Thank you for your time and reply. I did some modifcations and now the program is printing 3 times each value on match. I guess I am not putting the print at the right place.

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;
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;$pos<=$#temp;$pos++)
    {
        $arr[$seqcount][$pos] = $temp[$pos];
#        print "$pos\t$arr[$seqcount][$pos]\n";
    }
}

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++)
    {
#        print "$pos\t$s\t$arr[$s][$pos]\n";
        
        if ($arr[$s][$pos] ne $arr[$seqcount][$pos])
        {
            print "\n";            
            next;
        }
        else
        {
            print "$arr[$s][$pos]";
    
        }
    } print "\n";
}
[download]

Do I need to push in another array after there is a match of values? Thanks for your help.