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_051139-T1 (FUN_051139-T1), 486 bp.
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
Download TSV
Design results sorted by primer3 penalty, lowest first

Template 486 bp · parameter preset CnidoSite published protocol (Tm 60 [58-62] °C, 20 [18-24] bp, GC 40-60%) · 5 primer pairs returned.

Pair Left primer (5'→3') Position Len Tm (°C) GC (%) Right primer (5'→3') Position Len Tm (°C) GC (%) Product (bp) Penalty
1 ATGGGAGAACGTCTGAAGCG 1–20 20 60.109 55.000 AACCAGCAATTCCTACGCCA 84–103 20 59.962 50.000 103 0.146
2 ATGGGAGAACGTCTGAAGCG 1–20 20 60.109 55.000 CCCAAACGGCTGCATTGTAG 132–151 20 59.829 55.000 151 0.280
3 ATGGGAGAACGTCTGAAGCG 1–20 20 60.109 55.000 GCAACCAGCAATTCCTACGC 86–105 20 60.179 55.000 105 0.288
4 TGGCGTAGGAATTGCTGGTT 84–103 20 59.962 50.000 AAACCAATGAGCCCTGCCAT 277–296 20 60.252 50.000 213 0.290
5 ATGGGAGAACGTCTGAAGCG 1–20 20 60.109 55.000 GCAAAAGCAATGCAACCAGC 97–116 20 59.764 50.000 116 0.345
Primer map pair 1 (lowest penalty) · product 103 bp at template position 1–103 · the two tracks are drawn at different scales

Left primer — binds the template strand as listed (5′→3′)Right primer — its reverse complement binds hereProduct

Template486 bpproduct 103 bp · template 1–103product 103 bpleft primer, template 1–20right primer anneals here, template 84–1031122244365486Amplicon103 bpleft primer ATGGGAGAACGTCTGAAGCG · 5′→3′right primer AACCAGCAATTCCTACGCCA · its reverse complement binds the template strandATGGGAGAACGTCTGAAGCGAACCAGCAATTCCTACGCCAinterior 63 bp1275278103
Left primer
ATGGGAGAACGTCTGAAGCG
template 1–20 · 20 bp · Tm 60.109 °C · GC 55.000 %
Right primer
AACCAGCAATTCCTACGCCA
template 84–103 · 20 bp · Tm 59.962 °C · GC 50.000 %

Amplicon sequence (5′→3′ on the template strand, 103 bp) — blue is the left primer, red is where the right primer anneals. Copy from here to order or to check a base by eye.

ATGGGAGAACGTCTGAAGCGAGCATGGATAGGATACAAAAAATACAAGTTGGTGTTGAGGATTATTGCAGCGTTTGTGGGAGCTGGCGTAGGAATTGCTGGTT

The right primer is listed as its own 5'→3' sequence; what anneals to the template strand shown here is its reverse complement, so the highlighted stretch is complementary to the listed sequence. That is expected.

How to read this table. Position is a 1-based interval on the template, and both primers use the same convention: it is the stretch the primer occupies on the template strand (for the left primer, starting at its 5’ end; for the right primer, the region it anneals to, i.e. where the reverse complement of the listed sequence sits on the template). The two coordinates in a row can therefore be subtracted directly, and the amplicon view above marks both of them so you can check them by eye. Penalty is primer3’s weighted sum of the deviations from your constraints — lower is better, and the pairs are returned in that order. Tm is computed by primer3 from the SantaLucia thermodynamic parameters at the salt and primer concentrations in effect. The primer sequences themselves are 5’→3′ and can be ordered as they stand; the right primer anneals to the template as its reverse complement.

Specificity has not been assessed. This page only designs primers; it does not check whether they also anneal elsewhere in the genome or transcriptome. Once you have candidates, confirm each primer sequence with this site’s BLAST. The Tm and GC settings above are the design targets, and the annealing temperature still has to be optimised at the bench.

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