Similar regions between promoters of hisZ


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<          
sub       ATAACGCCTGAAAGAATCATCAGGACACATAGAGTTCGCAGTGTTTTCATCTTTATCTCC
hal       ........................................................CTAC
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TTGTTCTCTATTTGATTTGTATTATAGCATGCCAAACATAAAGAATTTGAGATATTACGT
hal       TAATCCTTTATCTTGTTAGTATATTAGCGAACTAAA...............ATATTAGCG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       ACCTTTAATACATTATTCATGATTTTTTCATAATGAGGAGAAGGATATTTG--AACTAAA
hal       AACTAAAGTATCTGTTTGTTGAT..................AGTATATTAGCGAACTAAA
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       AATATCCTTACTGAAGTTAAGCGTTGATTTTCATTCTTTCATCTGCTAACATATTATCAT
hal       ......................................TAATCCTTTATCTTGTTAGTAT
         -120      -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       ATTAGCGAACTAAAGGATTCGGAATTTTCCTTCATAAGATAACAGCGGAGGTGCTCGGGT
hal       ATTAGCGAACTAAAGTAT-CTGTTTGTTGATCCTAAAGCTAGGAGTG.............
          -60       -50       -40       -30       -20       -10       


            
            
sub       TG
hal       ..
          -1


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

About alignment...