#!/usr/bin/perl
use strict;
use warnings;
my %H;
open my $FH, '<', 'DNA_strings.dat' or die $!;
while (<$FH>) {
    s/\s+$//;
    for my $i (0 .. length($_)-1) {
        my $k = $_;
        substr($k,$i,1) = '*';
        push @{$H{$k}}, $_;
    }
}

for my $k (sort keys %H) {
    if ($#{$H{$k}} > 1) {
        print "$k\t", join(",\n\t\t", @{$H{$k}}), "\n";
    }
}