Figure 5

Optimal but not safe integration. For genomes $A=\left(a\overline{c}bed\right)$ 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 ${\mathcal{C}}_1=\left\{C_1\right\}$ and one bad component ${\mathcal{C}}_2=\left\{C_2\right\}$. The marker y is a link of ${\mathcal{C}}_1$ and ${\mathcal{C}}_2$ 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.