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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [14] // Basepair C2 - G18 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011060734,0.014482797,0.014081613,0.030514044,0.000000000],[0.384664447,0.040594609,0.034497041,0.015724453,0.000000000],[0.014420209,0.029095250,0.003555382,0.015038155,0.000000000],[0.038339089,0.014329933,0.325345055,0.014257188,0.000000000],[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 [2] | Right Index [13] // Basepair C3 - A17 cWW 
ClusterNode  | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.392931951529007] // Cluster node 6HCT|1|E|G|4:6HCT|1|E|G|7 and 6HCT|1|F|A|16:6HCT|1|F|A|16
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.046690699,0.007676303,0.008842876,0.005613701,0.000000000],[0.005638926,0.001127785,0.098122071,0.001127785,0.000000000],[0.639250862,0.001127785,0.109634108,0.066124819,0.000000000],[0.005638926,0.001127785,0.001127785,0.001127785,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6HCT|1|E|G|4 - 6HCT|1|F|A|16 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 6HCT|1|E|G|7 - 6HCT|1|F|A|16 tSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6HCT|1|E|A|5
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 4, 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 [6] | Right Index [11] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.043595236,0.392756919,0.048305054,0.000000000],[0.045811089,0.045705009,0.003636307,0.045458262,0.000000000],[0.000519472,0.000519472,0.017776750,0.000519472,0.000000000],[0.002448275,0.000519472,0.308635994,0.000519472,0.000000000],[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 [11] // Basepair A8 - G15 tHS 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.113545609,0.113984241,0.117255805,0.201455165,0.000000000],[0.103712991,0.107248177,0.001260969,0.116551990,0.000000000],[0.001260969,0.001260969,0.007793409,0.001260969,0.000000000],[0.006202964,0.001260969,0.104683837,0.001260969,0.000000000],[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 [7] | Right Index [10] // Basepair A9 - U14 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008946623,0.017374423,0.009813872,0.194415132,0.000000000],[0.021829934,0.009736222,0.195069241,0.010937668,0.000000000],[0.009833013,0.192572728,0.002024403,0.022823782,0.000000000],[0.231566497,0.010273839,0.052777129,0.010005495,0.000000000],[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 [8] | Right Index [9] // Basepair U10 - A13 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
