$ perl -E '
$s1 = q{gctgc};
$s2 = q{gctcc};
$x  = $s1 ^ $s2;
say for map sprintf( q{0x%02x}, ord ), split m{}, $x;'
0x00
0x00
0x00
0x04
0x00
$

##</code><code>##

use strict;
use warnings;

use 5.014;

open my $inFH, q{<}, \ <<EOD or die $!;
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atagctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgtttggggctctgccgccctcttctccgcctgccgttcaggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctaccgccctcttctccgcctgccgttccggc
EOD

my $baseStr = <$inFH>;
chomp $baseStr;

while ( <$inFH> )
{
    chomp;
    $baseStr = flagDiffs( $baseStr, $_ );
}

close $inFH or die $!;

say for split m{X+}, $baseStr;

sub flagDiffs
{
    my( $baseStr, $nextStr ) = @_;

    my $diff = $baseStr ^ $nextStr;

    my @posns;
    push @posns, pos $diff while $diff =~ m{(?=[^\0])}g;

    substr $baseStr, $_, 1, q{X} for @posns;
    return $baseStr;
}

##</code><code>##

at
gctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcg
ttggggctct
ccgccctcttctccgcctgccgttc
ggc

##</code><code>##

use strict;
use warnings;

use 5.014;

open my $inFH, q{<}, \ <<EOD or die $!;
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atagctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgtttggggctctgccgccctcttctccgcctgccgttcaggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctaccgccctcttctccgcctgccgttccggc
EOD

my $baseStr = <$inFH>;
my %diffPosns;

while ( <$inFH> )
{
    findDiffPosns( $baseStr, $_ );
}

close $inFH or die $!;

chomp $baseStr;
substr $baseStr, $_, 1, q{X} for keys %diffPosns;

say for split m{X+}, $baseStr;

sub findDiffPosns
{
    my( $baseStr, $nextStr ) = @_;

    my $diff = $baseStr ^ $nextStr;

    $diffPosns{ pos $diff } ++ while $diff =~ m{(?=[^\0])}g;
}