Similar regions between promoters of yqkG

                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<                   
sub       CTAATGTCTAAATCAGATGTACCCAATTTGCGCTTTCTCATGTGCACACTCCTTTTTTAG
hal       ............................................................
ste       CTGACGTATAAGTCTGATGTGCCGATGCGGCGTTTGTTCATTT.................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GCTTTGTATTGACCGTAATATAAAGGAGCTAAAGTTTCAACTTTTATGGCTTTGAGATCC
hal       .......ATACACTTTTATGTAAAGGAACAA........ACTTTTATG..........CC
ste       .....................................................GCGCTCC
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       AATCTTTCACATATTGAAATGTGCGTCCATACTC-TTTTAACTTCGCTCGAATTTCCCAT
hal       ATTCTTTTACGGTGTCATAT-TGCTTGCCCATTTGTTTTAATTTTGCACGAATTTCCCAC
ste       AATGCTTCA..................................TCGATCCAATTT.....
       -180      -170      -160      -150       -140      -130        


                                                                      
                                                                      
sub       GCTTTTCCGACTAAGACAACACCTTTTGGCATGCGGTGCACTTTCACGAAGAAGCCCCCT
hal       GCTTTCCCTGATAACGCGATGCTTGTTTGCCT............................
ste       .....................................................GCCCCCT
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TTTGCTCTAGTATGATAAAATGT-ATGGGGCATCATATAGAGACAGAACGGGAGATGAAG
hal       ......CTAATGTGATACACTTTTATGTAAAGGAACAAGGAAATAGTACTGGAGAGGAAG
ste       TTCGCGATCG-ATGATGATATGT.....................................
         -60       -50       -40        -30       -20       -10       


            
            
sub       AA
hal       A.
ste       ..
          -1


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

About alignment...