my $procount2 = 1;

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

##</code><code>##

$ perl readingframe.pl
Enter file name
t.txt
Enter output file name
o.txt
string is MHGRRRRRRRRRRRRRRRRRRRRRRRRRRRRRD_MHGRRRRRRRRRRRRRRRRRRRRRRRRRRRRRD_
Use of uninitialized value $1 in concatenation (.) or string at readingframe.pl line 68, <> line 2.

motif is 1
length of motif is 1
string is CMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVTECMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAVT
string is AWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_LNAWPPPPPPPPPPPPPPPPPPPPPPPPPPPPP_L