If you're working with strings, then work with strings. A string uses less memory than an array of characters, and string operations are fast:

my $line1 = 'CABGFE';
my $line2 = 'DBF';

say for $line1 =~ /[$line2]/g;
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Even if you're working with arrays of characters, joining into strings will probably be faster:

my @line1 = qw(C A B G F E);
my @line2 = qw(D B F);

my $line1 = join '', @line1;
my $line2 = join '', @line2;

say for $line1 =~ /[$line2]/g;
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If you've only simplified your example to arrays of characters, but they're really arrays of something else, then use a hash, as others have already suggested.