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 [14] // Initial node G683 - C707 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009784429,0.021777989,0.011031390,0.208347691,0.000000000],[0.017985926,0.008620950,0.201027673,0.012148861,0.000000000],[0.010927772,0.225150163,0.002128171,0.027374013,0.000000000],[0.195241385,0.012608128,0.023487298,0.012358162,0.000000000],[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 [14] // Basepair G683 - C707 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [13] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [13] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.300000000,0.100000000,0.300000000,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [12] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.024365078,0.049254635,0.000551847,0.002964234,0.000000000],[0.024333849,0.025191930,0.000551847,0.000551847,0.000000000],[0.360272004,0.003862929,0.022477458,0.366756534,0.000000000],[0.036455331,0.025365961,0.000551847,0.056492670,0.000000000],[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 [12] // Basepair G685 - U705 tSH 
ClusterNode  | Deletion Probability [0.000000000000000000001936518681344305600000000000000000000000] | Num Left Bases [3] | Num Right Bases [5] | Left Index [4] | Right Index [11] | Norm Constant [0.059289822346423] // Cluster node U686:G688 and C699:A704
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G688 - C699 cWW 
Interaction  | Interacting Bases [2,5] | Pair Probability [[0.178334863,0.194159396,0.211510727,0.269655199,0.000000000],[0.002162307,0.002162307,0.002162307,0.002162307,0.000000000],[0.010959123,0.011829242,0.016274252,0.089978741,0.000000000],[0.002162307,0.002162307,0.002162307,0.002162307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A687 - G700 tSS 
Interaction  | Interacting Bases [2,7] | 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 A687 - G703 tHS 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.021610380,0.003754531,0.079044280,0.003754531,0.000000000],[0.153817650,0.026937290,0.127005017,0.003754531,0.000000000],[0.059695354,0.003754531,0.038161270,0.024230069,0.000000000],[0.278346563,0.003754531,0.037364260,0.135015212,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U686 - A704 tWH 
Interaction  | Interacting Bases [3,8] | Pair Probability [[0.012109700,0.013573278,0.016008335,0.013747056,0.000000000],[0.002917024,0.002917024,0.002917024,0.002917024,0.000000000],[0.367060650,0.259480989,0.262267704,0.032416099,0.000000000],[0.002917024,0.002917024,0.002917024,0.002917024,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G688 - A704 tSS 
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion C701
Insertion    | Location [6] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.300000000,0.100000000,0.300000000,0.300000000,0.000000000]// Insertion after nucleotide 9, position 6 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
