Select a Region
You can use the BLAST-Like Alignment Tool (BLAT) to find high-identity matches by indexing the genome, the tool is ideal for fast alignments and is typically faster than Basic Local Alignment Search Tool (BLAST) however is less sensitive to divergent sequences. (Kent, W. J. (2002). BLAT—the BLAST-like alignment tool. Genome research, 12(4), 656-664.)
Start by selecting a region, to do this zoom in until the displayed region is around 1400 bps, then right click the nucleic acid track at the top of the view window and select “BLAT read sequence” to perform the alignment of the in view sequence. This will open the BLAT modal box.
