#!/usr/bin/perl -w  
use strict;  
use warnings;
use Getopt::Long;
use Data::Dumper;
use FindBin qw($Bin $Script);
use File::Basename qw(basename dirname);
my $BEGIN_TIME=time();
my $version="1.0.0";
#######################################################################################

# ------------------------------------------------------------------
# GetOptions
# ------------------------------------------------------------------
my ($infile,$outfile);
GetOptions(
                            "help|?" =>\&USAGE,
                            "i:s"=>\$infile,
                            "o:s"=>\$outfile,
                            ) or &USAGE;
&USAGE unless ($infile );
#######################################################################################
# ------------------------------------------------------------------
# Main Body
# ------------------------------------------------------------------
open (IN,"<",$infile) or die $!;
open (OUT,">",$outfile) or die $!;
$/=">";
my %head_seq;
my @motif;
my %len_motif;
my $k=0;
while (<IN>) {
    	chomp;
next if (/^$/);
    $k++;
    my ($head,$seq)=split /\n/,$_,2;
    $seq=~s/\n//g;
    $head_seq{$head}=$seq;
    my @arr=split//,$seq;
    if ($k==1) {
            for (my $i=2;$i<@arr;$i++) {
                    for (my $j=0;$j<@arr;$j++) {
                            my $motif=substr("$seq",$j,$i);
                            push @motif,$motif;
                    }
            }
    }
    else{
            next;
    }
}
for my $motif (@motif) {
    $a=0;
    for my $key(keys %head_seq){
            if ($head_seq{$key}=~/$motif/) {
                    $a++;
            }
            else{
                    next;
            }
            if ($a==$k) {
                    $len_motif{length($motif)}{$motif}=1;
            }
    }
}
for my $key(sort {$b<=>$a} keys %len_motif) {
    for my $key1(keys %{$len_motif{$key}}) {
            print OUT $key,"\t",$key1,"\n";die;
    }
}
#######################################################################################
print STDOUT "\nDone. Total elapsed time : ",time()-$BEGIN_TIME,"s\n";
#######################################################################################

# ------------------------------------------------------------------


sub GetTime {
    my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst)=localtime(time());
    return sprintf("%4d-%02d-%02d %02d:%02d:%02d", $year+1900, $mon+1, $day, $hour, $min, $sec);
}


sub USAGE {#
    my $usage=<<"USAGE";
Program:
Version: $version
Contact: Wang_yingzhen<xiangshu007\@qq.com>
Description:

Usage:
 Options:
    -i      <infile>        input file,
    -o      <outfile>       output file,
    -h                              Help

USAGE
    print $usage;
    exit;
}