Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [19] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009435981,0.020308281,0.010584118,0.207749754,0.000000000],[0.016871843,0.009369986,0.196949712,0.012311312,0.000000000],[0.010488840,0.230753978,0.002037301,0.032735453,0.000000000],[0.194255155,0.012845795,0.022899797,0.010402692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [19] // Basepair A1772 - U1979 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.985294118,0.004901961,0.004901961,0.004901961,0.000000000] | Position [2] | Left Index [2] | Right Index [18] // Fixed node on right for 5J7L|1|DA|A|1978
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [17] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.276866016,0.016538825,0.002384045,0.012574684,0.000000000],[0.197977903,0.019619284,0.002384045,0.010698259,0.000000000],[0.191809165,0.002384045,0.002384045,0.008589080,0.000000000],[0.211751896,0.014270066,0.016428812,0.013339830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [17] // Basepair A1773 - A1977 tSW 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [16] // Junction node C1774 - U1976 ID J1965
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.063152187,0.111246340,0.139890384,0.135229735,0.000000000],[0.142824501,0.228475044,0.001589961,0.136250072,0.000000000],[0.001589961,0.001589961,0.006982214,0.001589961,0.000000000],[0.006617072,0.001589961,0.019792682,0.001589961,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // Basepair C1774 - C1790 tHS 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.024836608,0.020256618,0.019195810,0.020035663,0.000000000],[0.016912240,0.016950716,0.004072947,0.019292395,0.000000000],[0.004072947,0.004072947,0.367607232,0.004072947,0.000000000],[0.445756215,0.004072947,0.024718822,0.004072947,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair U1775 - A1789 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G1776 - C1788 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
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [16] // Initial node 5J7L|1|DA|A|1791 - 5J7L|1|DA|U|1976 from node 
JunctionNode | Branches [2]  | Left Index [9] | Right Index [16] // Junction node A1791 - U1976 ID J2510
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.042857649,0.043176051,0.398595795,0.047840582,0.000000000],[0.045370598,0.045265538,0.003601343,0.045021164,0.000000000],[0.000514478,0.000514478,0.017605820,0.000514478,0.000000000],[0.002424734,0.000514478,0.305668340,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // Basepair A1791 - G1828 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.014038037,0.223353685,0.013249451,0.111579454,0.000000000],[0.014286320,0.011747913,0.076578973,0.013853086,0.000000000],[0.012993645,0.091415691,0.002898775,0.274058703,0.000000000],[0.075636734,0.014954620,0.016343225,0.033011687,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Basepair G1792 - U1827 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [13] | Right Index [16] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.118076515,0.118532651,0.121934763,0.169590154,0.000000000],[0.107851538,0.111527792,0.001311286,0.121202863,0.000000000],[0.001311286,0.001311286,0.008104396,0.001311286,0.000000000],[0.006450486,0.001311286,0.108861124,0.001311286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [16] // Basepair A1829 - U1976 tHS 
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.003672434,0.006585557,0.004221915,0.076551649,0.000000000],[0.054657564,0.026181875,0.601780983,0.037174395,0.000000000],[0.004269328,0.078201131,0.000804742,0.009036584,0.000000000],[0.077544064,0.005116688,0.010309321,0.003891769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [15] // Basepair C1830 - G1975 cWW 
HairpinNode  | Num Bases [1] | Left Index [15] | Right Index [15] | 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
