kdt2006, please correct if I'm wrong, but I read your last reply to mean that you want the maximal match in each subset of sequences. For example, I added a new sequence to my code and got the following results:

my $seq = [ [ qw(A C G C A T T C A) ],
            [ qw(A C T G G A T A C) ],
            [ qw(T C A G C C A T C) ],
            [ qw(C T G G A T C G C) ] ];
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Outputs:

..G.AT... occurs in 0,3
...G....C occurs in 1,2,3
.C......C occurs in 1,2
A.....T.. occurs in 0,1
........C occurs in 1,2,3
...G..... occurs in 1,2,3
A........ occurs in 0,1
....AT... occurs in 0,3
AC....... occurs in 0,1
..G.A.... occurs in 0,3
..G..T... occurs in 0,3
.C.G....C occurs in 1,2
..G...... occurs in 0,3
......T.. occurs in 0,1
.C.G..... occurs in 1,2
.C....T.. occurs in 0,1
AC....T.. occurs in 0,1
.....T... occurs in 0,3
....A.... occurs in 0,3
.C....... occurs in 0,1,2
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Notice above how the maximal match between 1 and 2 is .C.G....C, while a submatch of this, ...G....C, is the maximal match between 1, 2, and 3. From what I understand you would want both of these, even though one is a submatch of the other. You would not, however, want ........C or ...G..... because these are submatches of the maximal match for 1,2,3. I still believe this is a better way to find all possible matches. Perhaps the way to best suit it to your needs would be to implement a filter that finds the maximal match for each sequence subset. The following update to my original code does the trick. (Note that true and uniq require List::MoreUtils.

my %maxMatch;
for my $key (keys %$match) { 
  @{$match->{$key}} = uniq @{$match->{$key}};
  my $seqSet = join ",", @{$match->{$key}};
  unless ($maxMatch{$seqSet}) { $maxMatch{$seqSet} = $key; next; }
  my $old = true { /[^\.]/ } split //, $maxMatch{$seqSet};
  my $new = true { /[^\.]/ } split //, $key;
  $maxMatch{$seqSet} = $key if $new > $old;
}
for my $key (keys %maxMatch) { 
  print $maxMatch{$key}, " occurs in $key \n";
}
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Prints (for the four sequence set above):

..G.AT... occurs in 0,3 
.C.G....C occurs in 1,2 
...G....C occurs in 1,2,3 
.C....... occurs in 0,1,2 
AC....T.. occurs in 0,1
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Update: I was flipping through my Perl in a Nutshell text and discovered that grep could (and probably should) be used in place of true in the code above. I tested both and they work the same, although grep may run a little faster since it's a built-in command.