Homeologous regions in the Atlantic salmon genome, subdivided into 98 collinear blocks along the 29 European Atlantic salmon chromosomes. Red rectangles represent blocks of sequence without identifiable duplicated regions elsewhere in the genome. The innermost track (a) distinguishes regions of: red = high (>95% DNA sequence similarity), orange = elevated (90-95% sequence similarity), gre=low (~87% sequence similarity), yellow=telomeric regions (10-megabase bins) characterized by highly elevated male recombination. The middle track (b) shows genomic similarity (in 1 Mb intervals) between duplicated regions (red=high, yellow=medium, green=low sequence similarity). The outermost track (c) shows frequencey of Tc1-mariner transposon elements in the Atlantic salmon genome.