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
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [7] | Norm Constant [0.250792367330097] // Cluster node 5J7L|1|AA|U|1380:5J7L|1|AA|C|1383 and 5J7L|1|AA|A|935:5J7L|1|AA|A|935
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009203552,0.018544658,0.010295215,0.194997478,0.000000000],[0.019194364,0.009501956,0.196157927,0.011930519,0.000000000],[0.010244330,0.217046390,0.002027020,0.024427390,0.000000000],[0.216938755,0.011848709,0.037639682,0.010002057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|U|1380 - 5J7L|1|AA|A|935 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.107170601,0.136946515,0.105968530,0.107198193,0.000000000],[0.156383098,0.128528656,0.002339675,0.129920131,0.000000000],[0.023155686,0.002339675,0.040695929,0.010128882,0.000000000],[0.012119336,0.016512008,0.009212388,0.011380697,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|AA|C|1383 - 5J7L|1|AA|A|935 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.477272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.022727273,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.022727273,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.477272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|AA|U|1381
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|AA|C|1382
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 [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009106890,0.016989933,0.010236072,0.193756118,0.000000000],[0.020753249,0.009584275,0.218305904,0.012178967,0.000000000],[0.010305927,0.194944276,0.002027252,0.022809627,0.000000000],[0.218224654,0.011603275,0.039263037,0.009910544,0.000000000],[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 [5] | Right Index [6] // Basepair C1384 - G933 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
