#!/usr/bin/perl
use warnings;
use strict;
my $seqcount; my $pos; my $arrlen;
my @arr = ();
open (B, "temp.dat");
while (my $line=<B>)
{
	chomp $line;
	$seqcount++;
	$line =~ s/\s//g;
	my @temp = split (//, $line);
	$arrlen = scalar(@temp);
	for ($pos=0;$pos<=scalar(@temp);$pos++)
	{
		$arr[$seqcount][$pos] = $temp[$pos];
	}
}
my $max_position = 0;
$max_position = $arrlen if($arrlen > $max_position);
for ($pos=0;$pos<=$max_position;$pos++)
{
	for (my $s=1;$s<=$seqcount;$s++)
	{
		if ($arr[$s][$pos] ne $arr[$seqcount][$pos])
		{
			print "\n";			
			next;
		}
		else
		{
			print "$arr[$s][$pos]";
		}
	}
}

##</code><code>##

temp.dat
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atagctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgtttggggctctgccgccctcttctccgcctgccgttcaggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctgccgccctcttctccgcctgccgttccggc
atggctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcgcttggggctctaccgccctcttctccgcctgccgttccggc

##</code><code>##

Desired output
at
gctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcctgcggacgacccctctcgtggtcg
ttggggctct
ccgccctcttctccgcctgccgttc
ggc