We show that ignoring repeat-overlapping seeds misses between 22 and 84 Mb of mostly repetitive elements that actually align between mammals and we provide a tool, called RepeatFiller, to incorporate such repeat-overlapping alignments into genome alignments. Here, we investigated to what extent aligning repetitive sequences are missed in whole-genome alignments. This can be problematic if the regions flanking a repeat have been diverged to an extent that no seed in the vicinity of the repeat can be found. Consequently, alignments between repeats are only found during the extension phase, initiated from seeds outside the repeat boundaries. Therefore, seeds that overlap repetitive regions are not used to start a local alignment phase, either by masking repetitive regions before aligning genomes or by dynamically adapting seeding parameters by the observed seed frequencies. Given that repetitive sequences provide numerous seed matches to paralogous repeat copies in a whole-genome comparison, it is computationally infeasible to start a local alignment from seeds located in repetitive sequences. Seed detection is then followed by a computationally more expensive alignment extension step that considers ungapped and gapped local alignments. The seeding step of this heuristic detects short words or patterns (called seeds) that match between the sequences of the 2 genomes. Most methods for aligning entire genomes use a seed-and-extend heuristic, originally implemented in BLAST, to find local alignments between the sequences of 2 genomes. The nature of repetitive sequences such as transposons, however, leads to many paralogous alignments, which pose a challenge for comprehensively aligning orthologous repeats between vertebrate genomes. Studying how ancestral transposons and other repeats were co-opted into functional roles requires whole-genome alignments that comprehensively align orthologous repeats. Importantly, a sizeable portion of evolutionarily constrained regions arose from ancestral transposon sequences. By contributing transcription factor binding sites, promoters, and distal regulatory elements, co-opted transposons are involved in rewiring of regulatory networks and drive regulatory innovation. For example, transposon-derived sequences contribute to the transcriptome by providing alternatively spliced exons. While most repeats are estimated to evolve neutrally, transposons are important substrates for evolutionary tinkering. A substantial portion of vertebrate genomes consist of transposons and other repetitive sequences.