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 [9] // Initial node C1417 - G1581 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008962558,0.014859592,0.010393278,0.150315095,0.000000000],[0.076913212,0.008817731,0.243398715,0.011987446,0.000000000],[0.010528894,0.148385406,0.002088945,0.018854073,0.000000000],[0.143605439,0.011357816,0.129384680,0.010147120,0.000000000],[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 [9] // Basepair C1417 - G1581 cWW 
BasepairNode | Deletion Probability [0.0000147294218142] | Pair Probability [[0.059544634,0.053787320,0.000584169,0.003300211,0.000000000],[0.037422832,0.037770072,0.000443210,0.000443210,0.000000000],[0.452776205,0.002961509,0.014438148,0.244674219,0.000000000],[0.052405994,0.038561849,0.000443210,0.000443210,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.902527688,0.097127447,0.000333558,0.000011307] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | 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 [8] // Basepair G1418 - A1580 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.760869565,0.065217391,0.021739130,0.152173913,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000000741983018] | Pair Probability [[0.021051522,0.043854046,0.031539389,0.565466781,0.000000000],[0.004414998,0.050217320,0.004414998,0.004414998,0.000000000],[0.021656535,0.029306072,0.078793737,0.054465806,0.000000000],[0.004414998,0.004414998,0.034156873,0.047416927,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.191104012,0.616996179,0.096534053,0.095117422,0.000237046,0.000011288] | Left Letter Distribution [0.620000000,0.100000000,0.060000000,0.220000000,0.000000000] | 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 [6] // Basepair A1419 - U1578 tHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008622968,0.028889233,0.009691427,0.168375221,0.000000000],[0.015965643,0.007442493,0.182909660,0.010737626,0.000000000],[0.009614004,0.276828393,0.001864995,0.043338082,0.000000000],[0.193378178,0.011086787,0.020653500,0.010601790,0.000000000],[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 [4] | Right Index [5] // Basepair G1421 - C1577 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
