Similar regions between promoters of fbaA


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       GAGCTCGACATGATCCAGGAATCGAAGGAATTGGGCGCTCTGACGCACTTTGCCAAGCCG
hal       ....................................GCTCTGATGCA.............
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       TTTGACATCGACGAAATCAGAGACGCCGTCAAAAAATATCTGCCCCTGAAGTCTAACTGA
hal       ...GTCATTGCCGAAAACA.........................CATGAAGTCCTCATGA
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CAAAAAGAAGAAACAA-ATGAATCATGTCATTATGTTGCCGATTTGTCGAAAAGTTGGTA
hal       CCGATAGGGATATGATCATAAATGTTATCGCTTCCATCTTGAAATGTTGAAAAGATC-TC
       -180      -170       -160      -150      -140      -130        


                                                                      
                                                                      
sub       TCCTAGTTATGGAGAAAAAGCGATCTGAGTATTTACATATGACAGCAATATATGGGTCAT
hal       ACCAATCTAGGGTGAAA....GTTATGAGCATTTTTTTATGAC..............CAA
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       GCTAGGGTGGAAAGCTTTTTTCGCTAGAAGACAATCAGGCTACATAAGGAGGACATTCGA
hal       TCTAGGGTGAAA.............................ACAGAAGGAGGA.......
         -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...