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;
}