Repeat-match finds all maximal exact matches in the reference genome-file - so, essentially it will find all repeated sequences of specific length in a given genome file (similar to kmer search). Repeat-match is a suffix tree algorithm designed to find maximal exact repeats within a single input sequence. It uses a similar algorithm to mummer, but altered slightly to find maximal exact matches within a single sequence. The program will report both forward and reverse complement repeats by default unless the -f option is used. While the -t option identifies tandem repeats, the exact-tandems script is a wrapper for repeat-match and does a more graceful job of reporting the tandem repeats.
Parent program: MUMmer
MUMmer or 'Maximal Unique Matches' is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program.