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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) ] ];

..G.AT... occurs in 0,3
...G....C occurs in 1,2,3
...
.....T... occurs in 0,3
....A.... occurs in 0,3
.C....... occurs in 0,1,2

my %maxMatch;
for my $key (keys %$match) { 
...
for my $key (keys %maxMatch) { 
  print $maxMatch{$key}, " occurs in $key \n";
}

..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