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 [20] // Initial node
ClusterNode  | Deletion Probability [0.000000000000015524427799645559379460012814890536486428420510] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [20] | Norm Constant [0.015988623090801] // Cluster node 5J7L|1|DA|C|1833:5J7L|1|DA|U|1834 and 5J7L|1|DA|A|1969:5J7L|1|DA|G|1972
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.060096154,0.060096154,0.060096154,0.060096154,0.000000000],[0.088942308,0.060096154,0.060096154,0.060096154,0.000000000],[0.060096154,0.060096154,0.060096154,0.060096154,0.000000000],[0.069711538,0.060096154,0.060096154,0.060096154,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1833 - 5J7L|1|DA|A|1969 tSS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.003009274,0.003009274,0.012968037,0.013028877,0.000000000],[0.003009274,0.014471321,0.003009274,0.285028871,0.000000000],[0.011086743,0.003009274,0.010400724,0.003009274,0.000000000],[0.339388921,0.003009274,0.278445149,0.014116440,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1834 - 5J7L|1|DA|A|1970 cWH 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009230036,0.016881218,0.010494353,0.194361300,0.000000000],[0.020319858,0.009555111,0.230862069,0.012852202,0.000000000],[0.010589659,0.197055880,0.002038410,0.022912280,0.000000000],[0.207859340,0.012317386,0.032759727,0.009911172,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1833 - 5J7L|1|DA|G|1972 cWW 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.086472048,0.076104746,0.108659211,0.072073014,0.000000000],[0.075412287,0.076719486,0.003403014,0.064300174,0.000000000],[0.073023686,0.003465765,0.007400953,0.060867279,0.000000000],[0.074810444,0.068877759,0.077447827,0.070962307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1969 - 5J7L|1|DA|G|1972 cSS 
Insertion    | Location [4] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 19, position 4 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [17] // Initial node 5J7L|1|DA|2MG|1835 - 5J7L|1|DA|G|1968 from node 
JunctionNode | Branches [2]  | Left Index [3] | Right Index [17] // Junction node G1835 - G1968 ID J5852
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [3] | Right Index [4] // Basepair G1835 - C1905 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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 [5] | Right Index [17] // Initial node 5J7L|1|DA|G|1906 - 5J7L|1|DA|G|1968 from node 
JunctionNode | Branches [2]  | Left Index [5] | Right Index [17] // Junction node G1906 - G1968 ID J5497
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 G1906 - C1924 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 [17] // Initial node 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1968 from node 
ClusterNode  | Deletion Probability [0.000000000000000000001953125000000000515889489244815448855715] | Num Left Bases [8] | Num Right Bases [1] | Left Index [7] | Right Index [17] | Norm Constant [1.000000000000000] // Cluster node 5J7L|1|DA|C|1925:5J7L|1|DA|A|1932 and 5J7L|1|DA|G|1968:5J7L|1|DA|G|1968
Interaction  | Interacting Bases [8,9] | Pair Probability [[0.042857649,0.043176051,0.398595795,0.047840582,0.000000000],[0.045370598,0.045265538,0.003601343,0.045021164,0.000000000],[0.000514478,0.000514478,0.017605820,0.000514478,0.000000000],[0.002424734,0.000514478,0.305668340,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1932 - 5J7L|1|DA|G|1968 tHS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.072312829,0.013210163,0.000160612,0.000790086,0.000000000],[0.072592178,0.013660448,0.000160612,0.000160612,0.000000000],[0.074675711,0.000160612,0.000992664,0.013333822,0.000000000],[0.631622605,0.103918470,0.001124287,0.001124287,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1926 - 5J7L|1|DA|A|1928 tSH 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.017121410,0.016023235,0.004960794,0.021367648,0.000000000],[0.100702211,0.023585581,0.426645111,0.023424167,0.000000000],[0.004960794,0.019524850,0.021175153,0.017390558,0.000000000],[0.094150901,0.024535264,0.159816286,0.024616037,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1929 tWW 
Interaction  | Interacting Bases [6,7] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1930 - 5J7L|1|DA|U|1931 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|1927
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [16] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012540860,0.155529775,0.012456608,0.140202703,0.000000000],[0.015113779,0.010952378,0.117426741,0.013578237,0.000000000],[0.012245828,0.142067698,0.002615550,0.191455955,0.000000000],[0.115398566,0.014477202,0.018565386,0.025372734,0.000000000],[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 [15] | Right Index [16] // Basepair G1933 - C1967 cWW 
HairpinNode  | Num Bases [1] | Left Index [16] | Right Index [16] | 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
