An estimation of copy number of sequences present in three sorghum genomic sequences in sorghum and Miscanthus × giganteus ( Mxg ). Copy number was estimated for regions of the sorghum genome in both sorghum and Mxg. Shown are three completed sorghum BAC sequences, one centromeric and two euchromatic. Sorghum copy number was estimated by matching to a sequence dataset of whole-genome sorghum shotgun sequences (red) and the Mxg copy number estimated by comparison to the 454 survey reads (blue) using a blastZ alignment within a 1,000-bp sliding window. The estimated genomic copy number based on the number of reads matching each window (y-axis) is plotted against the position of the window on the BAC (x-axis). The nucleotide identity cutoff for this analysis was 90%. The regions of greatest copy number on BACs AC169372 and AC169376 predominantly match miniature inverted repeat transposable elements (MITEs), transposons and retrotransposons, which are significantly more abundant in sorghum, while AC169373 contains highly abundant centromeric repeats, for which the Mxg and sorghum copy numbers agree closely.