Obtain identity of sequences aligned by msa in r

Question

[Debjyoti]

I have a sequence data consisting of reads which I have stored as character strings in a list. The reads are basically amplicon sequences. My data will have a mix of different amplicons each with different primer pairs. I want to find out the sequences that correspond to a particular primer pair. When I search just with primer sequence using grep command

list<-"My sequence"
grep("primer_seq", list)

I only get the sequences that matches exactly and not the ones that differ by a few bases. Since I expect few mismatches because of pcr, is there a way I can obtain reads even if they differ by a certain amount of bases that I will specify. Can it be done through msa package using clustalw or any other method in r?

[cpad0112]

I think cutadapt or seqkit is the right tool for this. Please post primer sequences, few reads and expected output for better solution.