But  qr/^(\w*)/ won't capture anything — or more precisely, it will match and capture the empty string. Maybe try something like  qr/^>(\w*)/ instead:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $line = '>CATCATCATCAT';
 ;;
 my $pattern = qr/^>(\w*)/;
 if ($line =~ /$pattern/) {
   my $id = $1;
   print qq{got: '$id'};
   }
"
got: 'CATCATCATCAT'
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