my $one = "1  AGCTGATCGAGCTAGTACCCTAGCTC 26";
my $two = "15 AGCTGATCGAGCTAGTACCCTATCTC 40";

my @one = split '\s+', $one;
my @two = split '\s+', $two;

if ($one[1] ne $two[1]) {
    my $matchlen = ($one[1] ^ $two[1]) =~ /\A(\0+)/ 
                   ? length($1) 
                   : 0;
    print "Mismatch at ",
       $one[0] + $matchlen, ' and ', 
       $two[0] + $matchlen, "\n";
}
else  {
    print "full match\n";
}
[download]

see Bitwise-String-Operators