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 [13] // Initial node C239 - G258 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009331601,0.017144707,0.010710502,0.174400287,0.000000000],[0.059304213,0.008909929,0.208735593,0.012170573,0.000000000],[0.010778878,0.189337741,0.002131960,0.021653241,0.000000000],[0.166105499,0.011847821,0.086431832,0.011005623,0.000000000],[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 [13] // Basepair C239 - G258 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.104529735,0.113299638,0.001277766,0.006118877,0.000000000],[0.110346799,0.139011852,0.001277766,0.001277766,0.000000000],[0.142769417,0.001277766,0.006329975,0.044930558,0.000000000],[0.125686650,0.199309903,0.001277766,0.001277766,0.000000000],[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 [12] // Basepair C240 - C257 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.452436966,0.270694434,0.023721799,0.023598430,0.000000000],[0.027506654,0.000722793,0.061292121,0.035597978,0.000000000],[0.004033740,0.051298036,0.001989661,0.000722793,0.000000000],[0.003962864,0.040976145,0.000722793,0.000722793,0.000000000],[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 [3] | Right Index [11] // Basepair A241 - A256 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.502422063208130] // Cluster node G242:U243 and A255:A255
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.023443571,0.004916667,0.024117331,0.004916667,0.000000000],[0.048837108,0.040820184,0.032636071,0.004916667,0.000000000],[0.004916667,0.004916667,0.057540447,0.022934816,0.000000000],[0.606710971,0.004916667,0.060654664,0.052804832,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U243 - A255 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.049766715,0.051268642,0.002796023,0.002313363,0.000000000],[0.048139606,0.055918343,0.000594689,0.056354723,0.000000000],[0.034035869,0.018612615,0.038046497,0.531326889,0.000000000],[0.004282260,0.049868653,0.000594689,0.056080422,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G242 - U243 cSH 
InitialNode  | 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 [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.070082871,0.041560238,0.417526916,0.044166373,0.000000000],[0.062344794,0.040489348,0.003121759,0.042544838,0.000000000],[0.000686958,0.000488494,0.015314889,0.000488494,0.000000000],[0.004053340,0.000488494,0.256153702,0.000488494,0.000000000],[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 [6] | Right Index [9] // Basepair A244 - G254 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009377379,0.038078223,0.010451230,0.185556239,0.000000000],[0.017484928,0.008065063,0.219573479,0.011737618,0.000000000],[0.010436472,0.210767302,0.002031067,0.054246668,0.000000000],[0.175757611,0.011812423,0.022442019,0.012182279,0.000000000],[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 [7] | Right Index [8] // Basepair G245 - C253 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
