# we don't need this in the loop as we know when we increment (unless forking)
  # also syntax IS WRONG in original - need array context on LHS to get val
  # otherwise you are always going to get the val 1
  ($h_title_counter) = $dbh->selectrow_array("SELECT MAX(id) FROM head_index");

  # this should be a sth with bind not $dbh->selectrow_array every time
  my $sthX = $dbh->prepare("SELECT 1 FROM e_match_word WHERE word = ?");

  LONG:
    while (<READ>) {
          next if $. <= $rows2jump;
            $counter2++; #number of lines processed           
            #Lets deal with the sequences head here, marked by > so this will
            # only exec if we have that marker
            if ( s/^>// ) {
                $sth1->execute($_) or print "$DBI::errstr";
                $h_title_counter++;
              next LONG;
            }

            #Here we will deal with the actal sequence
            chop; #To remove the > at the end of the line
            #Input stuff in mysql
             for my $x (0 ... (length($line) - ($word_length)-1)) {
                my $word = substr($_, $x, $word_length);
                #Now we have it with a big cache, hope to speed things up
                if ($most_used_words{$word}) {
                    #UPDATE e_match_word set counter = counter+1 WHERE word = ?
                    $sth3->execute($word) or print "$DBI::errstr";
                    #print "cached result\n";
                    
                } elsif ( $sthX->execute($word)) {
                    #UPDATE e_match_word set counter = counter+1 WHERE word = ?
                    $sth3->execute($word) or print "$DBI::errstr";
                    #print "not cached result\n";
                    
                } else {                    
                    #INSERT INTO e_match_word VALUES (?,?)
                    $sth2->execute($word, 1) or print "$DBI::errstr";
                    $wordcounter++;
                    #print "new word\n";                    
                }           
                #INSERT INTO e_match_info values (?,?,?)
                $sth4->execute($word, $h_title_counter, $x) or print "$DBI::errstr";
            }            
            #$percent_done = int(($counter2/$counter) * 100);
            # you are setting status but never use it......
            #$status = "Searching for exact patterns.. processing line $counter2 of $counter"; 
            $mw->update();
            # $mw->update;      <--- duplicate
            # exit if ($stop);  <--- never set in loop
    }
    close (READ);