Hi

I think you can use the following for bacterial and viral business

In silico PCR amplification

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

Hello,

I know this question was asked five days ago, but if you still need some guidance you could use the UCSC Genome Browser in-silico PCR tool. Here is the link if you decide to check it out: https://genome.ucsc.edu/cgi-bin/hgPcr. However, this tool will not give digestion patterns (at least to my knowledge). Regardless, it could yield some useful information depending on your study's goal.

As previously suggested by Zahra Al-Khafaji you could use the in-silico PCR amplification tool. I have actually used that web tool several times and I highly recommend it, especially for in-silico PCR.

Just know, the in-silico PCR tool offered by UCSC is a little more biased towards eukaryotic organisms whereas the in-silico PCR amplification tool is completely biased towards bacteria.

If you want to look at banding patterns from an in-silico PCR, then I suggest using the following: http://insilico.ehu.es/PCR-RFLP/. It is freely available to use and I believe it allows for some degree of primer mismatches as well.

If you want to look at banding patterns from strictly whole genomes, then I suggest using the following: http://insilico.ehu.es/digest/. This is also freely available to use.

Lastly, if you want to use any of the following tools it is going to depend on the organism(s) you're currently studying. You did not mention this information in your question; therefore, it's possible none of these tools will help you. But hopefully, that's not the case here.

Best of luck!

-Noah :)