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 [7] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000027443570427925820176520957936016555856547] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.063637507107939] // Cluster node 4WF9|1|X|G|1356:4WF9|1|X|G|1360 and 4WF9|1|X|C|1368:4WF9|1|X|C|1370
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.191467916,0.148237255,0.008456450,0.008784229,0.000000000],[0.156026810,0.001823930,0.161255026,0.017110886,0.000000000],[0.008653821,0.213908124,0.004461081,0.001823930,0.000000000],[0.010983560,0.063359124,0.001823930,0.001823930,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1357 - 4WF9|1|X|C|1368 tHH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1360 - 4WF9|1|X|C|1368 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|G|1356 - 4WF9|1|X|C|1370 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.128816013,0.159083246,0.128591472,0.126381572,0.000000000],[0.017038636,0.015415878,0.002401666,0.015499352,0.000000000],[0.014867564,0.002110425,0.037081679,0.008721315,0.000000000],[0.129082442,0.071931339,0.065521870,0.077455532,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|A|1359 - 4WF9|1|X|C|1370 cWS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4WF9|1|X|A|1358
Insertion    | Location [6] | Length Distribution [0.006093845,0.493601463,0.493601463,0.006398537,0.000304692] | Letter Distribution [0.062500000,0.562500000,0.312500000,0.062500000,0.000000000]// Insertion after nucleotide 6, position 6 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 [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
