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;
}