From JalView you can copy the consensus sequence using right-click on the word consensus near the consensus histogram (on mac it is the command key (⌘) and click). This opens up a menu where you select the Copy Consensus Sequence as seen in the screenshot. You can then paste your consensus sequence into a text editor or your primer design program.

One option would be to use the EMBOSS tool cons to generate the consensus sequence from the alignment.

The EMBOSS tools are available on-line in a wide range of places, for example:

• http://emboss.bioinformatics.nl/
• http://bioinfo.nhri.org.tw/gui/
• http://imed.med.ucm.es/EMBOSS/
• http://wsembnet.vital-it.ch/soaplab2/

If you want to install EMBOSS locally you have a number of options:

• On Debian based Linux distributions (e.g. Ubuntu, Linux Mint, Bio-Linux, etc.) the standard repositories include an EMBOSS package: emboss
• For RPM based Linux distributions (e.g. RedHat, Fedora, SuSE, etc.) packages are available: see http://rpm.pbone.net/index.php3?stat=3&search=EMBOSS
• Build from source. The source distribution is available from the EMBOSS web site, and can also be obtained from a mirror on the EMBL-EBI FTP site: ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS