The Seven State Aligner uses a dynamic programming algorithm to find the best alignment between two pieces of DNA. This is designed for genomic to genomic comparisons, especially across species. Along with the alignment it classifies areas as either coding (symbols 1,2,3), heavily conserved (symbol H), lightly conserved (symbol L) or extended insert in either query or target (Q,T). The coding areas shouldn't be taken as gospel - this isn't a gene finder, at least not yet. Please limit the size of the sequences you put in to less than 10,000 bases each. The time it takes is proportional to the product of the two sequence sizes. Two 10,000 base sequences will take approximately ten minutes to align. Two 1,000 base sequences will take approximately six seconds.
Pattern to find (query):
DNA to search through (target):
Another WWW biological utility by Jim Kent.