Similar regions between promoters of ybgJ


                                                                      
                                                                      
sub       AGGGCCAGTATATATCCGTCTTTTTCAATAAACCGTTCCAGTTTTATGTTGATCACATCC
hal       .....CAGCATAACGCCATCCTTATGGCGGATACGTTTAGTTTTTATATT..........
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TCGCTTTTTATTTTGGGGAATCGGGAGAAAACCTGCAAATTGCTTTTGACCCAGAACATG
hal       TCACTTCCTATTATGTGAAAAATTCAGCATAACGCCA---TCCTTATGGCGGATACGTTT
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       AGGTTTTTATAAATCTTACTGCTTATTTTCAAAATGTTTTTGTCGTATTTTGTATGATTC
hal       AG-TTTTTATA.............................TGTAGTCTTCTGTTTCTTTC
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       TGTAGTCTCCATTATACAGTAATTATACCTTCCGCTATTATGAAAGCGTTTAACGCCCCC
hal       TGTAGCCTCCATCATAGACTAGACTTACC...............................
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       TTAGCCTTCGTTTTGATACACCTCAGTCCTTTAAGAAAAAAATCAGTGAGGAGGAATTCG
hal       ......TTAGTTTTTATATTCCT.....................................
        -60       -50       -40       -30       -20       -10       -1


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

About alignment...