Similar regions between promoters of yvqG


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         
sub       CGGACACTTTCACTGCAAAAATCAGACCAGACAAAAGCGGCAAATGAATAAGCGGAACGG
hal       ....................ATCAGAACAGGCGCAATAAGAAAAAGGAAGAGGGG.....
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GGAAGGATTTGCG-GTCAAGTCCTTCCCTTCCGCACGTATCAATTCGCAAGCTTTTCCTT
hal       .GAAGGCTCTGAGCGTCAATTCC.....................................
       -240      -230       -220      -210      -200      -190        


                                                                      
                                                                      
sub       TATAATAGAATGAATGAGAAGGATGAAACCGAATGAAAAAAATGCTTGGCAAACTGTTGA
hal       ......AGAATGCATCAGAA............ATGAAAAAATCGCTTG............
        -180      -170      -160      -150      -140      -130        


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


                                                                      
                                                                      
sub       TAGGTTCATAAATGGCACAGAAGCTGATTCAGCCAGCGCATCGCCGCGGGACATTGACAG
hal       ............................................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       C
hal       .
         -1


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

About alignment...