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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000049795766094] | Pair Probability [[0.008296274,0.016079379,0.009532980,0.156326100,0.000000000],[0.039696207,0.009728470,0.175317062,0.011282741,0.000000000],[0.009504468,0.268976635,0.001873621,0.020968068,0.000000000],[0.185312914,0.011317480,0.066801669,0.008985932,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.698392924,0.300735019,0.000834683,0.000037374] | Left Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | 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 [7] // Basepair G738 - C758 cWW 
ClusterNode  | Deletion Probability [0.0000000193172804] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.343191264578553] // Cluster node 9DFE|1|1A|G|739:9DFE|1|1A|U|740 and 9DFE|1|1A|U|757:9DFE|1|1A|U|757
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.012969457,0.250787748,0.011579538,0.020224389,0.000000000],[0.014334329,0.015455952,0.017287022,0.025623745,0.000000000],[0.011337681,0.017610232,0.003574619,0.045666438,0.000000000],[0.017667351,0.013766715,0.014652856,0.507461926,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|740 - 9DFE|1|1A|U|757 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076991900,0.069414143,0.003947522,0.063819619,0.000000000],[0.056053966,0.075662938,0.000836233,0.060049250,0.000000000],[0.053968695,0.000836233,0.071714411,0.189305808,0.000000000],[0.069505340,0.077477395,0.000836233,0.129580317,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|739 - 9DFE|1|1A|U|740 cSH 
Insertion    | Location [1] | Length Distribution [0.648604883,0.350398605,0.000952915,0.000043597] | Letter Distribution [0.055555556,0.166666667,0.055555556,0.722222222,0.000000000]// Insertion after nucleotide 2, position 1 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008254631,0.015194963,0.009508769,0.148501521,0.000000000],[0.052728315,0.010561558,0.184890064,0.011157201,0.000000000],[0.009537860,0.209332735,0.001919637,0.019699699,0.000000000],[0.206476664,0.010877682,0.092274218,0.009084483,0.000000000],[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 [4] | Right Index [5] // Basepair G741 - C756 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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
