Here are the kmer programs I mentioned in class.
Of course you will have to seperate them and change the first line.

#!/pkg/bin/perl -w
#Here we try to find all the k-mers of a string. It
#only finds non-overlapping ones, but later it will
#be modified to find the overlapping ones as well.
#dg

$dnastring = <>;
print "What length k-mer?\n";
$k = <>;  
chomp $k; # without this, the next line finds no matches.
while ($dnastring =~ m/(.{$k})/g) {
 print "$1 \n";
}



#!/pkg/bin/perl -w
# This finds and prints all the overlapping k-mers of the input string.
#dg

print "Input the string\n";
$dna = <>;
chomp $dna;
print "Input the length of the window\n"; 
$k = <>;
chomp $k;

while (length($dna) >= $k) {
$dna =~ m/(.{$k})/; 
print "$1 \n";
$dna = substr($dna, 1, length($dna) -1);;
}



#!/pkg/bin/perl -w
#This program expands on kmer1.pl which expands on kmer.pl
# This finds all the overlapping k-mers of the input string. It builds
# an associative array (a hash) where each key is one distinct k-mer in the string,
# and the associated value is the last starting position where that
#k-mer is found. For example, if the input is ACACTCA and k is 2, then
#one key is AC with  value 3; another key is CA with value 6;
#another key is CT with value 4; and one key is TC with value 5.
#dg

print "Input the string\n";
$dna = <>;
chomp $dna;
print "Input the length of the window\n"; 
$k = <>;
chomp $k;

%kmer = ();
$i = 1;
while (length($dna) >= $k) {
  $dna =~ m/(.{$k})/; 
  print "$1, $i \n";
  $kmer{$1} = $i;
  $i++;
  $dna = substr($dna, 1, length($dna) -1);;
}

foreach $kmerkey (keys(%kmer)) {
print "The last occurrence of string $kmerkey is in position 
$kmer{$kmerkey}\n";
}


#!/pkg/bin/perl -w
#program kmerfirst.pl
# This program finds all the overlapping k-mers of the input string. It builds
# an associative array where each key is one distinct k-mer in the string,
# and the associated value is the starting position where that
#k-mer is FIRST found.  Compare this to kmer2.pl

print "Input the string\n";
$dna = <>;
chomp $dna;
print "Input the length of the window\n"; 
$k = <>;
chomp $k;

%kmer = ();                      # This initializes the hash called kmer.
$i = 1;
while (length($dna) >= $k) {
  $dna =~ m/(.{$k})/; 
  print "$1, $i \n";
   if (! defined $kmer{$1}) {     #defined is a function that returns true
                                  # if a value has already been assigned to
                                  # $kmer{$1}, otherwise it returns false. 
                                  # the ! character is the negation, so
                                  # if $kmer{$1} has no value, then it will
                                  # be assigned the value of $i, the position
                                  # where the k-mer is first found.
    $kmer{$1} = $i;       
   }
 $i++;
  $dna = substr($dna, 1, length($dna) -1);;
}

foreach $kmerkey (keys(%kmer)) {
 print "The first occurrence of string $kmerkey is in position 
 $kmer{$kmerkey}\n";
}