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 [11] // Initial node
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.008971369,0.016871195,0.010036256,0.191671055,0.000000000],[0.020727304,0.009504551,0.215061691,0.011796248,0.000000000],[0.010095364,0.192251066,0.002003525,0.022551723,0.000000000],[0.225967248,0.011209843,0.041465653,0.009815909,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1018 - G1144 cWW 
ClusterNode  | Deletion Probability [0.0000000000001252] | Num Left Bases [3] | Num Right Bases [2] | Left Index [2] | Right Index [10] | Norm Constant [0.107967099456197] // Cluster node 9DFE|1|1A|U|1019:9DFE|1|1A|A|1021 and 9DFE|1|1A|U|1141:9DFE|1|1A|A|1142|||A
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.015670192,0.038722823,0.003278045,0.434947362,0.000000000],[0.015388165,0.035313208,0.013651465,0.037860784,0.000000000],[0.003278045,0.016248833,0.015689392,0.262586703,0.000000000],[0.037446804,0.031435146,0.016159964,0.022323068,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|1021 - 9DFE|1|1A|U|1141 tWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.015560842,0.015299030,0.003259057,0.037229894,0.000000000],[0.038498522,0.033098522,0.016154712,0.031253058,0.000000000],[0.003259057,0.013572389,0.016620668,0.016066358,0.000000000],[0.433048562,0.037641476,0.261065675,0.028372175,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|1019 - 9DFE|1|1A|A|1142|||A tWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.102154859,0.096752380,0.004944901,0.013796476,0.000000000],[0.099777216,0.093373493,0.001061587,0.008888900,0.000000000],[0.009061197,0.001061587,0.089431332,0.086905524,0.000000000],[0.213301508,0.091099193,0.001061587,0.087328260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|1019 - 9DFE|1|1A|A|1021 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 9DFE|1|1A|A|1020
Insertion    | Location [4] | Length Distribution [0.399409739,0.594195770,0.006099361,0.000295130] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 4 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 [5] | Right Index [8] // Initial node 9DFE|1|1A|G|1022 - 9DFE|1|1A|C|1140 from node 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node 9DFE|1|1A|G|1022:9DFE|1|1A|G|1024 and 9DFE|1|1A|C|1140:9DFE|1|1A|C|1140
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.004692894,0.009773618,0.005343954,0.097062545,0.000000000],[0.008243196,0.004601854,0.097885001,0.006404600,0.000000000],[0.026423031,0.551270192,0.005036511,0.064521312,0.000000000],[0.095820331,0.006647357,0.011311167,0.004962438,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1024 - 9DFE|1|1A|C|1140 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.077031253,0.078491313,0.004315696,0.076708478,0.000000000],[0.057508863,0.086666866,0.000955568,0.076869287,0.000000000],[0.067302366,0.000955568,0.082097414,0.143175873,0.000000000],[0.078226465,0.077756860,0.000955568,0.090982561,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|1022 - 9DFE|1|1A|U|1023 cSH 
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 [8] | Right Index [7] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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
