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 [14] // Initial node G887 - C910 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003876703,0.055283349,0.004488645,0.073569181,0.000000000],[0.006541094,0.022376317,0.079237697,0.005043447,0.000000000],[0.004432143,0.610609112,0.000817354,0.010483940,0.000000000],[0.073144353,0.037059067,0.009043524,0.003994075,0.000000000],[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 [14] // Basepair G887 - C910 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.130969856,0.127242150,0.001382179,0.007812668,0.000000000],[0.120901106,0.102549889,0.001382179,0.001382179,0.000000000],[0.160425389,0.001382179,0.008196369,0.087318529,0.000000000],[0.125458163,0.120832807,0.001382179,0.001382179,0.000000000],[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 [13] // Basepair G888 - A909 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.570678958,0.107433541,0.026568743,0.026609119,0.000000000],[0.009819045,0.000760311,0.065362604,0.054006351,0.000000000],[0.004749819,0.063087677,0.001862668,0.000760311,0.000000000],[0.004672114,0.062108118,0.000760311,0.000760311,0.000000000],[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 [12] // Basepair A889 - A908 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [11] | Norm Constant [0.471704422088098] // Cluster node G890:U891 and A907:A907
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.025472342,0.005342148,0.026204408,0.005342148,0.000000000],[0.053063396,0.044352700,0.035460347,0.005342148,0.000000000],[0.005342148,0.005342148,0.062519909,0.024919560,0.000000000],[0.572676343,0.005342148,0.065903626,0.057374481,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U891 - A907 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.054073450,0.055705351,0.003037987,0.002513558,0.000000000],[0.052305533,0.060757431,0.000646153,0.061231574,0.000000000],[0.036981281,0.020223322,0.041338982,0.490768639,0.000000000],[0.004652840,0.054184209,0.000646153,0.060933536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G890 - U891 cSH 
InitialNode  | 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 [6] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.137917373,0.045760669,0.311458334,0.047613612,0.000000000],[0.114554217,0.039460194,0.002849476,0.045859042,0.000000000],[0.001348900,0.000524797,0.014332810,0.000524797,0.000000000],[0.009454491,0.000524797,0.227291694,0.000524797,0.000000000],[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 [6] | Right Index [10] // Basepair A892 - G906 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016183114,0.304321651,0.015271658,0.043813033,0.000000000],[0.014196807,0.011327490,0.037477687,0.015135201,0.000000000],[0.014933673,0.043446980,0.003387233,0.377184865,0.000000000],[0.037192849,0.016768018,0.014870400,0.034489340,0.000000000],[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 [8] | Right Index [9] // Basepair G894 - U905 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
