my $procount2 = 1; foreach my $readingframe2(@protein){ my $protein; print "string is $_\n"; if(/MHGR/){ print "$1\n","motif is $_\n"; ##### <----- if(length($_)>=1){ print "length of motif is length($_)\n"; print OUT1 "Protein $procount2\n$_\n"; $procount2++; } } }