Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [11] // Initial node U113 - A290 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009383739,0.020149542,0.010379056,0.200722640,0.000000000],[0.021853259,0.009068682,0.196771190,0.011229117,0.000000000],[0.010341071,0.207909105,0.002131458,0.024714144,0.000000000],[0.225105357,0.011398645,0.026242775,0.012600221,0.000000000],[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 [11] // Basepair U113 - A290 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.099583908,0.086557364,0.158164716,0.024220246,0.000000000],[0.015062866,0.011799751,0.018800670,0.024418272,0.000000000],[0.142777257,0.019104895,0.003734971,0.030026250,0.000000000],[0.021360132,0.082092454,0.015680755,0.246615493,0.000000000],[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 [10] // Basepair U114 - U289 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
InitialNode  | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.025453598,0.088611510,0.084813384,0.026213276,0.000000000],[0.016484420,0.013468173,0.021954124,0.153449855,0.000000000],[0.027442117,0.022697844,0.004075038,0.032332908,0.000000000],[0.023304903,0.193624328,0.017284210,0.248790312,0.000000000],[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 [4] | Right Index [9] // Basepair U116 - C288 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.013792873,0.121236027,0.013575643,0.105505658,0.000000000],[0.019894961,0.016573698,0.079066334,0.014789670,0.000000000],[0.013369986,0.079724271,0.003963030,0.042304006,0.000000000],[0.089148150,0.015787988,0.021031523,0.350236181,0.000000000],[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 [5] | Right Index [8] // Basepair U117 - U287 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009027553,0.019940410,0.009723686,0.205285714,0.000000000],[0.024262390,0.009440542,0.191977271,0.010276342,0.000000000],[0.009740283,0.190868689,0.002132868,0.023419534,0.000000000],[0.242412981,0.010204177,0.027588121,0.013699440,0.000000000],[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 U118 - A286 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
