SUMMARY: Functional modules within protein sequences are often extracted by consensus sequence patterns representing a linear motif; however, other functional regions may only be described by combined features such as amino acid composition, profiles of amino acid properties and randomly distributed short sequence motifs. If only a small number of functional examples are well characterized, the researcher needs a tool to extract similar sequences for further investigation. AVAILABILITY AND IMPLEMENTATION: We provide the web application 'SAPA tool', which allows the user to search with combined properties, ranks the extracted target regions by an integrated score, estimates false discovery rates by using decoy sequences and provides them as a sequence file or spreadsheet. Source code, user manual and the web application implemented in Perl, HTML, CSS and JavaScript and running on Apache are freely available at http://sapa-tool.uio.no/sapa/