I am unable to use a file specifying possible primers with the GCG program
PRIME. The program loads in the primers (or at least, identifies how many
there are), but apparently fails to test them. Below is an example of the
sort of output I get; genosys.dat is a GCG file, so it ought to be in the
correct format!
I'd be grateful if anyone can suggest whether there is anything I might be
doing wrong or tell me if there is a bug in the program. My apologies if I
am making an obvious mistake.
Thanks,
Ethan Hack | E-mail: Ethan.Hack at ncl.ac.uk
Dept. of Biological & Nutritional Sciences | Phone: +44 91 222 8576
University of Newcastle | Fax: +44 91 222 8684
Newcastle upon Tyne NE1 7RU, UK
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PRIME of: nturf13.gcgn ck: 1357 from: 1 to: 679 December 20, 1994 16:55
INPUT SUMMARY
-------------
Input sequence: nturf13.gcgn
Input primer list: genosys.dat with 2391 primers.
Primer constraints:
primer size: 9 - 9
primer 3' clamp: S
primer sequence ambiguity: NOT ALLOWED
primer GC content: 40.0 - 55.0%
primer Tm: 10.0 - 65.0 degrees Celsius
primer self-annealing. . .
3' end: < 8.0 (weight: 2.0)
total: < 14.0 (weight: 1.0)
unique primer binding sites: not required
primer-template and primer-repeat annealing. . .
3' end: ignored
total: ignored
repeated sequences screened: none specified
Product constraints:
product length: 100 - 600
product GC content: 40.0 - 55.0
product Tm: 70.0 - 95.0 degrees Celsius
duplicate primer endpoints: NOT ALLOWED
difference in primer Tm: < 2.0 degrees Celsius
primer-primer annealing. . .
3' end: < 8.0 (weight: 2.0)
total: < 14.0 (weight: 1.0)
PRIMER SUMMARY
--------------
forward reverse
Number of primers considered: 0 0
Number of primers rejected for . . .
primer 3' clamp: 0 0
primer sequence ambiguity: 0 0
primer GC content: 0 0
primer Tm: 0 0
non-unique binding sites: 0 0
primer self-annealing: 0 0
primer-template annealing: 0 0
primer-repeat annealing: 0 0
Number of primers accepted: 0 0
PRODUCT SUMMARY
---------------
Number of products considered: 0
Number of products rejected for. . .
product length: 0
product GC content: 0
product Tm: 0
product position: 0
duplicate primer endpoints: 0
difference in primer Tm: 0
primer-primer annealing: 0
Number of products accepted: 0
Number of products saved: 0
