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: g18643.t2 (chr8Alt.g18643.t2), 1,116 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 1,116 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 TGTCAGAGGTGCTCTACGGA 149–168 20 59.962 55.000 ACCGAGTCGAATTGTGCTGT 238–257 20 59.966 50.000 109 0.071
2 GAACTGGATGCGAATTGGCC 806–825 20 59.899 55.000 GAAACGAGTGCCTCTGGGAA 981–1000 20 59.965 55.000 195 0.136
3 GAACTGGATGCGAATTGGCC 806–825 20 59.899 55.000 CGAGGAAGCAAGGTGGAGTT 1022–1041 20 59.965 55.000 236 0.137
4 GAACTGGATGCGAATTGGCC 806–825 20 59.899 55.000 GTTGAATGGTGCCTCGAGGA 1036–1055 20 60.036 55.000 250 0.138
5 ATGAAGGAATGCTGGGGCTC 769–788 20 60.106 55.000 GAAACGAGTGCCTCTGGGAA 981–1000 20 59.965 55.000 232 0.141
Primer map pair 1 (lowest penalty) · product 109 bp at template position 149–257 · 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

Template1,116 bpproduct 109 bp · template 149–257product 109 bpleft primer, template 149–168right primer anneals here, template 238–25712805598371,116Amplicon109 bpleft primer TGTCAGAGGTGCTCTACGGA · 5′→3′right primer ACCGAGTCGAATTGTGCTGT · its reverse complement binds the template strandTGTCAGAGGTGCTCTACGGAACCGAGTCGAATTGTGCTGTinterior 69 bp149176203230257
Left primer
TGTCAGAGGTGCTCTACGGA
template 149–168 · 20 bp · Tm 59.962 °C · GC 55.000 %
Right primer
ACCGAGTCGAATTGTGCTGT
template 238–257 · 20 bp · Tm 59.966 °C · GC 50.000 %

Amplicon sequence (5′→3′ on the template strand, 109 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.

TGTCAGAGGTGCTCTACGGATTCTCTCAGAGGAAGGCCTCAGGGGCCTTTACAAGGGTCTTGTACCGTCACTTATGAGAGAAGGGTCTTACAGCACAATTCGACTCGGT

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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