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: Porites_compressa_HIv1___RNAseq.g17733.t1 (Porites_compressa_HIv1___RNAseq.g17733.t1), 222 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 222 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 TCACTTGTAATGATCGGCTTGGA 11–33 23 60.055 43.478 GTTCCGGTCTGAGCTGCAAT 91–110 20 60.675 55.000 100 3.730
2 TCACTTGTAATGATCGGCTTGGA 11–33 23 60.055 43.478 TTTGTTCCGGTCTGAGCTGC 94–113 20 60.885 55.000 103 3.940
3 TCACTTGTAATGATCGGCTTGG 11–32 22 58.730 45.455 GTTCCGGTCTGAGCTGCAAT 91–110 20 60.675 55.000 100 3.945
4 TGGAAAGAAAGTGCGGGTGA 30–49 20 59.818 50.000 GCTCCAAGTTCATTCCATCATGA 186–208 23 59.050 43.478 179 4.131
5 TGGAAAGAAAGTGCGGGTGA 30–49 20 59.818 50.000 AGCTCCAAGTTCATTCCATCATG 187–209 23 59.048 43.478 180 4.134
Primer map pair 1 (lowest penalty) · product 100 bp at template position 11–110 · 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

Template222 bpproduct 100 bp · template 11–110product 100 bpleft primer, template 11–33right primer anneals here, template 91–110156112167222Amplicon100 bpleft primer TCACTTGTAATGATCGGCTTGGA · 5′→3′right primer GTTCCGGTCTGAGCTGCAAT · its reverse complement binds the template strandTCACTTGTAATGATCGGCTTGGAGTTCCGGTCTGAGCTGCAATinterior 57 bp11366185110
Left primer
TCACTTGTAATGATCGGCTTGGA
template 11–33 · 23 bp · Tm 60.055 °C · GC 43.478 %
Right primer
GTTCCGGTCTGAGCTGCAAT
template 91–110 · 20 bp · Tm 60.675 °C · GC 55.000 %

Amplicon sequence (5′→3′ on the template strand, 100 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.

TCACTTGTAATGATCGGCTTGGAAAGAAAGTGCGGGTGAAGTGCAATCCAGATGACACAGTGGGAGATTTGAAAAAACTGATTGCAGCTCAGACCGGAAC

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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