Primer Map

Visualize PCR primer annealing positions on DNA sequences. Map forward and reverse primers, display their binding sites, and analyze amplicon regions.

Enter template sequence and primers to generate map...

What is Primer Map?

Primer Map is a tool for visualizing PCR primer binding positions on DNA template sequences. It shows where forward and reverse primers anneal, their orientations, and the predicted amplicon region. This helps verify primer design and understand the PCR product structure.

How to Use This Tool

Map your primers:

  1. Paste your DNA template sequence
  2. Enter forward primer sequence (5' to 3')
  3. Enter reverse primer sequence (5' to 3')
  4. View the map with primer positions
  5. Check amplicon size and coordinates

When to Use

This tool is useful when you need to:

  • Verify primer binding sites on target sequences
  • Visualize PCR amplicon boundaries
  • Check primer orientation and spacing
  • Validate primer design before ordering
  • Troubleshoot PCR amplification issues

Example Primers

Standard PCR primer pair:

Forward: 5'-ATGCGTACGATCG-3'
Reverse: 5'-TCGATCGTACGCA-3'

The reverse primer binds to the complementary strand.

Understanding the Map

The primer map shows:

  • FWD →: Forward primer binding (5' to 3' on top strand)
  • ← REV: Reverse primer binding (binds to bottom strand)
  • Amplicon: Region between primers that gets amplified
  • Positions: Base pair coordinates in the sequence

FAQ

Q: How does reverse primer binding work?
A: The reverse primer binds to the reverse complement of the template. Enter it in the 5' to 3' direction as synthesized.

Q: What if primers don't bind?
A: The tool will indicate if primers cannot be found on the template sequence.