UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgPcr?command=start -> PCR: gives only perfect matches with a defined product size cutoff

better use PrimerBlast http://www.ncbi.nlm.nih.gov/tools/primer-blast/ and insert your primer sequences -> gives you all possible pcr products from either genome or cDNA with a defined cutoff (see advanced parameters on that page).

Hello Ravindra, I use this: http://eu.idtdna.com/analyzer/applications/oligoanalyzer/

UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgPcr?command=start -> PCR: gives only perfect matches with a defined product size cutoff

better use PrimerBlast http://www.ncbi.nlm.nih.gov/tools/primer-blast/ and insert your primer sequences -> gives you all possible pcr products from either genome or cDNA with a defined cutoff (see advanced parameters on that page).

The e-pcr of UCSC works very well. If you want to evaluate possible aspecific amplification products, you can use MFEprimer2 ( http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0/).

Hi, Please check this....(if you are working with Prokaryotic genomes)

http://insilico.ehu.es/PCR/

Another tool (Java based) with multiple options. http://primerdigital.com/tools/.

Also, as Mr.Stephan said, NCBI's other options are primer balst or Primer 3 (http://frodo.wi.mit.edu/) to check or design primers

Thank u everybody..

You may use primer blast.

http://www.bioinformatics.org/sms2/pcr_products.html

It will give the product size and sequence if the primers work correctly in the PCR. It does not give BLAST results and I think your question was just verifying PCR amplification.

OR

Software http://primerdigital.com/fastpcr.html

http://www.ncbi.nlm.nih.gov/tools/primer-blast/ does not allow to use a bacterial genome as a template. The size limit is 5000 bp

UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgPcr?command=start> only allow pre loaded genomes and it is not possible to upload "your" genome

http://insilico.ehu.es/PCR/ you can upload genomes but it is limited to 5 million nucleotides

Try

-snapgene ( portable software). Tutorial

https://www.youtube.com/user/SnapGene/videos

Or -primer map (online)