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 C2156 - G2180 from junction 
BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.009573432,0.018670696,0.010738592,0.199847452,0.000000000],[0.022636955,0.009050270,0.214230681,0.012151330,0.000000000],[0.010821283,0.200582138,0.002151860,0.023718468,0.000000000],[0.214249849,0.011785171,0.027717608,0.012074217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C2156 - G2180 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [2] | Right Index [10] // 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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.000828022,0.001039259,0.008821390,0.001017059,0.000000000],[0.000180669,0.000180669,0.000903347,0.000180669,0.000000000],[0.113707142,0.117192079,0.651951059,0.102553278,0.000000000],[0.000180669,0.000180669,0.000903347,0.000180669,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair G2157 - G2177 tSS 
BasepairNode | Deletion Probability [0.0000000006094467] | Pair Probability [[0.022062116,0.052061168,0.004657104,0.485318270,0.000000000],[0.021929599,0.060153984,0.019602286,0.060262558,0.000000000],[0.004657104,0.026684972,0.023169287,0.051844976,0.000000000],[0.048915432,0.051457529,0.021223473,0.046000141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A2158 - U2176 tWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.350791599,0.040670272,0.003713382,0.018474231,0.000000000],[0.038122680,0.015188207,0.012119555,0.015027400,0.000000000],[0.003713382,0.012224256,0.390946071,0.024547920,0.000000000],[0.018369341,0.015013760,0.022729598,0.018348346,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair G2160 - G2174 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[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 G2161 - U2173 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
