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my @data1 = ( "a 1 a", "a 2 T", "a 3 C" );
my @data2 = ( "a 2 Y", "a 3 R", "a 4 Q", "b 5 R" );
...
            print  "$_\n";
    }
}

$ perl compare.pl
a 2 Y
a 3 R

my @results;
for my $elem ( @data1 ) {
...
    @results = grep { /$match/ } @data2;
}
 print "$_\n" for @results;

$ perl compare.pl
a 3 R