Similar regions between promoters of yirY


                                                                      
                                                                      
sub       CAGCTGGCTGGATGAAGGCAGAGATCAGAATGCTTGGATTGACTTGGAAATCCGTGTCGC
ste       ...CTGGTGTGAGGAAGGAAGAGACCAATCAAGCTGGATCGATTTGGAGATCCATGTGAC
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GGACCAGCTGTCACTTGAAGAGATTCACAGGCTGCGGAAGGCGCACCCGGGCTTTATCCA
ste       CGAGTCGTTGACAATGGAGGAAATTGATCGGCTGCGTAAGCTTCATCCCGGATTTGTCCA
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TATCAGGCCGGTTTTTGAAGAACAGAACAAAGACCGG---GAACGGATCGAGGTTAAACA
ste       CATTCGCCCGGTGCTTCCCAATCGGGAGGAAGAGATGATGGAAATGAGCCGCG---AGCC
       -180      -170      -160      -150         -140      -130      


                                                                      
                                                                      
sub       TGTCTCAATCGAGGACCGCTTTAAGAAATTTTATGAAAAACAAACTGGCGGTGCGGTGCC
ste       GCTTTCACTTGAAGAAATGTTTCACCGCTTTTACGAACGGCAGACTGGGGGACAAACGCC
          -120      -110      -100       -90       -80       -70      


                                                                      
                                                                      
sub       GGATGAAGAAATGGTGAGGCTGTTTTTAGAGCTTGCATCAGGCGTTGAAGAGGAGGATGC
ste       GGATGAAGAGCTCGTCCGCCTCTTTTTGGAGCTGGCGGCGGAAG---AAGAGAAGGAAGG
           -60       -50       -40       -30       -20       -10      


             
             
sub       GAA
ste       GGA
           -1


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

About alignment...