while(my ($key2,$value2)=each(%hash2)){
if($key1 eq $key2){

##</code><code>##

if(exists $hash2{$key1}){

##</code><code>##

open(FH,"file1.txt")or die "can not open file";
open(FH1,"file1.txt")or die "can not open file";

##</code><code>##

#push(@allhits,$key1);

##</code><code>##

foreach(@allhits){ 

##</code><code>##

push(@file1,$list1[1]."#".$list1[2],$list1[4]);

##</code><code>##

push(@file1,$list1[1]."#".$list1[2],[$list1[4],$list1[0]]);
and in 
my @val1=split("/",$value1);
use 
my @val1=split("/",$value1->[0]);

and in 
#push(@allhits,$key1);
use 
push(@allhits,[$key1,$value1->[1]]);#(correction from 0 to 1)

and in 
my($id,$location)=split("#",$_);
use
my($id,$location)=split("#",$_[0]);

and in 
print "$_";.
use
print "@{$_}"; # to what you got to write.

##</code><code>##

    while(my $str=<FH1>){