Is it possible to do alignment within Python? Check variants against reference?
As others have said, doing whole-genome (or even whole-chromosome) alignments is the wrong solution. Simply track where you're creating SNVs. If you wrote your SNV locations to a sorted BED file you could use something like the following:



#!/usr/bin/env python
minWidth = 100000  # Only report regions of &gt;=100kb
last = [None, None]
for line in open("some bed file"):
    cols = line.strip().split()
    if cols[0] != last[0]:
        if int(cols[2]) &gt;= minWidth:
            print("{}:1-{}".format(cols[0], cols[2]))
    else:
        if int(cols[2]) - last[1] &gt;= minWidth
            print("{}:{}-{}".format(cols[0], last[1], cols[2]))
    last = [cols[0], int(cols[2])]


This will miss the last part of each chromosome/contig, since it doesn't know how long they are, but you should be able to figure out how to handle that. The memory requirements of this are trivially small.

I suspect there's also a bedtools or bedops command that will directly give you the distance to the next downstream region. One could alternatively parse that (it's all the above code is doing, but using bedtools or bedops would produce more validated results than a quickly thrown together script).