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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair C38 - G21 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000001205418709556771524403256147503] | Num Left Bases [9] | Num Right Bases [3] | Left Index [2] | Right Index [13] | Norm Constant [0.119082120126475] // Cluster node 7TZS|1|X|U|39:7TZS|1|X|C|48 and 7TZS|1|X|G|18:7TZS|1|X|U|20
Interaction  | Interacting Bases [9,10] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|C|48 - 7TZS|1|X|G|18 cWW 
Interaction  | Interacting Bases [4,11] | Pair Probability [[0.020814325,0.017422103,0.019901827,0.012513985,0.000000000],[0.002436905,0.002436905,0.214331865,0.002436905,0.000000000],[0.236896108,0.002436905,0.263298345,0.195326202,0.000000000],[0.002436905,0.002436905,0.002436905,0.002436905,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|G|42 - 7TZS|1|X|G|19 tSS 
Interaction  | Interacting Bases [8,11] | Pair Probability [[0.014581319,0.007142534,0.900123518,0.008553754,0.000000000],[0.001394965,0.000950067,0.009238892,0.004152123,0.000000000],[0.033838546,0.001868529,0.001761031,0.001554301,0.000000000],[0.001707421,0.004387058,0.007605013,0.001140929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|A|47 - 7TZS|1|X|G|19 cWW 
Interaction  | Interacting Bases [7,12] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|A|45 - 7TZS|1|X|U|20 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|U|39 - 7TZS|1|X|A|43 tWH 
Interaction  | Interacting Bases [3,9] | Pair Probability [[0.080791748,0.104086035,0.081202799,0.080044060,0.000000000],[0.075160146,0.082258421,0.003424452,0.074358593,0.000000000],[0.077373217,0.003360263,0.007732479,0.076533923,0.000000000],[0.071118259,0.041391910,0.061967263,0.079196431,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7TZS|1|X|A|41 - 7TZS|1|X|C|48 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7TZS|1|X|G|40
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7TZS|1|X|A|44
Insertion    | Location [7] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 8, position 7 in cluster node
InitialNode  | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [10] // New Initial node after Cluster
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
