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 G674 - C806 from junction 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009810372,0.019985697,0.011358953,0.186173951,0.000000000],[0.016552873,0.008089349,0.200518679,0.012762933,0.000000000],[0.011215968,0.263443051,0.002068393,0.026530626,0.000000000],[0.185098881,0.013397366,0.022885515,0.010107394,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Left Index [1] | Right Index [11] // Basepair G674 - C806 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | 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 [0.997990020,0.001999980,0.000010000] | 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 [0.0000244705618206] | Pair Probability [[0.024010722,0.093152721,0.004771130,0.487955535,0.000000000],[0.004771130,0.038171791,0.004771130,0.004771130,0.000000000],[0.044022502,0.066387877,0.053871957,0.055814147,0.000000000],[0.004771130,0.004771130,0.024540096,0.083445872,0.000000000],[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 [2] | Right Index [9] // Basepair A675 - U803 tHW 
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.414957834,0.027524172,0.079529796,0.016623519,0.000000000],[0.003486342,0.012807437,0.003486342,0.003486342,0.000000000],[0.298959150,0.019956551,0.043185240,0.020639353,0.000000000],[0.003486342,0.003486342,0.031107565,0.017277672,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.437500000,0.062500000,0.437500000,0.062500000,0.000000000] | Left Index [3] | Right Index [8] // Basepair A676 - A802 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.360594839,0.031200513,0.003322930,0.091785179,0.000000000],[0.031239901,0.012871807,0.010108516,0.012694969,0.000000000],[0.003322930,0.010103019,0.313906749,0.018183499,0.000000000],[0.015745234,0.050716942,0.018200359,0.016002616,0.000000000],[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 [7] // Basepair A677 - A800 tWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009704981,0.017699381,0.011265142,0.185482208,0.000000000],[0.018844119,0.008192545,0.242496164,0.013187696,0.000000000],[0.011312823,0.221520521,0.002068672,0.024103639,0.000000000],[0.185840710,0.012976132,0.025319168,0.009986100,0.000000000],[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 C678 - G799 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
