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#! /usr/bin/perl

...
            }
    }
}

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cpt2jmo@phantom:~$ ./2_hashes.pl
Genename(file1) start  end ** Genename(file2)     start    end

CLS_S3_Contig2721 139 168** CLS_S3_Contig2721 142 169
CLS_S3_Contig2730 361 384** CLS_S3_Contig2730 365 389