Use this before ordering primers or troubleshooting PCR to check where one or multiple primer pairs bind on the same template.
Useful Checks
You can add multiple primer pairs and check them against the same template in one run.
After checking binding, the validated template can be opened in Primer Designer or Restriction Site Analyzer for the next primer-design or restriction-check step.
Primer Binding Checker can receive primer/template handoffs from Primer Designer and Sanger Primer Designer, so design and validation stay in one browser workflow.
Minimum Inputs Needed
Template DNA sequence.
One forward primer.
One reverse primer.
Optional Settings
Template topology
Use linear for fragments. Use circular for plasmids. In circular mode, the coordinate origin means base 1 / the start of the entered sequence, not the biological ori.
Add primer pair
Use this to check more than one primer pair on the same template.
Minimum binding length, bp
This is the shortest exact 3' match accepted as binding. Keep the default unless you are troubleshooting.
Max matches shown per primer
Limits long lists when a primer binds many places.
Open in other tools
Send the same template to Primer Designer or Restriction Site Analyzer.
How To Use
Paste or upload the template.
Choose linear or circular topology.
Enter primers in 5' to 3' direction.
Add more primer pairs if needed.
Click Check primer binding.
Understanding The Results
The quick result tells you whether a product is expected.
The map shows where the primers bind.
5' overhangs are shown separately from the template-binding part.
Multiple binding sites are a warning for nonspecific PCR.
The product size is the expected amplicon size for that primer pair.
Accepted Input Formats
Template: raw DNA sequence, FASTA, or supported GenBank.
Primers: raw DNA sequence, written 5' to 3'.
FASTA headers and GenBank annotations are ignored.
Assumptions And Limitations
The tool checks exact binding. It does not fully model mismatches.
A result with no binding warnings does not guarantee PCR success.
Use the result as a screening check, then confirm with your experiment conditions.
Example
Paste a plasmid sequence, enter your forward and reverse primers, choose circular topology, and check that each primer binds once with the expected product size.
Use note: These tools are for research and educational planning. Check important calculations and sequence designs before ordering reagents or running experiments.