I wish to design a common LAMP primer for multiple sequences by primer explorer v 5. I tried to upload multiple files in software like clustal omega alignment, Notepad file with multiple sequence etc but not getting the right result in display. Please guide, how to upload the multiple alignment sequences.
If I have understood your question correctly, you are looking to design primers for multiple species with high sequence similarity.
I guess a consensus sequence will be more suitable submission sequence to achieve what you are trying to get from primer explorer. The primers thus deduced can be evaluated to align to all the included sequences.
even suggesting the locations for primer designing to explorer may help.
Hope it helps and you have productive time....
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