Comparison of results from 454 sequencing with ABI-Sanger sequencing. a. Map of the previously published BAC 519J4. Genes are depicted by grey boxes with transcriptional orientations indicated by arrows. Transposable elements are depicted as coloured boxes with LTRs indicated as shaded areas. Nested transposable elements are raised above the ones into which they have inserted. Regions covered by 454 sequence contigs are depicted as blue and purple bars underneath the map. Note that single copy sequences are covered well whereas multicopy sequences such as transposons or tandem repeats contain a large number of gaps. Sequence contigs used for comparison of ABI-Sanger and 454 sequencing results are depicted in purple. b. Detailed map of the region of Gap1. Three tandem repeats were pooled into the consensus contig c68. c. Multiple sequence alignment of the three repeat units shown in (b.) and the resulting consensus contig. Differences between repeat units are highlighted. d. Sequence coverage provided by 454 sequencing (blue) and ABI-Sanger sequencing (black). Red lines indicate simulated coverages with the same number of sequences assuming a purely random distribution. Red arrows indicate gaps in the ABI-Sanger coverage. Grey lines indicate coverage with 454 sequences from an independent sequencing experiment with fewer reads. The region of clearly higher coverage with 454 sequences suggests the presence of a duplicated sequence that could not be resolved with ABI-Sanger sequencing. e. Map of BAC 773K14 with aligned 454 sequence contigs and coverage with individual 454 sequences (colours as in d).