Hi, here are some links I found quite helpful when I had to design PCRs

UCSC In-silico-PCR

(http://genome.ucsc.edu/cgi-bin/hgPcr?command=start)

This site allows you to retrieve DNA sequence using known primer. You may check for unique priming throughout the genome, check length of PCR products, check localisation on chromosome.

UCSC BLAT Search

(http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=Human&db=hg18&hgsid=120276419)

Here you can paste your sequence and have a look at regions (STR, SNP, genes, ...) nearby or within your sequence (zoom in/out).

Primer3

(http://frodo.wi.mit.edu)

This program allows you to search for primers within your sequence. You can define regions within your sequence that the program must or must not use for primer design. You may preselect annealing temperature ranges, range of primer lengths, ...

Webcutter 2.0

(http://rna.lundberg.gu.se/cutter2)

This program allows you to search for restriction sites within your sequence.