Optimal but not safe integration. For genomes and B = ( abxcydze ), an optimal but not safe integration of the singleton ( xyz ) produces A'. In R(A', B) we have two clean 2-cycles (C3 and C4), one good component and one bad component . The marker y is a link of and and is adjacent to d in genome B. This information is used to find an alternative optimal integration for the singleton (xyz), as we will show in Figure 6.