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use strict;
use warnings;
...
    } 
} 
print Dumper(\%key) ."\n";

$VAR1 = {
          'Contig25396' => [
...
                             'GGCTCTCTACCTATCTGTCTCTCTCTACCTCTCTCTCCTT
+TCACGCACAC'
                           ]
        };

use strict;
use warnings;
...
        print $out join("\n", $line{key}, $line{seq}) . "\n"; 
    } 
}