Microsatellite flanking regions are not necessarily unique sequences, but they may group into sequence families. Microsatellites occurring within such families are likely to give multiple banding patterns during polymerase chain reaction amplifications. microfamily (version 1) is a program that detects flanking-region similarities between different microsatellite-containing sequences, thus allowing for potentially problematic sequences to be eliminated prior to primer design. The program also accomplishes some otherwise tedious sequence editing, such as checking for nonpermitted characters, and eliminates poorly readable extremities or potential vector/adapter contamination.
microfamily is written in Perl and available for Linux and Windows systems at http://www.up.univ-mrs.fr/local/egee/dir/meglecz/microfamily.html.