Demo input and output

Test run on bacterial genome:
Test run without specificity check:
Multiple sequences test run:
Overlapping primers test run:

What does this server do?

PCRTiler is used to generate multiple, specific and physically similar PCR oligos for tiled analysis at a genomic locus. Given a sequence (or multiple sequences), this server will then:

  1. Split your region(s) of interest in multiple segments according to your specifications;
  2. Use Primer3 to design multiple primer pairs targeting each of those segments;
  3. Use BlastN to discard primer pairs with cross-hybridization potential. You may choose to skip this step;
  4. Generate a report recommending oligos for PCR tiling analysis.

NEW: a MacOSX package of the standalone application is now available from the download page.

Input sequence

You may provide one or multiple sequences. If you include multiple sequences, please make sure to use FASTA headers to distinguish them.

Tiling job name (optional):

Primer parameters

Minimum primer TM:
Maximum primer TM:
Minimum amplicon length:
Maximum amplicon length:

Tiling parameters

Specify either: What's this?

NOTE: Designing overlapping primer pairs is supported by the server. One way of achieving this is to specify that you want one primer pair at every 50 bps, along with a desired amplicon size of 100-150 bps.

Specificity verification parameters

Select the target organism to evaluate oligo specificity:

Filter this list using keyword:

Minimum total number of mismatches to unintended targets:

Minimum number of mismatches to unintended targets within the 5 bps at the 3' end of primers:

Number of candidate primer pairs to evaluate per region:

Distance threshold for misprimed amplicons:

Program used to evaluate specificity:
BlastN is more sensitive, but takes a longer time to run, than megablast.

Submit job

The job run time limit is currently set at 300 minutes. The maximum number of oligo pairs per jobs is currently limited to 1000. The server is currently idle and there are 0 jobs in queue.

Once the computation is done, send a notification email to (optional):
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