Could I get some help in the debugging, somehow, in the sequence after 1-10 character the 11th character is getting truncated.

The relevant part of the code has the following structure:

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

Incrementing the same variable (viz. $pos) in two places like this is asking for trouble. And, sure enough, within the inner for loop there are one too many increments, producing a typical off-by-one error. You can fix this by decrementing $pos immediately after the inner loop has completed:

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;
}
[download]

Note that it is not necessary to set $FLAG each time through the loop.

Hope that helps,