Step 1: Enter sequence information
	Enter sequence below in FASTA format: OR: Enter a filename:

Step 2: Set BLAT parameters

Select target database: U95A full-length targets U74abc murine series GNF clones, human GNF clones, mouse Return: top hit and 5% worse top hit and 10% worse top hit and 20% worse top hit and 30% worse top hit and 40% worse top hit and 50% worse top hit and 60% worse top hit and 70% worse top hit and 80% worse top hit and 90% worse all hits uniqueHit concise psLayout SNPs MinScore (if less than 80% coverage): 10 20 30 (Kent's default) 50 75 100 (recommended) 200 300 400 500 600 700 800 900 1000 (Kent's score= "matches - mismatches - some gap penalty") MinIdentity 0 10 20 30 40 50 60 70 80 90 (default) 95 96 97 98 99 99.5 99.9 100 %

BLAT on DNA is designed to quickly find sequences of 90-95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases, and sometimes find them down to 22 bases.

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats. The index takes up a bit less than a gigabyte of RAM. The genome itself is not kept in memory. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment.

BLAT was written by W.J.Kent (UCSC) and locally debugged/patched/maintained by S.Batalov.