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 [7] // Initial node G56 - C47 from junction 
ClusterNode  | Deletion Probability [0.0000000752256015] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.249241205320160] // Cluster node G56:G56 and A46:C47
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009643656,0.017743843,0.011116974,0.163701052,0.000000000],[0.067339819,0.009199884,0.180791773,0.012510100,0.000000000],[0.011138561,0.208425677,0.002205865,0.022375070,0.000000000],[0.164574954,0.012391145,0.095803274,0.011038354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G56 - C47 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.070820127,0.131469830,0.074440085,0.009251830,0.000000000],[0.075385232,0.070175051,0.001590324,0.093328000,0.000000000],[0.009938947,0.010256490,0.130627801,0.073632882,0.000000000],[0.076767980,0.080806256,0.022773670,0.068735496,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A46 - C47 cSH 
Insertion    | Location [2] | Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 6, position 2 in cluster node
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 [2] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.026190392,0.046162582,0.015757625,0.016835666,0.000000000],[0.015373566,0.014150407,0.003309124,0.016092581,0.000000000],[0.053502174,0.003309124,0.333812897,0.003309124,0.000000000],[0.401053931,0.003309124,0.019426036,0.028405649,0.000000000],[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 [5] // Basepair U57 - A45 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009286118,0.017299080,0.010773992,0.177247259,0.000000000],[0.017597460,0.007805594,0.248854464,0.012519905,0.000000000],[0.010786420,0.239296072,0.001975440,0.023439283,0.000000000],[0.177340704,0.012464760,0.023756114,0.009557335,0.000000000],[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 [3] | Right Index [4] // Basepair G58 - C44 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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
