choroba has provided a solution giving the number of mismatches but if you also want their positions (as I think you say) then a regex and pos might help. This code gives 1-based positions, just subtract 1 in the regex code block if you need 0-based.

$ perl -Mstrict -Mwarnings -E '
my @seqs  = qw{ ATGC TGCT GCTA CTAA TAAC };
my $match =  q{GTCA};

foreach my $seq ( @seqs )
{
    my @posns;
    my $diff = $seq ^ $match;
    my $nMismatches = () = $diff =~ m{([^\0])(?{ push @posns, pos $dif
+f })}g;
    say qq{$seq : $match -> $nMismatches at @posns};
}'
ATGC : GTCA -> 3 at 1 3 4
TGCT : GTCA -> 3 at 1 2 4
GCTA : GTCA -> 2 at 2 3
CTAA : GTCA -> 2 at 1 3
TAAC : GTCA -> 4 at 1 2 3 4
$
[download]

I hope this is helpful.

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