A convenient method for locating sets of related short sequences in DNA sequences of any length

In investigating sequence variants in a family of highly repeated rat DNA, we needed to search the consensus sequence of the repeat unit of this family for short sequences which would become, with one base change, recognition sites for various restriction endonucleases. To do this, we have designed a pair of programs to search DNA sequences of any length for sets of related short sequences, allowing user-specified mismatches in the short sequence. Since putative regulatory regions are generally short sequences, these programs are also useful for locating all possible versions of such sequences in any given DNA. We describe the programs, and present results of searches using the programs.