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.
Daniel
I suspect that if promoters and TF binding sites were identical, they would be much easier to find. Usually you get TF binding motifs that are enriched for certain bases at certain positions, but not identical.
True, and in addition those sequences are rather short and therefore less easy to find. If a read is sufficiently longer than the repeat element, multi-mapping won't occur.
I see, thank you both for your responses. A follow-up question, what accounts for the differences in promoters/TF binding sites that recruit similar/the same enzymes? Are there small differences that may relate to transcriptional regulation, or do some of the differences not make a huge impact?