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. Author manuscript; available in PMC: 2008 Nov 9.
Published in final edited form as: J Comput Biol. 2007 Dec;14(10):1247–1272. doi: 10.1089/cmb.2006.0137

Figure 3.

Figure 3

The sites in the two connected components from Figure 2. We denote the component with sites {1, 3, 4} as C, and the component with sites {2, 5} as C′. The dominant sequence for C is 010, and the dominant sequence for C′ is 00. The rows in D[C, C′] are {a, b, d}, and the rows in D[C′, C] are {e, f, g}. The rows and columns have been permuted from their natural order to collect together the sites in the two components, and the rows in D[C, C′] and D[C′, C]. Note that row c is in neither D[C, C′] nor D[C′, C], since row c has the dominant sequence in both its C and C′ sides.