Fuzzy Search DNA accepts a DNA sequence along with a query sequence and returns sites that are identical or similar to the query. You can use this program, for example, to find sequences that can be easily mutated into a useful restriction site.

Enter the sequence to search (in raw sequence or FASTA format) into the text area below. Input limit is 2000 characters.

Enter the query sequence into the text area below. Input limit is 30 characters.

Use the following parameters to specify how hits are scored, and to control which hits are returned.
  • Match value
  • Mismatch value
  • Gap penalty
  • Report the the top hits.


P. Stothard. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000; 28: 1102, 1104.