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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009225160,0.018461010,0.010533281,0.191223781,0.000000000],[0.017164362,0.009144562,0.213851238,0.012801243,0.000000000],[0.010482999,0.244299236,0.001991779,0.024615947,0.000000000],[0.190171317,0.013006918,0.023266199,0.009760966,0.000000000],[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 [11] // Basepair G799 - C678 cWW 
BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.382418162,0.026612044,0.003450350,0.016493869,0.000000000],[0.025922251,0.012577988,0.010275794,0.043667329,0.000000000],[0.003450350,0.010290577,0.319063553,0.019445836,0.000000000],[0.078634598,0.012584058,0.019025013,0.016088230,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.388888889,0.055555556,0.500000000,0.055555556,0.000000000] | 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 [10] // Basepair A800 - A677 tWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.405834395,0.003041302,0.268297449,0.003041302,0.000000000],[0.026031730,0.012906210,0.003041302,0.003041302,0.000000000],[0.076708152,0.007533718,0.111790406,0.032553138,0.000000000],[0.013742791,0.003041302,0.014576957,0.014818546,0.000000000],[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 [9] // Basepair A802 - A676 tWH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009963261,0.001767869,0.019984304,0.001767869,0.000000000],[0.071081112,0.106635815,0.001767869,0.001767869,0.000000000],[0.001767869,0.004772464,0.014122660,0.010194127,0.000000000],[0.616889197,0.006047715,0.034449920,0.097020078,0.000000000],[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 [8] // Basepair U803 - A675 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.959459459,0.013513514,0.013513514,0.013513514,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 5J7L|1|DA|C|678
InitialNode  | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 [6] | Right Index [7] // Basepair C806 - G674 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
