perl -nle 'chomp;tr/a-z/A-Z/;next if /[^ATCG]/;$l=length();$c=0;for $m(5..$l){print substr($_,$c++,5)}' uniBNL_SSR_fasta.txt.input_library.txt | perl -nle '$c{$_}++ for split/\W/;}print map {"$_:$c{$_}\n"} sort{$c{$b}<=>$c{$a}}keys %c;{' -

##</code><code>##

...
AGAGA:5334
GAGAG:5124
TCTCT:1938
AAAAA:1908
ACACA:1884
TTTTT:1851
CTCTC:1798
...

##</code><code>##

#!/usr/bin/perl
#
# simple fasta input file cleaver
# usage: cleaver.pl --format OUTPUT_FILE_PREFIX --number X input_file
# where X is the number of files to split input_file into
#
# note: you can optionally pass more than one input file 
#       to (re)combine into X files

use strict;
use warnings;

use Getopt::Long;

my ($number,$format)=(2,"output");
GetOptions(
	"number=i" => \$number,
	"format=s" => \$format,
);

my @output_file;
foreach my $num(1..$number) {
	my $file ="$format.$num";
	open($output_file[$num-1],">",$file) or die;
}

my $file_num = 0;
while(<>) {
	$/='>';
	chomp;
	my $pre = ($. != 2 ? ">" : ""); 
	print {$output_file[$file_num]} "$pre$_";
	next if $. == 1;
	$file_num +=1;
	$file_num %= $number;
}