Similar regions between promoters of yjaU


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<        
sub       ATGCCATATGTGATAAAAGGAACGTCCAAATAAAGGCAATAATATATCGCACGTTTCCAC
hal       .............TGAAAGGAATAGGCAAATTA--TCAATTCTATA..............
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       CTCGTCCTTCTCATTCTATTCTAAAAGTTATCA-TACCATACAAAAAG-CGAAGGGGGAA
hal       ........................AAATTATCAATTCTATAAAAAACGACGAAGCTTGAT
       -240      -230      -220      -210       -200       -190       


                                                                      
                                                                      
sub       TCCAATTTTAGCAGAAAGTGAGGTGACAAAAGAGTCTGATTCGTCACACTTTAATGGTAA
hal       TCCGTTTTT..............TGACAAAAAAGCCT...........CTTTAAAGACAT
         -180      -170      -160      -150      -140      -130       


                                                                      
                                                                      
sub       AATATAAAACGTCAATCAGTATAATAGCCAAAAATGTAAAAGGCTAGGACTTTACCTTAT
hal       AACAATAGAAGTTGCTGCATAGGATGATCAAAACCTGAAAGGAATAGG.....AGCTCCT
         -120      -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       TCGTTTCTTTTCTATTTACATAAGATAGCGTGAGATGAAGTGTGAAAGGAGGCGGGCAAG
hal       TTATTTGTCGTTTCATGACAAAAAAGCCTATCCTATTACGTTTGAAAGCA..........
          -60       -50       -40       -30       -20       -10       


            
            
sub       CG
hal       ..
          -1


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

About alignment...