Similar regions between promoters of yfkN


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<  
sub       CAGTGTACTCGCTGTCCTCAAAATAATATGTTAAAACAACTGCAATTTTTTTCCCCATGA
hal       .......................................................CATGA
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TTCATAACCTCCCGCTTTATATGTCTACATAAAACACTCTACCCCAGCCACACTAAAATA
hal       TTTGCAACGTCTC........TGACTATATGAAAGACGGTCATCTCGCCGCA........
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       AACATTCCGCGATTGTGACAAACGATAAGCATAAATGCCCAGTATTTGTCGTTTGATACT
hal       ...................................................TTTGCGACT
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       GCTACATAATACTCATTTTTCTCCCTTTTACAATAATCATAAAGAAACACCTACAAATAG
hal       GATAAAT...........TTCTTTTTTTAACAATAG--ATTAATTTATTGTTACACATCG
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       TTACAAA------ATATTCT--TACAATAGGAGCTGTAACACAAATTTCGTTGAAAGGTG
hal       TTGGAAATCGGCTATCTTCTGGTACACTAGAAAAAG-ATCACCATTTTAAT-GAAAGGAT
        -60             -50         -40       -30       -20       -10 


                  
                  
sub       GAGAACTG
hal       GA......
                -1


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

About alignment...