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my $Are = '^(.*)' . join('(.*)', @A) . '(.*)$';

my $Are = join '(.*)', '^', @A, '$';

my $Are = join '(.*?)', '^', (map "($_)", $A =~ /(.)/sg), '$';

#!/usr/bin/perl -w
use strict;
...
__END__
ATGGAGTCGACGAATTTGAAGAAT
xxxxxx ATGGAG yxxx TCGA zxxxx CGAATTTGAA xxw GAAT