Similar regions between promoters of yhaH


                                                                      
                                                                      
sub       AAAAAGATAAGACATAGTGTAAAGGCGGTTCCGGTTGAACAAACAAGCGCTTTCTGCCGG
hal       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       ATAACCCTCTTGGGCGGATAAGAAGCAGCCTGGCTGAGAAGTTTGATATAGTAAACAGCG
hal       .......TCTTTTGCG-ATTAAATACAAGGTGTGTAAAAAGGCATATATAGATAAAAGCG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CCTGAAGCGAAGGCAAGGGTGATGCAGGATAATACAATCAAAAAGACAGACAACCTTCTC
hal       ..........AGATAAAAGCGAAACAGAAAAAAGAAATAAAA..............TTTT
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       CCTCCTTTTCACT-TAAAAAATATGCTAAAATAAAGCAAGCTATGTATAGAAGTTCAGGC
hal       CCTCCTTTTTCCTATCACTTATATGTGAACATAAGGGAATTCATGACTCTAATTTAAG..
       -120      -110       -100       -90       -80       -70        


                                                                      
                                                                      
sub       TTTCAACAAAAATGAAAAATGCTGAATGAATCCTATTTTGAAGAAAAGACGGGTGATTGT
hal       ....AACAGAAAAAAGAAAT........................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
hal       .
         -1


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

About alignment...