Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [13] // Initial node U1798 - A1821 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000000239456582305914910000000000000000] | Num Left Bases [4] | Num Right Bases [5] | Left Index [1] | Right Index [13] | Norm Constant [0.038961326718714] // Cluster node U1798:A1802 and A1815:A1821
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.441749542,0.015205919,0.075103199,0.098489209,0.000000000],[0.056325096,0.001443277,0.053941313,0.088214880,0.000000000],[0.029154810,0.052792421,0.002289604,0.001443277,0.000000000],[0.028991690,0.051969210,0.001443277,0.001443277,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1802 - A1815 tHH 
Interaction  | Interacting Bases [3,6] | Pair Probability [[0.019014290,0.019018870,0.006250487,0.026309014,0.000000000],[0.024244124,0.028687159,0.663510195,0.029548129,0.000000000],[0.006250487,0.025586574,0.020400031,0.018196760,0.000000000],[0.035814972,0.030755175,0.024764652,0.021649081,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1800 - G1817 tWW 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.001549151,0.002727414,0.015998825,0.013617496,0.000000000],[0.000211773,0.000211773,0.000211773,0.001058865,0.000000000],[0.016473642,0.046369184,0.120208586,0.779667332,0.000000000],[0.000211773,0.000211773,0.000211773,0.001058865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1799 - U1818 tSS 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.079674918,0.078577819,0.003724751,0.003645748,0.000000000],[0.655402229,0.000881344,0.041046967,0.005187295,0.000000000],[0.025118855,0.072642517,0.002497325,0.000881344,0.000000000],[0.024567540,0.004388660,0.000881344,0.000881344,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1800 - A1819 tHH 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.009165038,0.019030160,0.010081135,0.199658022,0.000000000],[0.023115364,0.009112997,0.204928790,0.011047591,0.000000000],[0.010129904,0.192879101,0.002111419,0.023228345,0.000000000],[0.234721258,0.010832296,0.027253714,0.012704867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1798 - A1821 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.069564796,0.064432445,0.066759450,0.067283927,0.000000000],[0.080157187,0.061605000,0.064605906,0.031370144,0.000000000],[0.067351560,0.005632734,0.058859672,0.059614966,0.000000000],[0.100984120,0.065911246,0.066185624,0.069681223,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1798 - A1802 cSS 
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.416666667,0.250000000,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
Insertion    | Location [5] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.583333333,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 9, position 5 in cluster node
Insertion    | Location [8] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 12, position 8 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 [5] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.041492445,0.082494358,0.378797887,0.045100819,0.000000000],[0.048364757,0.043877065,0.003499517,0.043448887,0.000000000],[0.000499931,0.000499931,0.016954426,0.000499931,0.000000000],[0.002380608,0.000499931,0.291089576,0.000499931,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [5] | Right Index [8] // Basepair A1803 - G1814 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009613617,0.017593128,0.010983027,0.192350441,0.000000000],[0.021287894,0.008639455,0.234523700,0.012787711,0.000000000],[0.011096459,0.200570476,0.002109537,0.023296342,0.000000000],[0.204768830,0.012284769,0.027115440,0.010979173,0.000000000],[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 [6] | Right Index [7] // Basepair C1804 - G1813 cWW 
HairpinNode  | Num Bases [1] | Left Index [7] | Right Index [7] | 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
