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 [[0.009596250,0.016007098,0.011294117,0.161729647,0.000000000],[0.074536499,0.012978608,0.208727819,0.013832501,0.000000000],[0.011450528,0.165029434,0.002266375,0.021087156,0.000000000],[0.173236538,0.013177859,0.094562621,0.010486950,0.000000000],[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 C2631 - G2647 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.214285714,0.071428571,0.642857143,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 7A0S|1|X|U|2632
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 [3] | Right Index [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 7A0S|1|X|A|2633
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 [12] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.013513514,0.959459459,0.013513514,0.013513514,0.000000000] | Position [2] | Left Index [4] | Right Index [12] // Fixed node on right for 7A0S|1|X|C|2646
InitialNode  | Left Length Distribution [1.000000000] | 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 [11] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right for 7A0S|1|X|C|2645
InitialNode  | Left Length Distribution [1.000000000] | 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 [10] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.279407267137871] // Cluster node 7A0S|1|X|G|2634:7A0S|1|X|U|2635 and 7A0S|1|X|A|2644:7A0S|1|X|A|2644
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018239161,0.004036356,0.018944354,0.004036356,0.000000000],[0.040590873,0.325253122,0.004036356,0.004036356,0.000000000],[0.004036356,0.009675411,0.030696143,0.017952320,0.000000000],[0.451254601,0.004036356,0.023418451,0.039757431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|2635 - 7A0S|1|X|A|2644 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.029480255,0.030039027,0.001651639,0.029356727,0.000000000],[0.022008936,0.033167853,0.000365701,0.029418270,0.000000000],[0.180298720,0.002559906,0.219933704,0.326838453,0.000000000],[0.029937668,0.029757948,0.000365701,0.034819492,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|2634 - 7A0S|1|X|U|2635 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 [[0.042449481,0.042764850,0.404323454,0.047384957,0.000000000],[0.044938497,0.044834438,0.003567044,0.044592391,0.000000000],[0.000509578,0.000509578,0.017438145,0.000509578,0.000000000],[0.002401641,0.000509578,0.302757213,0.000509578,0.000000000],[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 A2636 - G2643 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.004713507,0.009494604,0.005271585,0.109838539,0.000000000],[0.046713143,0.022607327,0.522182511,0.031468857,0.000000000],[0.005305405,0.100177811,0.001034229,0.017499094,0.000000000],[0.099529028,0.006196980,0.012639932,0.005327448,0.000000000],[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 C2637 - G2642 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
