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 [15] // Initial node
BasepairNode | Deletion Probability [0.0000119734646324] | Pair Probability [[0.008406848,0.016994520,0.009428215,0.221669729,0.000000000],[0.016792868,0.008555751,0.249835392,0.011157163,0.000000000],[0.009466194,0.196311342,0.001839096,0.029998578,0.000000000],[0.176713565,0.011176359,0.022242198,0.009412181,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.863704278,0.135687012,0.000586575,0.000022135] | Left Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | 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 [15] // Basepair C201 - G194 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012160827,0.195122844,0.012005175,0.020950047,0.000000000],[0.022937778,0.129790632,0.018543042,0.013683443,0.000000000],[0.011916535,0.018723588,0.003873259,0.040650650,0.000000000],[0.035987605,0.082184646,0.020230959,0.361238969,0.000000000],[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 [14] // Basepair U202 - U193 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.100135932,0.115971362,0.001358589,0.006285828,0.000000000],[0.103887646,0.153417806,0.001358589,0.001358589,0.000000000],[0.167626521,0.001358589,0.006952824,0.061391833,0.000000000],[0.130718205,0.145460507,0.001358589,0.001358589,0.000000000],[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 [13] // Basepair C203 - C192 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.499670618,0.291677097,0.017407094,0.017759386,0.000000000],[0.045630118,0.000518670,0.044216956,0.004928444,0.000000000],[0.002585943,0.043651869,0.001294599,0.000518670,0.000000000],[0.003522840,0.025580359,0.000518670,0.000518670,0.000000000],[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 [4] | Right Index [12] // Basepair A204 - A191 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.311752728833310] // Cluster node 9DFE|1|1A|G|205:9DFE|1|1A|U|206 and 9DFE|1|1A|A|190:9DFE|1|1A|A|190
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.016535040,0.003659231,0.017174345,0.003659231,0.000000000],[0.036798387,0.294864070,0.003659231,0.003659231,0.000000000],[0.003659231,0.008771418,0.027828141,0.016274998,0.000000000],[0.502524985,0.003659231,0.021230418,0.036042815,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|206 - 9DFE|1|1A|A|190 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.027394002,0.027913231,0.001534756,0.027279216,0.000000000],[0.020451412,0.030820637,0.000339821,0.027336403,0.000000000],[0.167539375,0.002378747,0.204369478,0.374476620,0.000000000],[0.027819045,0.027652044,0.000339821,0.032355393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|205 - 9DFE|1|1A|U|206 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 [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.038758222,0.039046168,0.456121414,0.043264526,0.000000000],[0.041030801,0.040935791,0.003256866,0.040714791,0.000000000],[0.000465267,0.000465267,0.015921785,0.000465267,0.000000000],[0.002192803,0.000465267,0.276430499,0.000465267,0.000000000],[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 [7] | Right Index [10] // Basepair A207 - G189 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008803172,0.033358955,0.009702592,0.197048926,0.000000000],[0.016460115,0.008740523,0.222580180,0.011377063,0.000000000],[0.009696742,0.205091361,0.001910371,0.053338299,0.000000000],[0.176167818,0.011475196,0.023131906,0.011116780,0.000000000],[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 C208 - G188 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
