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 [18] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [18] // Basepair C21 - G11 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.028776211,0.032326394,0.007021393,0.007021393,0.000000000],[0.712040258,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.044950176,0.000000000],[0.007021393,0.007021393,0.007021393,0.007021393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [17] // Basepair C22 - A10 bif 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [3] | Right Index [16] // Fixed node on left for 8DK7|1|C|U|6
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [4] | Right Index [16] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000009533766986221214533025748902239021246] | Num Left Bases [5] | Num Right Bases [4] | Left Index [4] | Right Index [16] | Norm Constant [0.000378449897444] // Cluster node 8DK7|1|C|U|24:8DK7|1|C|A|29 and 8DK7|1|C|U|6:8DK7|1|C|C|9
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.019248377,0.341640756,0.003950463,0.038911407,0.000000000],[0.003950463,0.046098892,0.012361189,0.003950463,0.000000000],[0.034274119,0.003950463,0.025404521,0.016144783,0.000000000],[0.003950463,0.003950463,0.037265855,0.404947322,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|U|24 - 8DK7|1|C|U|6 tHW 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.121583738,0.122053423,0.125556588,0.144924515,0.000000000],[0.111055049,0.114840499,0.001350235,0.124802948,0.000000000],[0.001350235,0.001350235,0.008345120,0.001350235,0.000000000],[0.006642085,0.001350235,0.112094623,0.001350235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|A|29 - 8DK7|1|C|U|6 tHS 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|G|26 - 8DK7|1|C|A|7 cWW 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.004841606,0.050416664,0.005513298,0.100138349,0.000000000],[0.008504413,0.023738407,0.100986868,0.006607555,0.000000000],[0.005452069,0.529512277,0.001039223,0.013313184,0.000000000],[0.098856770,0.034290020,0.011669605,0.005119692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|G|27 - 8DK7|1|C|C|8 cWW 
Interaction  | Interacting Bases [3,9] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|G|26 - 8DK7|1|C|C|9 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.003098658,0.003098658,0.013353226,0.013415874,0.000000000],[0.003098658,0.014901162,0.003098658,0.293495075,0.000000000],[0.011416052,0.003098658,0.010709656,0.003098658,0.000000000],[0.319766810,0.003098658,0.286715797,0.014535741,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|U|24 - 8DK7|1|C|A|29 cWH 
Interaction  | Interacting Bases [7,8] | Pair Probability [[0.104166825,0.124612443,0.005621093,0.043860124,0.000000000],[0.100542670,0.099286043,0.001147115,0.009317734,0.000000000],[0.010004306,0.001147115,0.104180479,0.094225112,0.000000000],[0.104547355,0.103291070,0.001147115,0.092903402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8DK7|1|C|A|7 - 8DK7|1|C|C|8 cSH 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8DK7|1|C|U|25
Insertion    | Location [4] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 7, position 4 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.023164190,0.014489905,0.351490869,0.017735478,0.000000000],[0.014838319,0.010255708,0.019408962,0.045569652,0.000000000],[0.375747942,0.019193415,0.003658470,0.015799099,0.000000000],[0.017770069,0.043129315,0.016144978,0.011603631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [12] // Basepair G30 - A5 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [10] | Right Index [11] // Basepair C31 - G4 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | 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
