for (my $pos = 1; $pos <= length($sequence); $pos++) {
    ...
    foreach my $k (...) {
        ...
        if ($pos == $p1) {
            ...
            for (my $p = ...) {
                ...
                $pos++;
            }
        }
    }
    ...
}

##</code><code>##

if ($pos == $p1)
{
    $FLAG = 1;
    push @temp, $red;

    for my $p ($p1 .. $p2)
    {
        my $s = substr($sequence, $p - 1, 1);
        push @temp, $s;
        push @temp, $brk if $p == int($p / 50) * 50;

        $pos++;
    }

    $pos--;    # <-- ADD THIS

    push @temp, $span;
}