Similar regions between promoters of prsA


                                                                      
                                                                      
sub       TAGGCGCTAGTGAAAATAAAGGATCGCTTATGTTGCAAGCGATCCTCGGGCTGCTTAGTA
hal       ......CTTATGAAAA-AAAGGAAC...................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GATGTAAGCTGCACCTACGATGATAAGCAAAATGAACAGTACTACGAGCAACGCGAATCC
hal       ...............................ATGAACAGCACAACGATTAACGCGAATCC
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       GTTAGAGTATCCTCCGCTCATGTTACATACCTCCTTTTCTTGATCAATATATAAGTATGT
hal       ACCGTGGTAAGCGCCAGACATGCTA-ACACCTCCTCT.......................
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       CATCAGCAAAAGTTTGACTAGACGAATGCCCTTTATTTAAAATCTTTTTACAGAAAGCCA
hal       .......AAAAGTTGCGCCAAATGAA--CCCTTTTTT.......................
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       CAATATGTTATGATACGCATAGGTAATTTAATTTGGAAT-GATTAGGAGTGTTTGAAAAC
hal       .......................TACTTCAATTTGTTTTTGATAATGAGGGAGTGGAAA.
        -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...