I have to carry out an in silico PCR on the 16S-rRNA gene of 5 random bacteria strains.
I would like to evaluate the resulting amplicon of different primer pairs. Because I can only use free software, I chose SerialCloner (2.6.1). The primer pairs contain several degenerate nucleotides but SerialCloner doesn't allow the input of bases other than actg. I receive the error message:
"Serial Cloner could not find the sequence corresponding to Primer 1. Check matrix and primer sequences and try again."
Could anyone explain whether there is a possibility to apply degenerate primers in SerialCloner or either another software that can solve my problem?
I attached two text files containing the 16S-rRNA sequence of Escherichia coli and two different degenerate primer pairs to apply.