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 [16] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Basepair G496 - C484 cWW 
ClusterNode  | Deletion Probability [0.000000000000000000000000000000000000151268825322266833831369] | Num Left Bases [11] | Num Right Bases [3] | Left Index [2] | Right Index [15] | Norm Constant [0.005678442180201] // Cluster node 5J7L|1|DA|A|497:5J7L|1|DA|C|509 and 5J7L|1|DA|G|481:5J7L|1|DA|A|483
Interaction  | Interacting Bases [9,12] | Pair Probability [[0.020028879,0.016764665,0.019150815,0.012041759,0.000000000],[0.002344946,0.002344946,0.206243870,0.002344946,0.000000000],[0.227956632,0.002344946,0.291098408,0.187955402,0.000000000],[0.002344946,0.002344946,0.002344946,0.002344946,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|506 - 5J7L|1|DA|G|481 tSS 
Interaction  | Interacting Bases [11,12] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|509 - 5J7L|1|DA|G|481 cWW 
Interaction  | Interacting Bases [1,13] | Pair Probability [[0.255486950,0.206401155,0.203351950,0.197013984,0.000000000],[0.016065555,0.013327012,0.002111047,0.013414598,0.000000000],[0.020426943,0.002111047,0.031068959,0.009926371,0.000000000],[0.007554652,0.007985333,0.006326349,0.007428094,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|497 - 5J7L|1|DA|A|482 cWS 
Interaction  | Interacting Bases [10,13] | Pair Probability [[0.388045295,0.332153463,0.018827954,0.023585663,0.000000000],[0.037274805,0.000540626,0.045519613,0.015373214,0.000000000],[0.002638001,0.045342292,0.001154794,0.000540626,0.000000000],[0.067172032,0.020750368,0.000540626,0.000540626,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|507 - 5J7L|1|DA|A|482 tHH 
Interaction  | Interacting Bases [1,14] | Pair Probability [[0.226839908,0.019867145,0.001702361,0.010380907,0.000000000],[0.165066191,0.067616638,0.001702361,0.001702361,0.000000000],[0.141812235,0.001702361,0.014787991,0.037155137,0.000000000],[0.153291403,0.152968278,0.001702361,0.001702361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|497 - 5J7L|1|DA|A|483 tSH 
Interaction  | Interacting Bases [3,7] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|499 - 5J7L|1|DA|A|503 tWH 
Interaction  | Interacting Bases [4,8] | Pair Probability [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|500 - 5J7L|1|DA|A|505 tSH 
Interaction  | Interacting Bases [2,9] | Pair Probability [[0.273328021,0.197478018,0.002879291,0.002879291,0.000000000],[0.012082009,0.008456580,0.002879291,0.002879291,0.000000000],[0.002879291,0.002879291,0.344532838,0.135329628,0.000000000],[0.002879291,0.002879291,0.002879291,0.002879291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|498 - 5J7L|1|DA|G|506 bif 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|501
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|502
Insertion    | Location [7] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.437500000,0.062500000,0.187500000,0.312500000,0.000000000]// Insertion after nucleotide 8, position 7 in cluster node
Insertion    | Location [10] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000]// Insertion after nucleotide 11, position 10 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 [13] | Right Index [12] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [13] | Right Index [13] | 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
