TECHVAULT > FAQ > APPLICATION SUPPORT > PCR AND SEQUENCING

Can you design and synthesize a set of sequencing primers?

IDT does not have a sequencing primer design service. We recommend using the PrimerQuest software available for free on our website to help you choose the primers.

Position:
The best sequencing data is found in the region 80-150bp away from the primer. It is difficult to get good base calls less than 50bp away from the primer and greater than 300bp away.

Primer design:
Length should be between 18 and 30 nt, with optimal being 20-25 nt.
G-C content of 40-60% is desirable.
The Tm should be between 55°C and 65°C.
Avoid primers with strong self-dimers or hairpins. You can use our OligoAnalyzer located on our website to check for this.
You also want to avoid primers which are >90% homologous to other regions within your sample. A BLAST search will alert you to this problem.

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