my @out = push @{
    $data[ $fileCount ]->{
...

##</code><code>##

#!/usr/bin/perl
#29/06/2011

#use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data, my @col, my @fields;
my $dataset;
#my %out;
my $Hashref;
my $fileCount;
my @out; 
my @results;

open INFILE, "<Primer-Rev1" or die $!;
open my $outfh, '>', "outputfile.txt" or die $!;

	for my $nr (1..2) {
	 for my $line (read_file('Primer-For'.$nr)) {
	  my @col = split(/\t/,$line);


	  push @{$data[$nr - 1]->{shift(@col)}},\@col;
	 }
	}


while (<INFILE>){

		@col = split(/\t+/, $_);
		chomp (@col);
	 	my ($header, $length, $tm, $sequence) = @col[0..3];

		# expecting file3 line in @col

#}

my @results = ( $col[0], $col[3] );
for my $dataset (@data) {
    my @beef = @{ $dataset->{ $col[0] } };
    @beef = 
        sort {
            my $diff_a = $col[2] - $a->[1];
            $diff_a *= -1 if $diff_a < 0;
            my $diff_b = $col[2] - $b->[1];
            $diff_b *= -1 if $diff_b < 0;
            $diff_a <=> $diff_b;
          }   @beef;

    push @results, $beef[0]->[2];
#print Dumper (\@results);

 foreach (@results){
		    print $_."\n";}
 
}
}


##</code><code>##

contig03841
CCAGGTTATTTATTTCAGCGGGAACT
AGTAGTTCATAATAAAGAGGAGGCTGGT
contig03841
CCAGGTTATTTATTTCAGCGGGAACT
AGTAGTTCATAATAAAGAGGAGGCTGGT
AGTAGTTCATAATAAAGAGGAGGCTGGA
contig06486
GCAAATGGCTCTAAGGATCAGCC
TTTTCCTGAGCGTTTTCCTGAGC
contig06486
GCAAATGGCTCTAAGGATCAGCC
TTTTCCTGAGCGTTTTCCTGAGC
CATTTTTCCTGAGCGTTTTCCTGAGT
contig09294
GTCGGAGCTCTCTCAGAACCC
GCCCCAGAAGACATCACCTTCAT
contig09294
GTCGGAGCTCTCTCAGAACCC
GCCCCAGAAGACATCACCTTCAT

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT


##</code><code>##

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT


##</code><code>##

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT