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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006106609,0.011394277,0.021230713,0.129932994,0.000000000],[0.013919657,0.006427520,0.426766304,0.008164019,0.000000000],[0.006909893,0.130722191,0.004098058,0.015295994,0.000000000],[0.143161101,0.007777744,0.061446752,0.006646171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair C1605 - G1309 cWW 
ClusterNode  | Deletion Probability [0.0000000196259322] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.295960532366638] // Cluster node 5J7L|1|DA|C|1606:5J7L|1|DA|A|1608 and 5J7L|1|DA|A|1308:5J7L|1|DA|A|1308
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.048369009,0.033068095,0.000547627,0.002633400,0.000000000],[0.179690744,0.129067806,0.001755500,0.001755500,0.000000000],[0.278732492,0.002625517,0.013248063,0.208305932,0.000000000],[0.050400819,0.048704241,0.000547627,0.000547627,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1606 - 5J7L|1|DA|A|1308 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.414443196,0.029718936,0.003853170,0.018419488,0.000000000],[0.028948610,0.014046437,0.011475468,0.014056646,0.000000000],[0.003853170,0.011491976,0.356313449,0.021716090,0.000000000],[0.018397520,0.014053216,0.021246137,0.017966491,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1608 - 5J7L|1|DA|A|1308 tWW 
Insertion    | Location [1] | Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | Left Length Distribution [0.005372012,0.333064733,0.650013430,0.011012624,0.000537201] | Left Letter Distribution [0.500000000,0.071428571,0.214285714,0.214285714,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // Initial node 5J7L|1|DA|A|1610 - 5J7L|1|DA|A|1307 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 5J7L|1|DA|G|1309
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [5] | Right Index [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [5] | Right Index [10] // Fixed node on right for 5J7L|1|DA|A|1610
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node
JunctionNode | Branches [2]  | Left Index [5] | Right Index [9] // Junction node C1611 - C1306 ID J3170
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.003708089,0.006649494,0.004262905,0.077294868,0.000000000],[0.055188220,0.026436068,0.597914779,0.037535311,0.000000000],[0.004310778,0.078960365,0.000812555,0.009124318,0.000000000],[0.078296919,0.005166364,0.010409412,0.003929554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair C1611 - G1620 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
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] | Right Index [9] // Initial node 5J7L|1|DA|U|1621 - 5J7L|1|DA|C|1306 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 5J7L|1|DA|C|1607
InitialNode  | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011589741,0.110338296,0.012004041,0.159995716,0.000000000],[0.016866856,0.010578618,0.157735464,0.013692293,0.000000000],[0.011902799,0.159428801,0.002450451,0.133386380,0.000000000],[0.144149775,0.014131177,0.021334200,0.020415391,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // Basepair G1622 - C1306 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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
