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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006272399,0.011247917,0.021578432,0.130747736,0.000000000],[0.013336193,0.006388256,0.440434150,0.009070380,0.000000000],[0.007291875,0.133564998,0.004113079,0.015434193,0.000000000],[0.132442750,0.008739137,0.052691487,0.006647016,0.000000000],[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 [1] | Right Index [11] // Basepair C16 - G33 cWW 
ClusterNode  | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [10] | Norm Constant [0.332341503555430] // Cluster node 5XTM|1|B|G|17:5XTM|1|B|G|20 and 5XTM|1|B|A|32:5XTM|1|B|A|32
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.039758362,0.011189224,0.012889659,0.008182709,0.000000000],[0.004801694,0.001643896,0.143025861,0.001643896,0.000000000],[0.509295606,0.001643896,0.159806172,0.096385645,0.000000000],[0.004801694,0.001643896,0.001643896,0.001643896,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5XTM|1|B|G|17 - 5XTM|1|B|A|32 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.054373565,0.057561746,0.000652718,0.003076264,0.000000000],[0.054777521,0.057428457,0.000652718,0.000652718,0.000000000],[0.355485412,0.003263592,0.015954665,0.277001348,0.000000000],[0.060695419,0.057118419,0.000652718,0.000652718,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5XTM|1|B|G|20 - 5XTM|1|B|A|32 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.911764706,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5XTM|1|B|G|18
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 3, position 2 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 [5] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.054373565,0.054777521,0.355485412,0.060695419,0.000000000],[0.057561746,0.057428457,0.003263592,0.057118419,0.000000000],[0.000652718,0.000652718,0.015954665,0.000652718,0.000000000],[0.003076264,0.000652718,0.277001348,0.000652718,0.000000000],[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 [5] | Right Index [9] // Basepair A21 - G31 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 5XTM|1|B|A|21
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 G23 - C30 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
