Hello onlyIDleft,

Not an answer, just a couple of observations. This code (comments removed):

while(<IN1>)        {
chomp;    
    if ($_=~ m/\>/)        {
        }
    elsif ($_!~ m/\>/)        {
    push @lengths, length($_);
        }
}
[download]

can be replaced with the equivalent:

while (<IN1>)
{
    chomp;
    push @lengths, length $_ unless />/;
}
[download]

Update: No need to escape > in a regex.

And similarly, this code (comments removed):

while(<IN2>)        {
chomp;    
    if ($_=~ m/\>/)        {
    push @source, $_;
        }
    elsif ($_!~ m/\>/)        {
    push @source, $_;
        }
}
[download]

is equivalent to:

chomp, push @source, $_ while <IN2>;
[download]

:-)

Hope that helps,