Unknown DNA — Rational Primer Design and Analysis — the ...

When the program successfully finishes and the output is displayed, look through the various files. My
complete successful Prime output file is shown below. I’ve again indicated parameter changes with bold:
PRIME of: input_14.rsf{BSC5936.week3.entire} ck: 513 from: 1 to: 1581 January
19, 2003 15:47
INPUT SUMMARY
-------------
Input sequence: /users/thompson/.seqlab-mendel/input_14.rsf{BSC5936.week3.entir
e}
Input forward primer list: /home/thompson/BSC5936.week3.prime.forward.dat with
25 primers.
Input reverse primer list: /home/thompson/BSC5936.week3.prime.reverse.dat with
25 primers.
Primer constraints:
primer size: 25 - 50
primer 3' clamp: S
primer sequence ambiguity: NOT ALLOWED
primer GC content: 40.0 - 55.0%
primer Tm: 50.0 - 65.0 degrees Celsius
primer self-annealing. . .
3' end: < 8 (weight: 2.0)
total: < 14 (weight: 1.0)
unique primer binding sites: required
primer-template and primer-repeat annealing. . .
3' end: ignored
total: ignored
repeated sequences screened: none specified
Product constraints:
product length: 100 - 1581
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 (weight: 2.0)
total: < 14 (weight: 1.0)
PRIMER SUMMARY
--------------
forward
reverse
Number of primers considered: 25 25
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: 25 25
PRODUCT SUMMARY
---------------
Number of products considered: 625
Number of products rejected for. . .
product length: 0
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