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 [12] // Initial node G17 - C38 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009734462,0.020214697,0.011090593,0.193143617,0.000000000],[0.018660673,0.008521127,0.200813940,0.012300663,0.000000000],[0.010985401,0.234217224,0.002109217,0.026079210,0.000000000],[0.203918224,0.012767771,0.024324928,0.011118254,0.000000000],[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 [1] | Right Index [12] // Basepair G17 - C38 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.059593935,0.069464361,0.000718031,0.003419172,0.000000000],[0.060124143,0.063018870,0.000718031,0.000718031,0.000000000],[0.342732568,0.003042710,0.014741292,0.253092402,0.000000000],[0.064776498,0.062403894,0.000718031,0.000718031,0.000000000],[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 [2] | Right Index [11] // Basepair G18 - A37 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.067789995,0.079017918,0.000816783,0.003889416,0.000000000],[0.068393123,0.071685967,0.000816783,0.000816783,0.000000000],[0.314619289,0.002761578,0.013379263,0.229707799,0.000000000],[0.073685325,0.070986412,0.000816783,0.000816783,0.000000000],[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 [3] | Right Index [10] // Basepair G19 - A36 tSH 
ClusterNode  | Deletion Probability [0.0000000000031049] | Num Left Bases [1] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.483768278986921] // Cluster node A20:A20 and G32:G35
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.199847682,0.220162527,0.263802060,0.230794523,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.004829830,0.005482656,0.008232375,0.059659296,0.000000000],[0.000898631,0.000898631,0.000898631,0.000898631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G32 tSS 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.106208866,0.107153807,0.197447047,0.115445278,0.000000000],[0.123800031,0.112312816,0.001279681,0.111216801,0.000000000],[0.001279681,0.001279681,0.006199787,0.001279681,0.000000000],[0.006093680,0.001279681,0.106443797,0.001279681,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A20 - G35 tHS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.416666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A33
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000]// Insertion after nucleotide 8, position 3 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 [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006165426,0.012560210,0.007138647,0.117002874,0.000000000],[0.010402818,0.005083832,0.126017962,0.008020992,0.000000000],[0.023812274,0.477595607,0.004391341,0.056326351,0.000000000],[0.116327236,0.008419708,0.014382630,0.006352092,0.000000000],[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 [5] | Right Index [6] // Basepair G21 - C31 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
