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    foreach my $samekeys (sort keys %hash1) {
        if (exists $hash2{$samekeys}){          
                
...
             }    
        }
}

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        1          2          3          4          5          6
Line 1234567890 1234567890 1234567890 1234567890 1234567890 1234567890
   1 GGAAAAACAT TTCATCTTAA AACTTTCCTA AGACAAGGGA AAACAAAAAA CCATGCTCTA
...


   etc.