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 [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000004582002] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.107464950003689] // Cluster node 1S03|1|A|A|12:1S03|1|A|A|14 and 1S03|1|A|U|38:1S03|1|A|U|38
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.008274522,0.017871821,0.009238324,0.225554088,0.000000000],[0.015053061,0.008268904,0.181704783,0.010664268,0.000000000],[0.009173652,0.270009765,0.001792143,0.030598357,0.000000000],[0.171137883,0.011098916,0.020309554,0.009249959,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|12 - 1S03|1|A|U|38 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.160143100,0.276728388,0.173510214,0.213180316,0.000000000],[0.015419283,0.013204997,0.001726291,0.013062945,0.000000000],[0.017567998,0.001726291,0.081091882,0.007977613,0.000000000],[0.006341574,0.006722267,0.005362359,0.006234482,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|14 - 1S03|1|A|U|38 cWS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.232381653,0.089297886,0.004500958,0.011701737,0.000000000],[0.090898062,0.084980468,0.000982283,0.007328610,0.000000000],[0.007392794,0.000982283,0.081960984,0.079558228,0.000000000],[0.144299930,0.083068623,0.000982283,0.079683217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|13 - 1S03|1|A|A|14 cSH 
Insertion    | Location [2] | Length Distribution [0.941706795,0.058000892,0.000284620,0.000007692] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 2, 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008232200,0.016237982,0.009326680,0.172454829,0.000000000],[0.016492653,0.008346045,0.218137694,0.011174322,0.000000000],[0.009306754,0.252685019,0.001797452,0.021629751,0.000000000],[0.207415017,0.011142248,0.026805368,0.008815987,0.000000000],[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 C15 - G37 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
