Similar regions between promoters of yufN


                                                                      
                                                                      
sub       TTGGTTAGTTGATCCCGAAAAACTAAGTCATAAGTCTTACTTCAGAAAACGATGTCACGG
ste       .............................................AAAACGATGAGCCGA
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TTTTCCGCCCGG--AACGCCTTCCGCATCCTTCTCTTCCCCGCCTTTCGAAGGAAATACT
ste       TTTTTTATTCCGTCAACTACTTCCGC..................................
       -240      -230        -220      -210      -200      -190       


                                                                      
                                                                      
sub       CACACCACGCTTATTCAGGGAAGAATAGAACTGTCTCAGCGCATTCCATTTGTTATTATC
ste       ...................................................GCTATCATG
         -180      -170      -160      -150      -140      -130       


                                                                      
                                                                      
sub       AGAAAATTTTATCGATTCTAAGAAATTGTTCAGGACAGCCCATCACATGACTGGCCGGAT
ste       AAAAAGTGTCGCCGATTTT.........................................
         -120      -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       CAGCTTTGAACCAAATTTTT---CTGGGGGGTTATATCT-TGAATAAACGAAAAATCGGA
ste       .........AACAAATTTTCAAGCTAGGGGGTAGTGAATGTGAAAAAGCGAA---TCGGA
          -60       -50          -40       -30        -20       -10   


                
                
sub       TTGGCG
ste       TTGGTG
              -1


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

About alignment...