Repeat motif examples from human chromosome 19. A) 35-bp repeat that frequently alternates with 171-bp centromeric alpha-satellite DNA. B) This repeat has no indels and point substitutions only occur in 3 of the 20 columns. C) It is common to see similar motifs contained in other repeats. This repeat shares the sequence GAGT with Figure 6B, but they are obviously different sequences with different patterns of variation. This sequence has irregularly spaced insertions of 4 nucleotides along with C often substituted for A. D) A repeat with many indels in multiples of 2. The various repeats align at 42, 44, and 46 bp. E and F) Two examples of a common repeat motif that occurs throughout the human genome. They are dominated by an internal AT repeat and generally have no single clear alignment.
Seaman and Sanford BMC Bioinformatics 2009 10:452 doi:10.1186/1471-2105-10-452