Similar regions between promoters of metB

                                                                      
                                                                      
sub       TTTAAATCGCAATTCAAAATGTAAACATCAATTAAGAACTCATAAGAAACCTAACGATAT
hal       ...............AAAAGATAAACGTAAA.............................
ste       ............TTTAAGGTCAAAAAATAAATTGAAGAATGTTGACAAA...........
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GAGCGTCAGTTCATTATCAATTCATATGGCTCGTTTTTTATCTTATCATTCTATAAAACA
hal       ..........................................................CA
ste       ..............TATCGCTCCTTCCAACACCGTTTTTAAATTGTCA............
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TTACAATTCCCTC-TTACATCTTTGAAAATCATTTTACTGTGAAACCAAAAGGCGTGTCA
hal       TGAAAATACCTCCGTTTGATCATTGCGAATTTTCTTATT...AAACGTAAAGGAGT....
ste       .........................................GAAATGAAATGGCGT....
       -180      -170       -160      -150      -140      -130        


                                                                      
                                                                      
sub       GTGCGTTTTATTTAAAGAGTTTTCTGTTGTTTCCCCCTCAACACGTATAGATAGATTGAA
hal       .............................................TATATATACATACAA
ste       ..............................................AAAAATAAATTGAA
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       AATTGGCGTGAAAATTCCTATAATGAAGAAAATTA--AACGGGGAAATAATGGAGGTGGC
hal       AA..........................................................
ste       GAATGTTGACAAAGTTTTTATAATTAAGGTATTTAGTAACGAGACAGAAACGGAGGGGAC
         -60       -50       -40       -30         -20       -10      


             
             
sub       ACG
hal       ...
ste       AC.
           -1


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

About alignment...