Wikipedia says there are three main types of repetitive regions (https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)), terminal repeats, tandem repeats, and interspersed repeats. However, I am wondering if promoter regions and other transcription factor binding sites will also be exactly the same between different genes? In some cases the exact enzymes that are recruited are exactly the same, making the recruitment regions also identical or at least very similar? We are working with whole genome metagenomic data from the surface of the eye and most of the reads that have multiple alignments are from similar strains/repetitive/low complexity sequences -- so what I'm asking about doesn't seem to be a problem, but I'm wondering why it isn't? Thanks.