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 [18] // 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 [18] // Basepair C53 - G41 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.030289734,0.068503029,0.000762594,0.003173752,0.000000000],[0.266785855,0.410423431,0.003812972,0.003812972,0.000000000],[0.067095736,0.000762594,0.003348885,0.009493180,0.000000000],[0.064860346,0.065349730,0.000762594,0.000762594,0.000000000],[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 [17] // Basepair C54 - C40 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.437389671,0.327985029,0.019573927,0.019970073,0.000000000],[0.051310150,0.000583234,0.049721078,0.005541936,0.000000000],[0.002907841,0.049085648,0.001455750,0.000583234,0.000000000],[0.003961363,0.028764599,0.000583234,0.000583234,0.000000000],[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 [16] // Basepair A55 - A39 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [15] | Norm Constant [0.266231322387786] // Cluster node 6UFG|1|A|G|56:6UFG|1|A|U|57 and 6UFG|1|A|A|38:6UFG|1|A|A|38
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFG|1|A|U|57 - 6UFG|1|A|A|38 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.030804004,0.031387867,0.001725802,0.030674930,0.000000000],[0.022997202,0.034657186,0.000382122,0.030739236,0.000000000],[0.188394657,0.002674853,0.229809368,0.296611539,0.000000000],[0.031281957,0.031094167,0.000382122,0.036382988,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFG|1|A|G|56 - 6UFG|1|A|U|57 cSH 
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 [14] // 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 [14] // Basepair A58 - G37 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [7] | Right Index [13] // Fixed node on left for 6UFG|1|A|C|40
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 [8] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [13] // Fixed node on left for 6UFG|1|A|G|41
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 [9] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [9] | Right Index [13] // Fixed node on right for 6UFG|1|A|U|57
InitialNode  | Left Length Distribution [1.000000000] | 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 [9] | Right Index [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.618999942,0.027411941,0.048841477,0.026826787,0.000000000],[0.018350871,0.010237698,0.026918842,0.026030599,0.000000000],[0.037348807,0.027481470,0.005898737,0.028798923,0.000000000],[0.026068812,0.029318190,0.020065065,0.021401838,0.000000000],[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 [9] | Right Index [12] // Basepair A61 - A35 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 [10] | Right Index [11] // Basepair C62 - G34 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
