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
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010008314,0.015906297,0.011951013,0.143543808,0.000000000],[0.113253323,0.015638746,0.171362823,0.014397321,0.000000000],[0.012135476,0.146322383,0.002470993,0.020335440,0.000000000],[0.161392960,0.013617556,0.136517933,0.011145613,0.000000000],[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 [12] // Basepair C1711 - G1733 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.050260457,0.063450175,0.058243639,0.013975854,0.000000000],[0.029153549,0.028666679,0.002302816,0.002302816,0.000000000],[0.195454347,0.002302816,0.016500022,0.249699113,0.000000000],[0.191176562,0.091905521,0.002302816,0.002302816,0.000000000],[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 [11] // Basepair G1712 - U1732 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[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 [3] | Right Index [10] // Basepair G1713 - A1731 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000384010711367214351577654699383264706497383] | Num Left Bases [3] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.201969868463057] // Cluster node 8P9A|1|AR|A|1714:8P9A|1|AR|U|1717 and 8P9A|1|AR|G|1727:8P9A|1|AR|G|1730
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.229900085,0.231041542,0.253649052,0.238080083,0.000000000],[0.000481407,0.000481407,0.004368547,0.000481407,0.000000000],[0.003300261,0.000481407,0.003429267,0.032379908,0.000000000],[0.000481407,0.000481407,0.000481407,0.000481407,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|1714 - 8P9A|1|AR|G|1727 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010488908,0.016497752,0.012698690,0.101695031,0.000000000],[0.205516623,0.021615334,0.092055563,0.014005064,0.000000000],[0.012898676,0.089434432,0.002856478,0.027252089,0.000000000],[0.121610822,0.013331452,0.245283817,0.012759270,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|1717 - 8P9A|1|AR|G|1727 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.121788976,0.122693781,0.461195057,0.135949022,0.000000000],[0.025786009,0.025726299,0.000864138,0.025587411,0.000000000],[0.000292399,0.000292399,0.004224495,0.000292399,0.000000000],[0.001378078,0.000292399,0.073344740,0.000292399,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|1714 - 8P9A|1|AR|G|1730 tHS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|AR|A|1715
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 8P9A|1|AR|G|1728
Insertion    | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node
Insertion    | Location [5] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 8, position 5 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 [7] | Right Index [6] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
