Surely that should be

for ( my $loc = 0; $loc <= length($dna) - 10; $loc += $increment ) {
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Otherwise his last few strings won't be 10 characters long. Even though I have done this exact thing (sliding window with overlaps) in the past using a C-style for loop, I think I'd probably write it like this these days:

my $end = int((length($dna) - 10)/3);
for my $i (0..$end) {
   push @windows, substr($dna,$i*3,10);
}
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or more likely

my @windows = map { substr($dna,$_*3,10) } 0..int((length($dna)-10)/3)
+;
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