Additional file 3 of Finding and extending ancient simple sequence repeat-derived regions in the human genome

Additional file 3: Figure S3. Asymmetric similarity to poly-A. The frequency of adenine nucleotides (A) at every site within 200 bp of perfect poly-A repeats. The solid line shows the frequency of A in a human genome where all transposable elements have been masked and the dotted line shows the frequency in an unmasked human genome. As a reference, the gray box represents a range of 3 standard deviations from the mean frequencies of A calculated in 700 bp windows from 300 to 1000 bp away from both ends of all perfect repeats. The strongly varying frequencies in the unmasked genome are mostly a symptom of the high copy number of retroelements such as Alu and Line1. The asymmetric frequency of A’s adjacent to perfect A repeats in the masked genome likely reflects incomplete masking of transposable elements and the existence of other unmasked retrotransposed sequences in what would have been the 5′ region of the retrotransposed poly-A mRNAs.