Examples of Structured Variation. The Nucleotide Display is on the left with their corresponding Repeat Maps on the right. A) Nucleotide covariance within a tandem repeat on human chromosome Y: 392,702-397,700 (March 2006 assembly). We can refer to each monomer position as a column labeled 1-44, starting with column 1 on the left. There are only four columns with any significant amount of variation (columns 8-10, and 33). The consensus in column 33 appears to be T (blue) but 26 out of the 27 point substitutions in that column are Gs (green). Columns 8-10 appear to have a consensus of TGA but all variation in these columns occurs when all three positions are simultaneously replaced with CAG 34 times over the course of the repeat. B) A complex tandem repeat pattern on human chromosome 19, with monomer widths of 41, 43, 45, 47, or 49. This pattern appears to have a strong dimer component running throughout. Notice that all shifts in the repeating pattern are in multiples of two, yet the pattern itself actually has an odd width around 45 nucleotides. This kind of indel offset consensus is a fairly common occurrence and can come in sets of 3 or more nucleotides as well. C) Shifting pattern in rice chromosome 12 centromere. This repeat has a dual frequency spacing of 155/165. The Repeat Map clearly shows two bands at these lengths. The nucleotide display is set to width 161. The overall picture is a zig-zag pattern which might arise via a series of systematic insertions or deletions. When the repeating monomer is 155 nucleotides long, the vertical bands slant to the right. When the monomer is 165 nucleotides long, it slants to the left.
Seaman and Sanford BMC Bioinformatics 2009 10:452 doi:10.1186/1471-2105-10-452