Figure 1.

Alternative alignments of the sequences CATCGA and CCGATA. The alignment on the left is colinear if the dinucleotides AT (red) are interpreted as insertion or deletion. Alternatively, the AT dinucleotides can be aligned and the CG dinucleotides interpreted as insertion or deletion. Non-colinear aligners that allow for translocations may align the AT dinucleotides in addition to the CG dinucleotides. The alignment on the right shows a non-colinear alternative that interprets the four nucleotides ATCG as inversion (reverse complement). In this example, we expect non-colinear aligners to prefer the inversion (right) over the translocation (left) since it creates fewer segments.