Similar regions between promoters of nrgA


                                                                      
          <<<<<<<<<<<<<<<<<<<                                         
sub       TGCCGCCTTTATTCATCATACATCCCCCTCAGTGTATTATTTGATGTAGTACACTTAATA
hal       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       CAGTATAGAGTATTCTAATTAATGTCAATTCCCTTTTCAGCTCATATGAATAGTTTCTTT
hal       ..................TTAATGTCA.................................
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TATAGATACAAAGTCTTATATCG-CAAAAAATGCCATTCTCCTTCCTTTCCATCCCTCGA
hal       .........AATGTCAGATATAGGCACAAAATACCAT.......................
       -180      -170      -160       -150      -140      -130        


                             @@@@@@@@@@@@@@@@@                        
                                                                      
sub       TAACATTTCTCAAAAACCATGTCAGGAAATCTTACATGAAAATGTTTTATCATTCTTTTT
hal       ...........AAATACCATGTCTGATTATCTGACATGGTTGTAGATTCAGAATATTTAG
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TCTCTATAATGAAGAAATATAATAATTGCTTTTTATTCTGAAAGATACGGAGGAATGAGA
hal       ACCTTATAAT-AAGGAGTACATCAACTG-TTCATATTAGAAAA.................
         -60       -50       -40       -30       -20       -10        


           
           
sub       C
hal       .
         -1


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

About alignment...