>perl -wMstrict -le
"my $seq1 = '--TAGAG--T';
 my $seq2 = '-ATTGAGATT';
 print 'question 1';
 (my $mask1 = $seq1) =~ tr{-ATGC}{\x00\xff};
 print qq{seq1 '$seq1'};
 print qq{seq2 '$seq2'};
 $seq2 &= $mask1;
 $seq2 =~ tr{\x00}{-};
 print qq{seq2 '$seq2'};
 print 'question 2';
 $seq1 = 'G-TATAG';
 $seq2 = 'GATCT-G';
 print qq{seq1 '$seq1'};
 print qq{seq2 '$seq2'};
 (   $mask1 = $seq1) =~ tr{-ATGC}{\x00\xff};
 (my $mask2 = $seq2) =~ tr{-ATGC}{\x00\xff};
 my $dmask = $mask1 & $mask2;
 $seq1 &= $dmask;
 $seq2 &= $dmask;
 my $diff = $seq1 ^ $seq2;
 $diff =~ tr{\x00-\xff}{=D};
 print qq{diff '$diff'};
"
question 1
seq1 '--TAGAG--T'
seq2 '-ATTGAGATT'
seq2 '--TTGAG--T'
question 2
seq1 'G-TATAG'
seq2 'GATCT-G'
diff '===D==='