081164325,0.088445651,0.004566895,0.060577510,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|2497 - 9DFE|1|1A|C|2498 cSH 
Insertion    | Location [1] | Length Distribution [0.974362859,0.025546540,0.000089116,0.000001485] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | Left Length Distribution [0.998645549,0.001293652,0.000060798] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.998645549,0.001293652,0.000060798] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
