Similar regions between promoters of narQ

                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     
sub       CGCAGCTATTGTGCTGTTTACGGTTCTGAAAAAGAATCAGCATAATCAAACATAGAGTCC
hal       ..........GAGCTTTTTTAGTTGATGAATAGG..........................
ste       ....GTTACTGTTCGTGGTATGCTTATGATATAG--TTAGCACGATGAAA..........
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TTTATACAGAGGTGTCTCAGCGTGTCGACAAACCCCGCGTTCGTTGTCAATGCACATTGG
hal       ........................................TCCTTCTCGA-GCAAAATGT
ste       ....................................GCGTTGGTT-TCGCTGCAGA....
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TGCTCACGTGTTATAAAAGGAACGGCGGCTAAATGCTTAGGCGTCCTGCCTAAACACCGC
hal       TGCAAAATTGTGAATAAA..........................................
ste       .............TAGAAGCCTTGCCGGCTAAACGGTTTTGCCGCTTGGC..........
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       CGTCATCACATCCTGTAAAAGCCCTTTATATAGAGGGCTCTTTTTGTGTCTCAGAATTC-
hal       ..............................................TGTTGCAAAATTGT
ste       ............................................................
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       GACAAAATCCGAGGAGTGTGAAAAAATATAAAGGCAGGAACATTGCGGAGGGGAAGAGAC
hal       GAATAAATCCG...ATTGTGAATAAAT.................................
ste       ................TGTGAACAGAAACAA.GGCAGGCAGGTTTCGGA...........
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
hal       .
ste       .
         -1


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

About alignment...