Hello everyone. I'm working with primer analysis and design, and so far I've performing it in Excel but: a) I don't like Excel, b) I do it manually, c) I don't like Excel, d) it gets tedious when working with thousands of sequences and tens of primers. My analysis consists of establishing how many sequences have mismatches on each position of my primers, and also count how many mismatches each sequence has with the corresponding primers. This last analysis I've been able to (partially) solve it by using ncbi-blast+ tool. However, **I will find very helpful a program/script where you input your sequences and primers fasta files and retrieve the number of mismatches at every primer position. Does anyone know something that could help me achieve all this?** If it also has an output tab-separated file as the one attached that would be perfect for easy visualization of results. Suggestion/orientations are also grateful! I just want to know if there's something to help me out, otherwise I'll try writing a script to automatize my analysis. Thank you!

Thanks Mensur