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 [0.000000000000000000223328457280071460584722431189528970159112] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.008748336697488] // Cluster node 5J7L|1|DA|U|2680:5J7L|1|DA|U|2684 and 5J7L|1|DA|A|2725:5J7L|1|DA|A|2727
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.031843204,0.013485512,0.080527687,0.013485512,0.000000000],[0.379953218,0.028749934,0.047098957,0.013485512,0.000000000],[0.013485512,0.019535492,0.032895086,0.033442083,0.000000000],[0.035478394,0.013485512,0.021975449,0.221072936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2681 - 5J7L|1|DA|A|2725 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.007834346,0.014958357,0.008684444,0.168720670,0.000000000],[0.018575859,0.008405686,0.204619178,0.009962529,0.000000000],[0.008719741,0.168234648,0.001760426,0.019830586,0.000000000],[0.300719926,0.009418038,0.040894884,0.008660681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2684 - 5J7L|1|DA|A|2725 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.008105384,0.015473466,0.009186860,0.170405132,0.000000000],[0.017061420,0.008314162,0.250704869,0.011086930,0.000000000],[0.009213444,0.215457325,0.001780847,0.020763584,0.000000000],[0.214715044,0.010844820,0.028182785,0.008703929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2680 - 5J7L|1|DA|A|2727 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.063781716,0.055522707,0.054477794,0.046285617,0.000000000],[0.111493036,0.120168446,0.358827972,0.085221023,0.000000000],[0.018344455,0.010636512,0.018102324,0.015634134,0.000000000],[0.010691600,0.012588458,0.007964435,0.010259772,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2683 - 5J7L|1|DA|A|2727 cWS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.074156057,0.073555679,0.004043079,0.058987560,0.000000000],[0.110216985,0.217363980,0.000846835,0.044424285,0.000000000],[0.046981489,0.000846835,0.072885912,0.069571402,0.000000000],[0.075914703,0.074005313,0.000846835,0.075353051,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|2681 - 5J7L|1|DA|C|2683 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.417525773,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.108247423,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.056701031,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.417525773,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|2682
Insertion    | Location [6] | Length Distribution [0.002341937,0.890211394,0.107040274,0.000392619,0.000013776] | Letter Distribution [0.065217391,0.369565217,0.239130435,0.326086957,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
InitialNode  | Left Length Distribution [0.997221289,0.002647563,0.000131149] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997221289,0.002647563,0.000131149] | 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
