Similar regions between promoters of ahpC


                                                                      
                                                                      
sub       TATTCTGCTTTTGGCCATTGTCCTTTGCCCTTGACCATGGTGTCATAAAATGTTCAAATG
ste       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       CCAAAACGGCCTGGCATTCTGATTTACAAAAGTCCCTGAAAACCTTATCTAATTGAGAAT
ste       ..AAAAATCCATTGCATATGTATTGACAAA.....................ATTGACAAA
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CAGCCTCTCATTTATTATAA-AAGAAATGCCTAAATCCTACCTGTCACACCTTTATTAAG
ste       CATATGCCCCTATATGATAATAAGTATTGGTTTAA.......................AG
       -180      -170       -160      -150      -140      -130        


                                                                      
                                                                      
sub       ATGAAAAAAAGTAGGTTATGGCTTGACAAAAAATATATATTAATTAATAATTCATATATA
ste       AAAAAAATCCATTGCATATGTATTGACAAACATATGCCCCTATATGATAATAAGTATTGG
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       ATTAGAATTATTATTGAAAGCGATTATGCTTTCTAATACATTTTTAGGAGGAATATACAT
ste       TTTAAAATTATTAT..............................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       T
ste       .
         -1


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

About alignment...