Similar regions between promoters of ygaG


                                                                      
                                                                      
sub       GGAAGCATTTGATGT-GTGGAAGCTGAAGAAAAACTTCGGAAAAGAGTATATGGGAATCG
hal       GGAAGCGTGCGCCGTTGTGGAAG---AAAGAAAACAACGGAAAAACAAGCAAGCGCATCG
       -300      -290       -280      -270      -260      -250        


                                                                      
                                                                      
sub       AGCGTTCCACTTTTT--TAATTGATAAAGA---AGGCCGGCTCATTAAAGAATGGAGAAA
hal       ATACACATCCTTTTTACTAGATGTAAAAGATACAGCCCCGCTCTTT......TGGAAGAA
        -240      -230        -220         -210      -200      -190   


                                                                      
                                                                      
sub       AGTAAA-AGTAAAGGACCATGTAGCCGAAGCGCTTCAAACCCTCAAAGATATGTCTGAAA
hal       AGAAAACAACGGAAAAACAAGCAAGCGCATCGATACACATCCT.................
              -180      -170      -160      -150      -140      -130  


                                                                      
                                                                      
sub       AGTAAATCTCTATGAGCCTATGCTTACTTTTACCCTGATATCAATTGACAA-ATTATCGT
hal       ........................................TTAATTGACAATAATATCGG
              -120      -110      -100       -90       -80        -70 


                                                                      
                                                                      
sub       AGAAAGAGTTACACTAATTATAAACATTACAATGTAAGAATTTTTTTTAG----AAGAGA
hal       CTTCATACT-ATACTATTTATAAAGATTATAATGTAAGAATGTTTTTTTCTTGAAAGTGA
                -60       -50       -40       -30       -20           


                      
                      
sub       GGTGCATGACGG
hal       GGTGCATGACG.
          -10       -1


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

About alignment...