Similar regions between promoters of ytcF


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       ACTCCTGCAGAGTTGTTGATCTAATCCGCCATGTAGCGGCACGAATGAAACATCCGTCTG
hal       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>>>>                                                    
sub       CTGTATAAAATAAGGTCATGGACACATTTTAAAGAAAAAACCCTTAACAGCATATTTCTG
hal       ...TAAAAAAAGTGGTCAT.....CATATTCATAAAAAAA..................TG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       AAAAAACGCACCTTGCAAATTAGACTTAAACACAGTATACTATTTTTCGTGAACTTCTTG
hal       AAAAAGTTGTTATTGCAAAGAAGGATTAAACAAAGTATACTATTTTCCGTGAACATGAAA
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       CTTGAGACTGTTTCGGAAT--------TACTTAAAGGGTTAGGACCTCTCCGGACTAACT
hal       CGAAAG-CAAAATAGGAGTACGTTTACTACAGAAAGGGTTAGGACCTCTTTGGACTAACT
       -120      -110              -100       -90       -80       -70 


                                                                      
                                                                      
sub       TTCCCCCGTGGTAAATGGCCGACCCAGTTGTTGGA-ATTTCACTTTTTAATTCTTGTTAA
hal       TTCCCCCGTG-TAATAAACGTTCCTACATGCTTGAGAAGGCA---TGAATTTTTTGTAAA
                -60       -50       -40        -30       -20       -10


                   
                   
sub       GGGGGGTCC
hal       GGGGGATTC
                 -1


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

About alignment...