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

if(exists $hash2{$key1}){

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

#push(@allhits,$key1);

foreach(@allhits){

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

push(@file1,$list1[1]."#".$list1[2],[$list1[4],$list1[0]]);
and in 
...
print "$_";.
use
print "@{$_}"; # to what you got to write.

    while(my $str=<FH1>){