Additional file 2.
Histogram of the Repeat Overview pixel hue. This histogram is taken from Human Chromosome 4 as a typical example. There is a very significant peak at 135 which is caused by the di-mer structure of the Alu repeat. Next to it is a much smaller peak centered at 171 caused by the centromere alpha-satellite repeat. Much of the centromere is unsequenced so the number of copies is under-represented. When selecting the 'best frequency' the Repeat Overview starts at offset 1 and all future values must beat the previous by 10%. This is to ensure that it does not display multiples of repeats and also causes the graph to favor shorter repeats.
Format: TIFF Size: 239KB Download file
Seaman and Sanford BMC Bioinformatics 2009 10:452 doi:10.1186/1471-2105-10-452