in reply to Comparing 2 different-sized strings
So to "solve" your problem in the most easy way, matching your description:
my $s1='TCGAGTGGCCATGAACGTGCCAATTG'; my $s2='ATGATCCTG'; ($s1,$s2) = ($s2,$s1) if length($s1) > length($s2); my $len= length $s1; print "Matches:\n"; for (my $i=0; $i+$len+10 <= length $s2; ++$i) { print substr($s2, $i, $len+10),"\n"; }
prints:
Matches: TCGAGTGGCCATGAACGTG CGAGTGGCCATGAACGTGC GAGTGGCCATGAACGTGCC AGTGGCCATGAACGTGCCA GTGGCCATGAACGTGCCAA TGGCCATGAACGTGCCAAT GGCCATGAACGTGCCAATT GCCATGAACGTGCCAATTG
I didn't bother to put the number of mismatches. In most cases it will be length($s1) ;)
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