Spike Wuhan is [here][1] Using Python then use the BioPython `Bio.pairwise2` program [here][2] Yours sequence is the reference, the shorter Wuhan query is the query. The genomic positions `position1` and `position2` will then be defined via the output of `pairwise2`, then cut it by using the genomic position -1 as follows: spike = completegenome[int(position1)-1:int(position2)-1] `-1` is needed because lists start at 0 rather than 1. [1]: https://www.ncbi.nlm.nih.gov/nuccore/MN996527.1?from=21530&to=25351&report=fasta [2]: https://biopython.org/docs/1.75/api/Bio.pairwise2.html