As davido says, you can do this with a regex too. Either play with pos a little bit:

## capture 10 chars (with advancing), then move back 7:

while ( $dna =~ /(.{10})/g ) {
    print "current window = $1\n";
    pos $dna -= 7;
}
[download]

Or use a capture within a lookahead:

## capture next 10 chars without advancing, then advance by 3:

while ( $dna =~ /(?= (.{10}) ) .{3}/gx ) {
    print "current window: $1\n";
}
[download]

For maintenance/readability reasons, you may be better off using a for loop and substr. I don't know, though; I kinda like the lookahead solution... it's cute.