Restriction Site Finder

Paste unambiguous DNA in the 5′→3′ direction, as raw sequence or one FASTA record. Spaces and lower case are accepted. Ambiguous bases, digits, multiple records and inputs above {max} bases are rejected; the sequence is never silently altered or truncated.

Recognition and cuts

The common enzymes use their documented recognition motifs and cuts, shown with a slash, e.g. G/AATTC for EcoRI and /GATC for MboI. Start is the 1-based position of the leftmost base in the entered strand. Cut after gives the boundary after that base; Beginning means before base 1. For circular DNA, a cut after the final base is the bond back to the first base.

Both strands are searched, including overlapping sites. In circular DNA, sites may cross the sequence end, but a motif cannot be longer than the whole molecule. Palindromic sites are listed once. For asymmetric custom motifs, + is the entered orientation, − its reverse complement and ± both at the same start.

Custom motifs

Use 1–32 DNA IUPAC symbols: R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=C/G/T, D=A/G/T, H=A/C/T, V=A/C/G and N=any base. These motifs define recognition only, not a cleavage offset. They do not affect fragment lengths.

Digest

All selected enzymes form one combined digest. Equal cut boundaries are counted once. The fragment table groups equal lengths and shows their multiplicity; sizes are measured along the entered strand. With no enzyme cuts, one full-length molecule remains. A circular molecule with one cut becomes one linear full-length fragment. CSV exports every site, selected motifs without sites, and each individual fragment, independent of the visible page.

Limits

At most {hits} sites. Sites are paged in groups of 20. No methylation sensitivity, star activity, reaction conditions, digestion efficiency, fragment end chemistry or gel migration is modelled. Ends cut differently on the two strands are reduced to the entered-strand length convention; this is no base-exact double-stranded fragment chemistry prediction.