A representative genome alignment of a full-length gene and a sequence tag. The full-length gene encoding chromatin assembly factor 1, subunit A (Chaf1a), NCBI accession NM_013733, and the sequence tag BG-RRR265 align to a region of chromosome 17. (A) Overview showing the full region of the genome spanned by Chaf1a. Segments enlarged in the parts B-C are marked above the genome position. (B) Regions of genome that have been removed from the search space by repeat masking are shown in yellow, superimposed on the known gene track. The removal of these regions prevents correct localization of the full-length gene and sequence tag for these exons. (C) Magnification of the exon from region C illustrates differences between the alignment programs in aligning sequence to the edges of exons.