PCR Primer Design

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PCR Primer Design

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Intro & Info

Eurofins Genomics’ PCR Primer Design Tool enables you to design optimal PCR primer pairs using the advanced Primer3 algorithm Primer3 Manual.

The tool analyses your DNA sequence to identify primers with high specificity, efficiency, and product quality. Default parameter settings ensure reliable results, but you can adjust them to customise the analysis to your experimental needs.

Detailed Primer3 settings for each input field can be viewed by clicking the corresponding link.

Click “Design Primers” to generate a list of suitable PCR primer pairs. The output also includes the recommended annealing temperature for each pair.

PCR Primer Design

Assay Design

Primer Name(s):

1. Target Sequence:

2. Target Sequence:

Design Parameters open / close

1. Target Region:

Start position:

Length:

2. Target Region:

Start:

End:

Primer 3' GC clamp bases:

Primer 3' GC clamp bases

Primer maximal homopolymer repeat

Primer maximum number of G/C allowed in last five 3' bases

Max. Tm difference [°C] (default: 3°C):

qPCR Probe Criterias open / close

Minimum

Maximum

Probe Length (mer):

Probe GC (%):

Orientation open / close

Please specify the orientation of the qPCR probe on the target sequence:

Sense

Antisense

Primer Criterias open / close

Minimum

Maximum

Length (mer): Min | Max

Primer GC (%): Min | Max

Tm (°C) Min | Max

Amplicon Criterias open / close

Minimum

Maximum

GC Content (%):

Tm (°C): Min | Max

Reaction Conditions open / close

Monovalent salt concentration
(0.1 - 50 mM):

Primer concentration
(0.1 - 50 nM):

Output Parameters open / close

Permit multiple primer binding sites

Yes

No

Sort by Ta of the PCR products

Yes

No

* These fields are mandatory

Design Result

No.	Name	Sequence	Ta	Start..End	Length	GC	Tm	Order

					20	55.0	50.7
	Amplicon	xxx

No.	Name	Sequence	Ta	Start..End	Length	GC	Tm	Order
	qPCR Product	xxx

					20	55.0	50.7
					20	55.0	50.7

No.	Name	Sequence	Ta	Start..End	Length	GC	Tm	Order
	qPCR Product	xxx

					20	55.0	50.7
					20	55.0	50.7

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