BLAT produces two major classes of alignments:
- at the DNA level between two sequences that are of 95% or greater identity, but which may include large inserts;
- at the protein or translated DNA level between sequences that are of 80% or greater identity and may also include large inserts.
The output of BLAT is flexible. By default it is a simple tab-delimited file which describes the alignment, but which does not include the sequence of the alignment itself. Optionally it can produce BLAST and WU-BLAST compatible output as well as a number of other formats.