c:\@Work\Perl\monks>perl -wMstrict -le
"my $s1 = '---DAAAGLRG--G--G-P-LT-IGGY';
 my $s2 = '...XXXXXXXX..X..X.X.XX.X..X';
 print qq{'$s1'};
 print qq{'$s2'};
 ;;
 (my $mask = $s1) =~ tr{-\x00-,.-\xff}{\x00\xff};
 my $t1 = $s1 & $mask;
 my $t2 = $s2 & $mask;
 $t1 =~ tr{\x00}''d;
 $t2 =~ tr{\x00}''d;
 ;;
 print qq{'$t1'};
 print qq{'$t2'};
"
'---DAAAGLRG--G--G-P-LT-IGGY'
'...XXXXXXXX..X..X.X.XX.X..X'
'DAAAGLRGGGPLTIGGY'
'XXXXXXXXXXXXXX..X'