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 [12] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000000000331140036538882804049492080542852422011] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.047573018692215] // Cluster node 7A0S|1|X|C|96:7A0S|1|X|A|101 and 7A0S|1|X|G|82:7A0S|1|X|G|84
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.195772860,0.059551583,0.288030981,0.060516632,0.000000000],[0.048888255,0.042958949,0.002738635,0.058559089,0.000000000],[0.001918465,0.000660745,0.014582542,0.000660745,0.000000000],[0.011219066,0.000660745,0.212619965,0.000660745,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|101 - 7A0S|1|X|G|82 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.046690699,0.007676303,0.008842876,0.005613701,0.000000000],[0.005638926,0.001127785,0.098122071,0.001127785,0.000000000],[0.583310039,0.001127785,0.109634108,0.066124819,0.000000000],[0.061579749,0.001127785,0.001127785,0.001127785,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|97 - 7A0S|1|X|A|83 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.106334440,0.112569335,0.001276474,0.006016026,0.000000000],[0.107124428,0.112308671,0.001276474,0.001276474,0.000000000],[0.203005705,0.001276474,0.006240276,0.108342292,0.000000000],[0.118697632,0.111702351,0.001276474,0.001276474,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|100 - 7A0S|1|X|A|83 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.010572638,0.014877250,0.013044997,0.090228256,0.000000000],[0.206427106,0.021659062,0.106652866,0.015137891,0.000000000],[0.013291996,0.091543616,0.002872521,0.017432502,0.000000000],[0.123374477,0.014077094,0.246524532,0.012283196,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|C|96 - 7A0S|1|X|G|84 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.188190220,0.187739903,0.222253463,0.178040115,0.000000000],[0.001931272,0.001931272,0.020012296,0.001931272,0.000000000],[0.015142959,0.001931272,0.015772404,0.157398460,0.000000000],[0.001931272,0.001931272,0.001931272,0.001931272,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|101 - 7A0S|1|X|G|84 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|U|98
Insertion    | Location [3] | Length Distribution [0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.000536624,0.015765044,0.000192305,0.000192305,0.000000000],[0.004438582,0.971419293,0.001346133,0.001346133,0.000000000],[0.000192305,0.001346133,0.000564806,0.000192305,0.000000000],[0.000192305,0.001346133,0.000737291,0.000192305,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair C102 - C81 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009343268,0.018128250,0.010549122,0.196880225,0.000000000],[0.019613658,0.009602282,0.210732508,0.012583150,0.000000000],[0.010555512,0.209899895,0.002054288,0.024189159,0.000000000],[0.209264206,0.012361836,0.034173856,0.010068786,0.000000000],[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 [7] | Right Index [8] // Basepair U103 - A80 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
