Figure 5

The structure of alignment graphs and A-Bruijn graphs does not display inversions. Let $\overline{B}$ denote the reverse complemented block representation of a block B. The alignment graph structure and A-Bruijn graph structure for the two sequences ABC and A$\overline{\mathrm{B}}$C is the same as for the two sequences ABC and ABC. The orientation of blocks remains unclear in the graph structures. However, there are two Enredo graph structures for the alternative orientations of block B in one sequence. Thus, the transformation from the alignment graph structure or A-Bruijn graph structure to an Enredo graph structure is ambiguous with two alternatives.