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: aawi_s0227.g10.t1 (aawi_s0227.g10.t1), 6,231 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 6,231 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 CAACAACCGCATTGGCTTCA 4404–4423 20 59.968 50.000 ATTGCTGGACCTGGACCATG 4528–4547 20 60.034 55.000 144 0.066
2 GACCGAGTGGCAAAAGAGGA 5811–5830 20 59.965 55.000 CTTCCGTCGTCTATGGGCTC 6053–6072 20 59.969 60.000 262 0.066
3 GAGGACCGAGTGGCAAAAGA 5808–5827 20 59.965 55.000 CTTCCGTCGTCTATGGGCTC 6053–6072 20 59.969 60.000 265 0.066
4 GACCTCCTGGAAAATCGGCA 5892–5911 20 60.035 55.000 CTTCCGTCGTCTATGGGCTC 6053–6072 20 59.969 60.000 181 0.066
5 AGGACCGAGTGGCAAAAGAG 5809–5828 20 59.965 55.000 CTTCCGTCGTCTATGGGCTC 6053–6072 20 59.969 60.000 264 0.066
Primer map pair 1 (lowest penalty) · product 144 bp at template position 4,404–4,547 · the template track shows a 1,500 bp window of the 6,231 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 3,726–5,225 of 6,231Template1,500 bp windowproduct 144 bp · template 4,404–4,547product 144 bpleft primer, template 4,404–4,423right primer anneals here, template 4,528–4,5473,7264,1014,4764,8505,225Amplicon144 bpleft primer CAACAACCGCATTGGCTTCA · 5′→3′right primer ATTGCTGGACCTGGACCATG · its reverse complement binds the template strandCAACAACCGCATTGGCTTCAATTGCTGGACCTGGACCATGinterior 104 bp4,4044,4404,4764,5114,547
Left primer
CAACAACCGCATTGGCTTCA
template 4,404–4,423 · 20 bp · Tm 59.968 °C · GC 50.000 %
Right primer
ATTGCTGGACCTGGACCATG
template 4,528–4,547 · 20 bp · Tm 60.034 °C · GC 55.000 %

Amplicon sequence (5′→3′ on the template strand, 144 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.

CAACAACCGCATTGGCTTCATACTTGGAAAACATCCAAAAGATGTTTCAAGTGTTTTCTGTACATTCTGACAAGACGAAACACGGGTATACTAAGGACGTCGGCCTTGATGAGGTTATCGCCAACATGGTCCAGGTCCAGCAAT

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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