Telomerase is a reverse transcriptase which maintains a specific repeat sequence of DNA, the telomere, during development.

The paralogous segments can be repeat sequences with more than 90% sequence similarity.

SSM can result in an increase or decrease in the number of short repeat sequences.

The second way that SSM induces transcriptional regulation is by changing the short repeat sequences located outside the promoter.

If there is a change in the short repeat sequence it can affect the binding of a regulatory protein, such as an activator or repressor.

DNA transposons encode a transposase protein, which is flanked by inverted repeat sequences.

Hin functions by binding to two 26bp imperfect inverted repeat sequences as a homodimer.

Strong homologies to this repeat sequence are also present in several mammalian and avian elastins.

RepeatMasker uses a database of known repeat sequences and implements a string-matching algorithm to find copies of those repeats in a new sequence.

We found from 100,000 to 400,000 pairs of exact repeats in each chromosome using a minimum length of 25 bp (after filtering out simple repeat sequences).