An example of localization to a pseudogene. Localization results for the full-length gene encoding mitotic arrest deficient 1-like 1 (Mad1l1), GenBank accession NM_010752. All representations of alignments between query sequences and build 34 of the mouse genome were made using the UCSC Genome Browser Custom Tracks feature. Slight alterations have been made to the representations, including the removal of graphical elements to improve the clarity of the figure, but no changes were made to the alignments. (A) The coordinates of the known gene on the genome are listed at the top, and positions of exons are represented by colored blocks. A region of chromosome 5 is shown containing the known localization of NM_010752 (the Known Genes track at bottom) and the alignments of exons for NM_010752 to the genome by SSAHA, MegaBLAST, and BLAT. (B) A region of chromosome 9 containing a pseudogene related to NM_010752 is shown on the same scale as (A). Below this, the segment of chromosome 9 containing the pseudogene is enlarged. The highest-scoring MegaBLAST match, circled in cyan, localizes to this pseudogene rather than the real gene. The highest scoring matches returned by SSAHA and BLAT are located on chromosome 5 and overlap with the correct localization.