The Sequence Manipulation Suite:
Primer Map
Primer Map accepts a DNA sequence and returns a textual map showing the annealing positions of PCR primers. Restriction endonuclease cut sites, and the protein translations of the DNA sequence can also be shown. Use this program to produce a useful reference figure, particularly when you have designed a large number of primers for a particular template. Primer Map uses the standard genetic code and supports the entire IUPAC alphabet.

Paste a raw sequence or one or more FASTA sequences into the text area below. Input limit is 100000 characters.

Enter the primers you want to display. An example primer entry is: (T7) aatacgactcactatag. The round brackets surround the name of the primer, and the sequence is written in the 5' to 3' direction. Multiple entries are separated by commas.

Please check the browser compatibility page before using this program.
  • Show bases per line.
  • Show the translation for reading frame
  • Restriction sites should
  • Treat sequences as molecules.
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*You can mirror this page or use it off-line.
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