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 U3 - G8 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011524459,0.015996371,0.013606468,0.115568146,0.000000000],[0.168876048,0.012314695,0.139927955,0.015695487,0.000000000],[0.013856800,0.123730358,0.002839025,0.019638331,0.000000000],[0.119574633,0.014515400,0.199997678,0.012338148,0.000000000],[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 [1] | Right Index [12] // Basepair U3 - G8 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.129506361,0.126673089,0.001432729,0.008039397,0.000000000],[0.142111874,0.112243512,0.001432729,0.001432729,0.000000000],[0.140738059,0.001432729,0.008529896,0.064911900,0.000000000],[0.131659396,0.126990143,0.001432729,0.001432729,0.000000000],[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 [11] // Basepair C4 - A7 tSH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.218999763,0.151281779,0.003250143,0.021991785,0.000000000],[0.003250143,0.013270599,0.003250143,0.003250143,0.000000000],[0.241326746,0.127991387,0.033272604,0.017815985,0.000000000],[0.003250143,0.003250143,0.030767019,0.123781475,0.000000000],[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 [3] | Right Index [10] // Basepair A5 - C6 tHW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.218999763,0.003250143,0.241326746,0.003250143,0.000000000],[0.151281779,0.013270599,0.127991387,0.003250143,0.000000000],[0.003250143,0.003250143,0.033272604,0.030767019,0.000000000],[0.021991785,0.003250143,0.017815985,0.123781475,0.000000000],[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 [9] // Basepair C6 - A5 tWH 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.129506361,0.142111874,0.140738059,0.131659396,0.000000000],[0.126673089,0.112243512,0.001432729,0.126990143,0.000000000],[0.001432729,0.001432729,0.008529896,0.001432729,0.000000000],[0.008039397,0.001432729,0.064911900,0.001432729,0.000000000],[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 [5] | Right Index [8] // Basepair A7 - C4 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013347761,0.165529096,0.013687752,0.119073501,0.000000000],[0.015838591,0.009978088,0.123297350,0.014347705,0.000000000],[0.013441150,0.139428673,0.002801578,0.196271923,0.000000000],[0.115139890,0.015509778,0.019472481,0.022834682,0.000000000],[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 G8 - U3 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
