Similar regions between promoters of trxA

                                                                      
          ]]]]]]]]]]]]]                                               
sub       CATGCCGGCGCTCTTTTTCAGGTTTTAAAACAGCTCCGGCAGGGCATGGTAAAGTACATG
hal       ............................................................
ste       .............TTTTTGACGGATAAATTCCGCGGCAAAAGCGAATAGTAGA.......
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       ACAGTGAAGAGGAGATGTGATCTTATGCTTCGTACCATTTTAATGATTATTGGGGCAATT
hal       ..............AAGTGATCTTCTGC................................
ste       ............................................................
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       GTAGTGATCGGGGCCATTATCAGATTTGTGTTTTAAAAAAAGAGCATATCCCATTCAACC
hal       ........CGGTGGTATAATGCAAATTGTG.........AAGTGCAAACTTCTTGAAAAC
ste       ..AGTCATCGTCGCCATTAACAAA....................................
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       ATATAAAAATGAGTAAACCGGCTGTGATCAGGAAAAAATAATTTGTAAGCATTAAAATAG
hal       ATATAACAAT..................................................
ste       ............................................................
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       CGTGAACGAATGGGAGATGCTATACTAAAAATCATCATTTCACATTGGAGGAATTCAATA
hal       .............GCGGTGGTATAATGCAAAT............................
ste       ....AGCGAATAGTAGAAACGAAGCAAAACAT.........AGATGGGAGGGAATCGAT.
        -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...