Fig. 4.

Schematics for aligning sequences with tandem duplication and inversion. Color gradient reflects the directionality of sequences from the 5′-end to the 3′-end. (A) Aligning a contig/read spanning a duplication breakpoint can be no different than aligning sequences with a deletion/insertion. (B) For contigs spanning other duplication breakpoints, the order of the aligned fragments is different in the two se-quences. (C) Optimal split-alignment for sequences with inversions is calculated by aligning the 5′-end of the first sequence to the 5′-end of the second one and aligning the 3′-end of the first sequence to the 3′-end of the reverse complement of the second one.