Similar regions between promoters of yndD


                                                                      
          >>>>>>>>                                                    
sub       AATTTTAGTTTTCCCAGACTGCTAAAAGGCTCATTTTGTGTTAATTATGCAAAATGGTCA
hal       .ATTTTTGATTTCATCAACTTCATAAA.................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                           ]]]]]]]]]]]]]]]]]]]]]]]                    
sub       GGTTGATTTCTTTAAAAGCATGATGAAATGTTCATCATGCTTTTTTATTGAGAAAAAAGA
hal       ..TTGATTTCATCAACTTCATAA..............................ATAAAGA
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CGAACATAAAAAATAGGTATACGGGAAAAATAATC--CTATTAGAGAGAGGGGAACTGAC
hal       CGCACAAA.........TATTGGGGAAAAGTGAAGGACACTTGGAGCGATGAGGACGGAC
       -180      -170      -160      -150        -140      -130       


                                                                      
                                                                      
sub       AGATGGATAACATGATATCAACACTTACTGACTGGAATGTGTGGTTTCAAGCGTTAGTAG
hal       A...............................................AAGCGATAGAAG
         -120      -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       TATTTCTCGTTCCATATGTAATCTATAAAGTGTTTACTTGGATTCATGTATAAGAAGGTG
hal       AAAAGATTGAAAAACAAGCAAACGATATTGTG...............GAATTAGAAGGTG
          -60       -50       -40       -30       -20       -10       


            
            
sub       CA
hal       C.
          -1


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

About alignment...