Similar regions between promoters of rpoC

                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       AAGGCGACAATGTTCCTGAACCAGGTGTTCCGGAATCATTCAAAGTATTAATCAAAGAAC
hal       AGGGAGAAAACGTCCCTGAGCCTGGTGTTCCAGAATCATTTAAAGTTCTTATAAAAGAGC
ste       .......................GGTGTGCCGGAGTCGTTTAAAGTGTTGATCAAAGAGC
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       TTCAAAGCTTAGGTATGGATGTCAAAATCCTTTCTGGTGATGAAGAAGAAATAGAAATGA
hal       TACAGTCTCTCGGTATGGACGTCAAGATGCTATCAAGTACTGAGGAAGAGATTGAAATGA
ste       TGCAAAGCTTGGGCATGGACGTCACGATTTTGACGAGCGATGAACAAGAAGTGAACATGG
       -240      -230      -220      -210      -200      -190         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       GAGATTTAGAAGACGAAGAAGATGCGAAACAAGCTGACGGCCTGGCATTATCAGGTGATG
hal       AAGAGCTTGATGATGAGGATGA....................................TG
ste       AAAACTTTGATGATGATGATG------ACCATGC--ACCGGATGCCATCATG-GTGGACG
       -180      -170      -160      -150      -140      -130         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>
sub       AAGAGCCGGAAGAAACAGCATCTGCAGACGTTGAACGCGA-TGTAGTAACAAAAGAATAA
hal       ATGATGAGGATGAACAAGCAAGCG-ACAAATTGAACTTGAATATTGATTCAACAGAATCA
ste       TCAAACCGGCCGAACGGGAAGAAGCCGGTGAAGAGAAAGA-TGCGGTGACGAAAGAATAA
       -120      -110      -100       -90        -80       -70        


                                                                      
                                                                      
sub       TCTCTAGTTATAAAGGCAAGTGACATCGGTTAATCCGAAGATAAAAAGGGAGGTAGGCCC
hal       ....................................GGAAATCATAAGGGAGGTTGGCCC
ste       ACC--GGCCATAACGGCCAG......................AAAAAGGGAGGTATACCC
         -60       -50       -40       -30       -20       -10        


           
           
sub       C
hal       C
ste       C
         -1


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

About alignment...