Similar regions between promoters of yheN


                                                                      
          <<<<<<<<<<<<<<<<                                            
sub       TGACTAAAACCTTCATAAAAGCCCTCCCTTTTCGAGATGTCCCTGATGTCATTCAAGCTG
hal       ..........................................................TG
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TCATTATCACTAATTCTACCATATTGGACAAGCTGAAAAACAGAAAGATCAAGAGATCTA
hal       TCATTTTAACTATTT...............AGCAGAAACGTAGAAGGGTGAA........
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TAGCGGAAAGGAGTTTATTTTTTCCTTAAAATCTGACATTTCGACAAATTTTCTATGTGC
hal       ...CGGAAATTCGCTTTTCTTTT.....AATTGTGTCATTTTAACTATTTT.........
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       TTTCCAGTTTTA-TTCCTGTATACTTGACTGGTAATACATAGGTTGTAAACATAAGGCAT
hal       .TTCCAGTTGGAATTCATCTAT......................................
       -120      -110       -100       -90       -80       -70        


                                                                      
                                                                      
sub       CTTCATAAGCTGCCTGCTGTACAGCATTATGTAGAGATTTTATGCCAATGGAGAGATTGT
hal       ...........GTCTTCGTTACAGAATTGTGT............................
         -60       -50       -40       -30       -20       -10        


           
           
sub       T
hal       .
         -1


   >     : other CDS		-     : gaps within a similar region
   ]     : terminator		.     : gaps between similar regions
   }     : RNAs			@     : known binding sites
   <,[,{ : opposite direction

About alignment...