FuzzyFinder

FuzzyFinder will search a large piece of DNA (the haystack) for matches to a small piece of DNA (the needle). In the output matching areas will be blue, and UPPER case. A traditional alignment display appears on the bottom. This utility is particularly useful in mapping mRNA/cDNA sequences to Genomic data. (more info)

or

Pattern to find (the needle):

DNA to search through (the haystack):

strand match

Another WWW biological utility developed by Jim Kent, and local copy modified by Peter FitzGerald.