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: scaffold243.g14.t1 (scaffold243.g14.t1), 2,156 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 2,156 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 AGGCCTGCCTGGAACAATAC 748–767 20 60.034 55.000 TGATTGCGCAACTCTCCAGT 1028–1047 20 59.965 50.000 300 0.069
2 GATTCACTCAGTGGTGGGGG 1380–1399 20 60.035 60.000 TACCAGGGTGTTCATTCGGC 1485–1504 20 60.036 55.000 125 0.071
3 GTGCTTTCACCGCCATCTTG 496–515 20 60.110 55.000 CGCTCGCTCTTTCGATTGTG 612–631 20 59.976 55.000 136 0.134
4 GATTCACTCAGTGGTGGGGG 1380–1399 20 60.035 60.000 CTGCAACCTCGTTCCTAGGG 1592–1611 20 60.108 60.000 232 0.143
5 TGCCGGTGTTGTTCATACGA 246–265 20 59.966 50.000 CAAGATGGCGGTGAAAGCAC 496–515 20 60.110 55.000 270 0.143
Primer map pair 1 (lowest penalty) · product 300 bp at template position 748–1,047 · the template track shows a 1,500 bp window of the 2,156 bp template — the blue segment on the top bar is where that window sits, and every scale is in template coordinates · the two tracks are drawn at different scales

Left primer — binds the template strand as listed (5′→3′)Right primer — its reverse complement binds hereProductWindow drawn in the template track

whole templatethe 1,500 bp drawn in the track below · template 148–1,647 of 2,156Template1,500 bp windowproduct 300 bp · template 748–1,047product 300 bpleft primer, template 748–767right primer anneals here, template 1,028–1,0471485238981,2721,647Amplicon300 bpleft primer AGGCCTGCCTGGAACAATAC · 5′→3′right primer TGATTGCGCAACTCTCCAGT · its reverse complement binds the template strandinterior 260 bp7488238989721,047
Left primer
AGGCCTGCCTGGAACAATAC
template 748–767 · 20 bp · Tm 60.034 °C · GC 55.000 %
Right primer
TGATTGCGCAACTCTCCAGT
template 1,028–1,047 · 20 bp · Tm 59.965 °C · GC 50.000 %

Amplicon sequence (5′→3′ on the template strand, 300 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.

AGGCCTGCCTGGAACAATACGACGCAGACCTTCATGTGAGAGTCAGTTATAATTCGAGTAACGCCAACCCTAGGCAGTGATTCGATTGATGAATGCACAAAATAGGGCCAATGAAAACATTGTTCGTTATGAGTCCCTGTTGAGCAAGGTTTACCACATGGATGCAAGGAACTCAGGTAATCAGCCTAGAGAGGCTCTAACAATAGTGAAATCCCACTCCATTAGATGTGGTTTTGGCATTCCAAAATTTATTCCAGAATCCGTGAACCTTGAAGAGTCTACTGGAGAGTTGCGCAATCA

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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