cpt2jmo@phantom:~/misc$ ./2_hashes_with_arrays.pl
$VAR1 = {
          'CLS_S3_Contig2722' => [
                                   {
                                     'end' => '390',
                                     'start' => '375'
                                   }
                                 ],
          'CLS_S3_Contig2725' => [
                                   {
                                     'end' => '362',
                                     'start' => '323'
                                   },
                                   {
                                     'end' => '480',
                                     'start' => '455'
                                   }
                                 ],
          'CLS_S3_Contig2729' => [
                                   {
                                     'end' => '130',
                                     'start' => '119'
                                   },
                                   {
                                     'end' => '220',
                                     'start' => '163'
                                   }
                                 ],
          'CLS_S3_Contig2731' => [
                                   {
                                     'end' => '843',
                                     'start' => '824'
                                   },
                                   {
                                     'end' => '1201',
                                     'start' => '1150'
                                   }
                                 ],
          'CLS_S3_Contig2728' => [
                                   {
                                     'end' => '144',
                                     'start' => '117'
                                   },
                                   {
                                     'end' => '472',
                                     'start' => '437'
                                   }
                                 ],
          'CLS_S3_Contig2721' => [
                                   {
                                     'end' => '168',
                                     'start' => '139'
                                   }
                                 ],
          'CLS_S3_Contig2735' => [
                                   {
                                     'end' => '636',
                                     'start' => '571'
                                   },
                                   {
                                     'end' => '710',
                                     'start' => '677'
                                   },
                                   {
                                     'end' => '810',
                                     'start' => '775'
                                   }
                                 ],
          'CLS_S3_Contig2730' => [
                                   {
                                     'end' => '202',
                                     'start' => '181'
                                   },
                                   {
                                     'end' => '384',
                                     'start' => '361'
                                   }
                                 ]
        };
$VAR2 = {
          'CLS_S3_Contig2721' => [
                                   {
                                     'end' => '169',
                                     'start' => '142'
                                   }
                                 ],
          'CLS_S3_Contig6525' => [
                                   {
                                     'end' => '514',
                                     'start' => '509'
                                   },
                                   {
                                     'end' => '502',
                                     'start' => '493'
                                   },
                                   {
                                     'end' => '508',
                                     'start' => '503'
                                   }
                                 ],
          'CLS_S3_Contig2730' => [
                                   {
                                     'end' => '389',
                                     'start' => '365'
                                   }
                                 ],
          'CLS_S3_Contig4978' => [
                                   {
                                     'end' => '274',
                                     'start' => '271'
                                   },
                                   {
                                     'end' => '388',
                                     'start' => '385'
                                   }
                                 ],
          'CLS_S3_Contig2977' => [
                                   {
                                     'end' => '376',
                                     'start' => '365'
                                   },
                                   {
                                     'end' => '82',
                                     'start' => '77'
                                   },
                                   {
                                     'end' => '90',
                                     'start' => '83'
                                   }
                                 ]
        };
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