I'm not sure if I really understood your requirements or code. 
my $MAX = 10_000;
my $WINDOW_SIZE = 5;
my $MAX_MISMATCH = 1;

my $seq1 = join '', qw(A T G C)[ map int rand 4, 1 .. $MAX ];
my $seq2 = join '', qw(A T G C)[ map int rand 4, 1 .. $MAX ];

sub with_regexp {
    my ($seq1, $seq2, $window, $mismatch) = @_;
    my $retval = '';

    for my $start (0 .. length ($seq1) - $window - 1) {
        my $regex = build_regexp (substr ($seq1, $start, $window), $mi
+smatch);
        pos $seq2 = 0;

        do {
            $retval .= $seq2 =~ m/\G(?=$regex)/gc ? 1 : 0
        } while $seq2 =~ m/\G(?=.{$window})./g;
        $retval .= "\n";
    }

    $retval;
}
sub build_parts {
    my ($window, $mismatch) = @_;
    my $l = length $window;

    $mismatch = $l if $mismatch > $l;

    return $window unless $mismatch;
    return '.' x $l if $l == $mismatch;

    my ($first, $rest) = split //, $window, 2;

    return (
        (map $first . $_, build_parts ($rest, $mismatch)),
        (map '.' . $_, build_parts ($rest, $mismatch -1)),
    );
}
sub build_regexp {
    join '|', map '(?:' . $_ . ')', build_parts (@_);
}

print with_regexps ($seq1, $seq2, $WINDOW, $MAX_MISMATCH);

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In reply to Re: Speed up DNA dotplot by happy.barney
in thread Speed up DNA dotplot by Microcebus

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