Bioinformatics.Org Back to PrimerX homepage
Automated design of mutagenic primers for site-directed mutagenesis


Primer Design:

Primer Characterization




Primer Design Based on DNA Sequence

Step 1. Upload a text file containing your template DNA sequence, or paste the sequence onto the text area below. You may enter a raw or Fasta-formatted sequence.

1        10        20        30        40        50        60

Your sequence length should be between 40 and 8,000 bp. The target site for mutation should be flanked on both sides by a sufficient length of DNA. All non-GCAT characters in the sequence will automatically be removed.

Step 2. Enter a short code identifying your desired mutation. Follow the format described below.

Mutation code:     (optional)

Mutation type Mutation code Description
Substitution C15G Replaces a "C" at position 15 with a "G".
CG15AT Replaces "CG" at positions 15-16 with "AT".
Deletion C15del Deletes a "C" at position 15.
CG15del Deletes "CG" at positions 15-16.
Insertion C15insG Inserts a "G" at position 15, pushing the "C" to position 16.
CG15insAT Inserts "AT" at positions 15-16, pushing the "CG" to positions 17-18.

Step 3. Choose the mutagenesis protocol that you will be using, and click on "Next."

Primer design protocol:

Home | Help