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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009871049,0.046171971,0.010994713,0.160287119,0.000000000],[0.075938610,0.013151401,0.146576152,0.012330920,0.000000000],[0.011013021,0.156071426,0.002313617,0.067427105,0.000000000],[0.155186233,0.012309232,0.106586450,0.013770981,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C239 - G258 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.108290885,0.105412437,0.001332541,0.006252454,0.000000000],[0.114621927,0.126644956,0.001332541,0.001332541,0.000000000],[0.151011558,0.001332541,0.006924724,0.079367587,0.000000000],[0.142571113,0.150907115,0.001332541,0.001332541,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [12] // Basepair C240 - C257 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.468359047,0.309930808,0.018496463,0.018870803,0.000000000],[0.048485738,0.000551129,0.046984138,0.005236875,0.000000000],[0.002747776,0.046383686,0.001375617,0.000551129,0.000000000],[0.003743306,0.027181227,0.000551129,0.000551129,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // Basepair A241 - A256 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.287755810051411] // Cluster node 5J7L|1|DA|G|242:5J7L|1|DA|U|243 and 5J7L|1|DA|A|255:5J7L|1|DA|A|255
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.017569834,0.003888232,0.018249148,0.003888232,0.000000000],[0.039101300,0.313317227,0.003888232,0.003888232,0.000000000],[0.003888232,0.009320350,0.029569679,0.017293519,0.000000000],[0.471392047,0.003888232,0.022559058,0.038298443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|243 - 5J7L|1|DA|A|255 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.029108371,0.029660095,0.001630804,0.028986401,0.000000000],[0.021731301,0.032749451,0.000361088,0.029047168,0.000000000],[0.178024309,0.002527614,0.217159311,0.335330170,0.000000000],[0.029560014,0.029382561,0.000361088,0.034380255,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|242 - 5J7L|1|DA|U|243 cSH 
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.0000244705618206] | Pair Probability [[0.095042800,0.046221503,0.387079866,0.049492520,0.000000000],[0.044258638,0.042324170,0.003153390,0.047082533,0.000000000],[0.000931539,0.000535376,0.015792087,0.000535376,0.000000000],[0.005076173,0.000535376,0.261403276,0.000535376,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A244 - G254 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009582906,0.046969097,0.010439699,0.184672626,0.000000000],[0.016867708,0.009337652,0.190702311,0.012115851,0.000000000],[0.010382217,0.210810972,0.002065622,0.066848871,0.000000000],[0.179146945,0.012358680,0.024755653,0.012943189,0.000000000],[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 G245 - C253 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
