print "Input the K value \n";
$k = <>;
chomp $k;

print "Input T\n";
$t = <>;
chomp $t;

%Qkmer = ();                      
$i = 1;

$query=' ';
while ($line=<IN>) {
chomp($line);
 if ($line=~ m/^>/ ) {
 next;
}
$query=$query.$line;
$line=~ s/(^|\n)[\n\s]*/$1/g;

 while (length($line) >= $k) {
   $line =~ m/(.{$k})/;
   if (! defined $Qkmer{$1}) {#every key not deined as the first match
     $Qkmer{$1} = $i;
   }
   $i++;
   $line = substr($line, 1, length($line) -1);
 }
}

open(MYDATA, '<', "data.txt");

while ($line=<MYDATA>) { \
  chomp($line);
  %Skmer = ();           # This initializes the hash called Skmer.
  $j = 1;

  if ($line=~ m/^>/ ) { #if the line starts with >
    next; #start on next line #separated characters
  }
  $line=~ s/^\s+|\s+$//g ; #remove all spaces from file
  while (length($line) >= $k) {
    $line =~ m/(.{$k})/;#match any k characters and only k characters in dna
    $Skmer{$1} = $j; #set the key position to $j and increase for each new key
    $j++;
    $line = substr($line, 1, length($line) -1); #this removes the first character in the current string
  }

  ###(56)###for($Skmerkey(keys %Skmer)){
    $i=$Skmer{$Skmerkey};
    if(defined $Qkmer($Skmerkey)){
      $j=$Qkmer($Skmerkey);
      }
      $S1=$line;
      $S2=$query;
      @arrayS1= split(//, $S1);
      @array2= split(//, $S2);

      $l=0;
      while($arrayS1[$i-$l] eq $arrayS2[$j-$l]){
        $l++;
      }
      $start=$i-$l;
      $m=0;
      while ($arrayS1[$i+$k+$m] eq $arrayS2[$j+$k+$m]) {
        $m++;
      }
      $length=$l+$k+$m;
      $match= substr($S1, $start, $length);

      if($length>$t){
        $longest=length($match);
        print "Longest: $match of length $longest \n";
      }
  }

}###(83)###