use v5.12;
use warnings;

my $x ='ABCGE ABCGE';
my $y ='ABCGE FGCGB';
my $z ='ABCGE JHAGT';

say scalar ($x ^ $y) =~ tr/\0//c;
say scalar ($x ^ $z) =~ tr/\0//c;
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3
4
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edit

Oh I probably misread your examples, but if you compare first and second column you'll get the same results.

update

covering both cases

use v5.12;
use warnings;
use Data::Dump qw/pp dd/;
use Test::More;

sub distance {
    my ( $x,$y ) = @_ ;
    return scalar (("$x" ^ "$y") =~ tr/\0//c );
}


my $x ='ABCGE ABCGE';
my $y ='ABCGE FGCGB';
my $z ='ABCGE JHAGT';

is( distance($x,$y) => 3, "by row");
is( distance($x,$z) => 4, "by row");



while (<DATA>){
    my @col = split;
    is( distance($col[0],$col[1]) => $col[2],"by col");
}

done_testing;


__DATA__
ABCGE ABCGE 0
ABCGE FGCGB 3
ABCGE JHAGT 4
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