Checking quality of predesigned probes for multiplex qPCR

Question

[wijexex511]

Hello, we have a single common primer and a set of specific probes for a set of sequences (over 50). How can we check quality of this design, can you recommend us some software and remind us the steps we should definitely follow ? Thanks in advance

[gb]

Another option: https://www.drive5.com/usearch/manual/cmd_search_oligodb.html

Or make a multiple sequence alignment

Answer 1

[trausch]

I am not sure I fully understand your question. If you want all primer binding sites and possible amplicons across a genome for your multiplexed qPCR design then this tool should work: https://www.gear-genomics.com/silica/