Blakesley et al. BMC Genomics 2010, 11:21 http://www.biomedcentral.com/1471-2164/11/21 Page 7 of 15 Figure 2 Characteristics of gaps in comparative-grade finished BAC sequences from ENm001. Sequences within the gaps (blue bars) summarized in Figure 1 were analyzed with respect to GC (A) and simple repeat (B) content; similar analyses were performed for the entire human-grade finished BAC sequences (orange bars). Results for the 19 species with the greatest differences (i.e., gap sequences vs. total BAC sequences) for each analysis are shown. Each error bar represents the 95% confidence interval. with respect to this enrichment (Figure 2B) is even more dramatic. At the extreme, dog has an unusually high amount of simple repeats in its gap sequence (28%); by comparison, in 26 of 37 other species, this value is less than 10%. Table 4 details the repeat content within all the sequences of our first data set (taken as a whole) as well as that in captured and uncaptured gaps. In addition to again noting the significant enrichment of simple repeats within captured gaps, these data reveal that long interspersed repeats (LINES) are significantly enriched in uncaptured gaps. Captured versus uncaptured gaps An early step in sequence finishing involves ordering and orienting contigs within the initial sequence assem- bly. This process extensively utilizes information about the paired forward- and reverse-primed sequence reads generated from each plasmid template during the shot- gun phase. Two contig ends are considered adjacent to