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 supports the entire IUPAC alphabet and several genetic codes.

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.

  • Show bases per line.
  • Show the translation for reading frame
  • Use the genetic code.
  • Restriction sites should
  • Treat sequences as molecules.


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