Is there any tool for fuzzy sequence matching?
Python solution:
e&lt;=2 will allow up to 2 insertions, 2 deletions, or 2 SNPs in any 2 combinations

import regex
seq_list=["GGGAGGG", "GGGAAGGG", "GGGAAAGGG", "TTTATTT", "TTTAATTT", "TTTAAATTT", "GGGG", "GGG"]
for sequence in seq_list:
    if regex.search("(GGGGGG|TTTTTT){e&lt;=2}", sequence):
        print(sequence)


GGGAGGG
GGGAAGGG
TTTATTT
TTTAATTT
GGGG  

Can also include a wildcard

seq_list=["GGGAAAAAGGG", "GGGAAAAATGG", "GGGAAAAATTG", "GGGAAAAATTT"]
for sequence in seq_list:
    if regex.search("(GGG.*GGG|TTTTTT){e&lt;=2}", sequence):
        print(sequence)


GGGAAAAAGGG
GGGAAAAATGG
GGGAAAAATTG