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 U1735 - A1757 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010617565,0.017207514,0.012224139,0.144725988,0.000000000],[0.119578446,0.011276938,0.159608290,0.013787516,0.000000000],[0.012394940,0.145308958,0.002585264,0.020771623,0.000000000],[0.159746803,0.012984375,0.144469588,0.012712053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair U1735 - A1757 cWW 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.019680511,0.052135779,0.000598716,0.003321980,0.000000000],[0.019508401,0.020008761,0.000598716,0.000598716,0.000000000],[0.378788100,0.004191009,0.025571885,0.418046764,0.000000000],[0.035351914,0.020401319,0.000598716,0.000598716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair G1736 - U1756 tSH 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.168008325,0.137401149,0.001642125,0.011900428,0.000000000],[0.047047609,0.037864462,0.000532653,0.000532653,0.000000000],[0.278182915,0.002619096,0.013399396,0.204760253,0.000000000],[0.048415624,0.046628008,0.000532653,0.000532653,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair A1737 - A1755 tSH 
ClusterNode  | Deletion Probability [0.000000000000000002141016935993338200000000000000000000000000] | Num Left Bases [3] | Num Right Bases [3] | Left Index [4] | Right Index [9] | Norm Constant [0.203059297941871] // Cluster node A1738:U1741 and A1751:G1754
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.246133399,0.253695198,0.246453931,0.224620956,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.002474039,0.002668836,0.003464906,0.016323442,0.000000000],[0.000520662,0.000520662,0.000520662,0.000520662,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - A1751 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010671796,0.018383968,0.012272411,0.145081933,0.000000000],[0.118399456,0.011223837,0.147716963,0.013568949,0.000000000],[0.012345101,0.157172007,0.002585120,0.022020461,0.000000000],[0.159365085,0.013201127,0.143217320,0.012774467,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1741 - A1751 cWW 
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.186964122,0.188627543,0.254394136,0.203223383,0.000000000],[0.043586124,0.039541834,0.000450536,0.039155962,0.000000000],[0.000450536,0.000450536,0.002182752,0.000450536,0.000000000],[0.002145394,0.000450536,0.037475536,0.000450536,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1738 - G1754 tHS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1739
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G1752
Insertion    | Location [2] | Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node
Insertion    | Location [5] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 5 in cluster node
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 [7] | Right Index [6] // New Initial node after Cluster
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
