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while(my ($key1,$value1)=each(%hash1)){
while(my ($key2,$value2)=each(%hash2)){
...
         ...
}
}

while(my ($key1,$value1)=each(%hash1)){
    if (exists $hash2{$key} ) {
...
         ...
     }
}

foreach(@allhits){
    while(my $str=<FH1>){