Primer Design

Primers can be designed directly against the sequences annotated in CnidoSite, or against a sequence you paste in. Design is performed by primer3 (version 2.6.1) running on this server — your sequence is not sent to any third-party website. For reference, the primers released with this database were designed with an optimal melting temperature of 60°C (58–62 °C), an optimal primer length of 20 bp (18–24 bp), and a GC content between 40% and 60%, with self-complementarity restricted to limit primer-dimer formation; that parameter set is the CnidoSite published protocol preset below.

Template taken from CnidoSite: FUN_001290-T1 (FUN_001290-T1), 576 bp.
The engine ran normally but returned no primer pair under the current settings.
This is not a program error — the constraints are too strict for this template. The reasons, taken one by one from primer3’s EXPLAIN output:
Left primer: considered 3339, GC content failed 3310, low tm 29, ok 0
Right primer: considered 3339, GC content failed 3311, low tm 28, ok 0
Primer pair: considered 0, ok 0
Template

Two ways to supply a template: pick a species and a gene / transcript ID, or paste your own sequence. If the gene ID is found it is used; the pasted sequence is used otherwise. A template must be at least 30 bp.

Load example sequence
Primer parameters
Advanced parameters (any field left empty keeps the preset value)

A value that is not a number is ignored. The product size range is applied only when both of its fields are filled in and the maximum is at least the minimum.

Melting temperature
Primer length and GC content
Product and output
Self-complementarity and probe
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