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
ClusterNode  | Deletion Probability [0.0000000544785060] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.026384285500560] // Cluster node 6DLR|1|A|C|39:6DLR|1|A|U|40 and 6DLR|1|A|G|22:6DLR|1|A|G|22
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.006614080,0.012366324,0.007475838,0.148133616,0.000000000],[0.023377803,0.007425917,0.268524319,0.008824574,0.000000000],[0.007521544,0.155869528,0.001493007,0.017192719,0.000000000],[0.269702946,0.008478071,0.049729738,0.007269978,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|G|22 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.078658574,0.076390655,0.187722203,0.097106617,0.000000000],[0.184525663,0.072113430,0.019597915,0.094015495,0.000000000],[0.001297261,0.001297261,0.023570233,0.001297261,0.000000000],[0.038434952,0.001297261,0.121377959,0.001297261,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|U|40 - 6DLR|1|A|G|22 tHS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.042390954,0.063911666,0.005045895,0.069886495,0.000000000],[0.146727447,0.080996712,0.000821349,0.089193701,0.000000000],[0.066182965,0.000821349,0.047061250,0.066326255,0.000000000],[0.081194623,0.146797857,0.000821349,0.091820134,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|U|40 cSH 
Insertion    | Location [1] | Length Distribution [0.843487427,0.156284483,0.000219459,0.000008630] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.976638942,0.023280906,0.000078918,0.000001233] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006628422,0.012892329,0.007479019,0.175917433,0.000000000],[0.013829938,0.006800654,0.280794140,0.008941245,0.000000000],[0.007500515,0.210645333,0.001456266,0.018827313,0.000000000],[0.210023899,0.008796672,0.022252410,0.007214412,0.000000000],[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 [3] | Right Index [4] // Basepair G41 - C21 cWW 
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
