test sequence

[ableasby at hgmp.mrc.ac.uk]

There is probably not a problem. EMBOSS only reports one
isoschizomer for cases where several REs have the same cut
site. If the  -preferred   switch is given to these
programs then the more easily available of the isoschizomers
will be reported. This is controlled by the file:

   embossre.equ

where, for each RE, you can specify which isoschizomer should be
reported.

So, first try adding -preferred. If you just want to search for
a particular set of enzymes they can be given as a comma-separated
list using the -enzymes qualifier   e.g. -enzymes "ecori bamhi"

HTH

Alan Bleasby
HGMP


PS: NEB supply an emboss-format set of files which are just the most
    common REs. You can rename them (e.g. to embossre.enz/ref/sup)
    and overwrite your current set in the emboss REBASE directory.