Similar regions between promoters of yhxA


                                                                      
                                                                      
sub       TCGCCATTTCCTATATCATACAGAAAACGGCTAGGCTTCACATTGCTATTGCAATGGCTG
ste       ......................................................TGGCTG
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TCCAAGTTGTTTCGAGTGCGACCTTTATCAGTACGATGCTGAGCATTGTCACTTTGCCTG
ste       GAAAGATTCGTTTTACGGCGATCTTCAT......GATGTTGGGCATT.......TTCCCG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TTTTGCTTTGGAAGCTGCATCCTCTTTCTTCTTGAGAAAGGGGATGTT----TTATTATT
ste       GTTTGATTTTTAACCTG.........TCTTCATGTGAATGGAAAAGATGGCGTGAATTTT
       -180      -170      -160      -150      -140          -130     


                                                                      
                                                                      
sub       TACGCGGTTTATTGACTCTGACCCGGTCTGGCTTTATATTGAAGGCAGGGAAATCATCAC
ste       TACACG...............CCCGGTTTGATTTT.........................
           -120      -110      -100       -90       -80       -70     


                                                                      
                                                                      
sub       CAAGACATCACATAAAGAGAAGGTCTGTTTCAATTGAATTGGCATTATAGGGAACGCTAA
ste       ............................................................
            -60       -50       -40       -30       -20       -10     


              
              
sub       TGAA
ste       ....
            -1


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

About alignment...