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 [12] // Initial node C97 - G143 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011302835,0.015688748,0.013344805,0.113345681,0.000000000],[0.165628431,0.012077874,0.146852417,0.015393651,0.000000000],[0.013590323,0.121350928,0.002784428,0.019260671,0.000000000],[0.117275121,0.014236258,0.205766953,0.012100875,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C97 - G143 cWW 
BasepairNode | Deletion Probability [0.0000015977316803] | Pair Probability [[0.109749162,0.127926698,0.001322337,0.006296802,0.000000000],[0.110725601,0.116056577,0.001322337,0.001322337,0.000000000],[0.170695282,0.001322337,0.006406447,0.109991924,0.000000000],[0.119293454,0.114924027,0.001322337,0.001322337,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.738007380,0.012300123,0.246463715,0.003075031,0.000153752] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G98 - A142 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.106208866,0.107153807,0.197447047,0.115445278,0.000000000],[0.123800031,0.112312816,0.001279681,0.111216801,0.000000000],[0.001279681,0.001279681,0.006199787,0.001279681,0.000000000],[0.006093680,0.001279681,0.106443797,0.001279681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A99 - G141 tHS 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.099771965,0.100659637,0.139443264,0.161770273,0.000000000],[0.116296998,0.105505979,0.001202125,0.104476389,0.000000000],[0.001202125,0.001202125,0.059145721,0.001202125,0.000000000],[0.005724366,0.001202125,0.099992658,0.001202125,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A100 - G140 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [8] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [6] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.250000000,0.416666667,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [[0.009878188,0.017748468,0.011469828,0.188961043,0.000000000],[0.019498419,0.008363241,0.238084568,0.013495422,0.000000000],[0.011542717,0.215631747,0.002108490,0.024257963,0.000000000],[0.189509081,0.013172006,0.026116132,0.010162687,0.000000000],[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 C102 - G138 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
