Blakesley et al. BMC Genomics 2010, 11:21 http://www.biomedcentral.com/1471-2164/11/21 Page 6 of 15 Figure 1 Gaps in comparative-grade finished BAC sequences from ENm001. The human- and comparative-grade finished sequences of the 541 BACs summarized in Table 1 were compared, and the gaps detected in the comparative-grade finished sequence were analyzed. Indicated for each species are the total bases within gaps per Mb of human-grade finished sequence (A), the number of gaps per Mb of human-grade finished sequence (B), and the median size of the gaps in base pairs (C). Previously, we found that sequence within gaps is dis- proportionately more repetitive than non-gap sequence; specifically, total repetitive sequences identified by the program RepeatMasker [29] account for roughly 50% of gap bases in comparative-grade finished sequence, while the subset of simple repeat sequences (predominantly homopolymer, as well as di-, tri, and tetranucleotide repeats) account for 3.7% of gap bases [5]. Further, it is well-established that these simple repeat sequences present major challenges during sequence finishing (e.g., determining the exact length of a dinucleotide repeat). We thus compared the simple repeat content of gap sequences for the species in the first data set (Figure 2B). In aggregate for all species, 2% of the total sequence cor- responds to simple repeats, whereas 10% of the sequence in captured gaps corresponds to simple repeats. Thus, simple repeats are generally enriched within captured gaps. The considerable variability seen among species