Similar regions between promoters of yczE


                                                                      
                                                                      
sub       CAGCGCCCTGTTTCAGATTATTGACAAAATCCTAAAACGATATTCGTTTTAGGATTTTGT
hal       .................TTGTTGACCAATCACTTCATCAATGTTCGAT............
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GATTTTCAGCGTGATTGAAAACCTTTGAAGTCTAGGAAGGGCGAGCATTGGAGCACAGCT
hal       ..............TTGAAAACAATTCATG-CTAT-AATGGCAAGGACTTCAAGAGAGAG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       AATGTTAAATTCGTGAGCACCGAAGCACAGGCCTGACAACGAATGCAAGGGTTTGCCAAC
hal       AAGGGTA............................AAAACCAATGCAA............
       -180      -170      -160      -150      -140      -130         


                                                                      
                     ]]]]]]]]]]]]]]]]                                 
sub       ACGCTGAAACAGGGCGCCTGCGCGCCTGTTTTTTTGTTGAGCCCCTTTCGCCTATTCCGC
hal       .....................GTGGCTGTTTTTT..........................
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       CCTTCTGTCAGATGTGCTACAATGACAATCGACTGATTTTTACGAAAGAAGGGACCTCAC
hal       ..............TGCTATAATGGCAA...............GAGAGAAGGGTATTCA.
        -60       -50       -40       -30       -20       -10       -1


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

About alignment...