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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009999236,0.014956157,0.012144288,0.113577937,0.000000000],[0.155316435,0.018121105,0.149224604,0.014349655,0.000000000],[0.012353913,0.115566971,0.002596142,0.018349519,0.000000000],[0.138353991,0.013455419,0.200251764,0.011382864,0.000000000],[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 [10] // Basepair C1388 - G1417 cWW 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.307468761068205] // Cluster node 4WF9|1|X|U|1389:4WF9|1|X|U|1389 and 4WF9|1|X|A|1415:4WF9|1|X|U|1416
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.019942725,0.003678126,0.036925004,0.003678126,0.000000000],[0.152271055,0.236122282,0.003678126,0.003678126,0.000000000],[0.003678126,0.009716392,0.029112768,0.020281111,0.000000000],[0.354057298,0.003678126,0.020266348,0.099236264,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|1389 - 4WF9|1|X|A|1415 tWH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.131392922,0.044532614,0.001382892,0.006856603,0.000000000],[0.153412219,0.102638929,0.001382892,0.001382892,0.000000000],[0.119589980,0.001382892,0.009300133,0.044937517,0.000000000],[0.138184339,0.126792210,0.001382892,0.115448072,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|U|1389 - 4WF9|1|X|U|1416 tSH 
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 [3] | Right Index [7] // Initial node 4WF9|1|X|A|1390 - 4WF9|1|X|G|1414 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 4WF9|1|X|A|1390
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.040046680,0.040344198,0.438040994,0.044702790,0.000000000],[0.042394808,0.042296639,0.003365136,0.042068293,0.000000000],[0.000480734,0.000480734,0.016451081,0.000480734,0.000000000],[0.002265699,0.000480734,0.285620012,0.000480734,0.000000000],[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 [7] // Basepair A1391 - G1414 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010345669,0.063869632,0.011184400,0.175001619,0.000000000],[0.015911075,0.009705029,0.168647217,0.012962493,0.000000000],[0.011036499,0.221372192,0.002195693,0.082929291,0.000000000],[0.165236712,0.013579500,0.021122074,0.014900906,0.000000000],[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 [5] | Right Index [6] // Basepair G1392 - C1413 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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
