Hello

in addition to what has already been said about doing multiple times things that can be done only once (reading files many times, etc.), and although this is not directly what you are asking for, I would strongly recommend some changes to your coding style. Especially, you've got a lot of repeated code. Just to take an example, this big 30-line while loop:

        while (my @line=split (/\t/,<SEQ>)){#for each sequence record 
+the nmer information
            my $ct=0;
            my $start=$line[1];
            if ($start < $line[2]){##Watson Strand
            # ...
            }
            else{##Crick Strand
            # ...
            }
        }
[download]

is coming twice, with identical or almost identical code. Put that in a separate subroutine which you call then twice where you need. This will remove about 60 lines from your main code and make it much shorter and far easier to follow. It will also make it easier to figure out possible performance improvements. And, last but not least, if you have a bug in that code or need to re-factor it, you will need to correct it only once.