Similar regions between promoters of ydhB


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<        
sub       TATAAAATTGCAGGTAGTAGGGAGTCGGCTTATCTAATTTAAAATCGTCCATATATAATA
hal       .........................................AAATTGTTCATTTTTA...
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       CCTCTTTTGAATATATTCAAGGGCTTTTCTTCATCAAAATCAT-ATAACAGATGGTAATG
hal       .CTCATTTGAATGTCCTC............TAACCAAAATCATCATACTAGATTGTTA..
       -240      -230      -220      -210      -200       -190        


                                                                      
                                                                      
sub       GGAAGCAACAAACTGCCTTGTCAGATCCCTGAATTTGAGGTACGATATGTTTGCTGAACG
hal       ............................................................
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       ACGGTCGACGGACTACTGGCAACTGAAAAAACGGCGTGTTTTTCTTCGTCAATAGGACAC
hal       ............................................................
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       CATACCTCCGCCAGAATAGCGCACGATTACATTTTTACATCTTTTCAATGGAGGAAAAAA
hal       ...............ATAACGAAATTGTTCATTTTTACACTCTTTCA.............
         -60       -50       -40       -30       -20       -10        


           
           
sub       T
hal       .
         -1


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

About alignment...