Alignment Locations vs. Karyotype. The alignment [A] shows all hits on the genome. The best hit is boxed. In this case, BLAT shows one hit.
Alignment Locations vs. Query. The alignment [B] shows hits, or High Scoring Pairs (HSPs), as a red bar along the query sequence (the black and white bar below).
Alignment Summary. The summary [C] shows a table of hits, with customisable columns. Links are provided from the table. The link 'A' shows an alignment of the query and target sequence. 'G' shows the hit on the genome. 'C' brings you to the location tab, where you can see the BLAT hit in context of genes in that region.
Click 'C' in the Alignment Summary table to go to the Location tab (explored in The location tab section of this course). The location tab will allow you to find out if your BLAT hit matches any Ensembl genes.