#!/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";
    }
}

##</code><code>##

$ cat DNA_strings.dat
CTGAG
CGAGT
ACGCT
TATAC
CTGAA
GGAGC
ATACA
AAAAA
ACAAA
AGAAA
AATAA
AAAGA
ACCAA
AGCAC
CCACG
GCCAT
AGCAA
GGCAT
GTTTG

$ perl DNA_cmp.pl
A*AAA:	AAAAA, ACAAA, AGAAA
A*CAA:	ACCAA, AGCAA
AA*AA:	AAAAA, AATAA
AAA*A:	AAAAA, AAAGA
AC*AA:	ACAAA, ACCAA
AG*AA:	AGAAA, AGCAA
AGCA*:	AGCAC, AGCAA
CTGA*:	CTGAG, CTGAA
G*CAT:	GCCAT, GGCAT

##</code><code>##

$ perl gen_random_strings.pl 100000 20 20 ACGT >DNA_strings.dat

$ time perl DNA_cmp.pl

real    0m47.659s
user    0m46.395s
sys     0m1.252s