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
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010187606,0.061327314,0.011087687,0.172971723,0.000000000],[0.018460196,0.009839639,0.220587306,0.013368761,0.000000000],[0.011137225,0.169507099,0.002196073,0.080283893,0.000000000],[0.167339440,0.013178161,0.023776616,0.014751262,0.000000000],[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 [1] | Right Index [6] // Basepair C8 - G5 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.062500000,0.062500000,0.687500000,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left for 5VCI|1|A|U|9
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000493232005] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.020921021768211] // Cluster node 5VCI|1|A|A|10:5VCI|1|A|A|11 and 5VCI|1|B|U|4:5VCI|1|B|U|4
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.029167032,0.025707784,0.003594886,0.381883230,0.000000000],[0.021420106,0.018778763,0.003594886,0.003594886,0.000000000],[0.053873187,0.003594886,0.286180329,0.074524582,0.000000000],[0.053663672,0.033231998,0.003594886,0.003594886,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|B|U|4 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[0.016857107,0.009218740,0.186838956,0.009967940,0.000000000],[0.009521668,0.189261136,0.001964127,0.051205712,0.000000000],[0.188626503,0.010612004,0.022144213,0.011112588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|11 - 5VCI|1|B|U|4 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.159101612,0.101642687,0.005091781,0.012804749,0.000000000],[0.102869672,0.096130391,0.001119318,0.007905053,0.000000000],[0.035862729,0.001119318,0.093002231,0.090231618,0.000000000],[0.107710274,0.094047641,0.001119318,0.090241608,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|A|A|11 cSH 
Insertion    | Location [1] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
InitialNode  | Left Length Distribution [0.991157722,0.008431010,0.000411269] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991157722,0.008431010,0.000411269] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster
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
