Similar regions between promoters of ykyA


                                                                      
                                                                      
sub       GCAGCAGCCTCCGCCGTAACCATATCCATACATATTA-CATAACCTCCTCTTTTAATTAC
hal       .....AGCATCCATCAAAACCATATCCGTACATTGAGTCATTACCTCCTTTGATTAT...
       -300      -290      -280      -270       -260      -250        


                                                                      
                                                                      
sub       GCCAGAGCCTTTATAAGTAGGCATAGCGTCTAATATAACCTATGTAAAAACAAAAAAGTT
hal       .........TGTATAAGGGGGCAT.........TACAACATATGCGGTAATTACATGATT
        -240      -230      -220      -210      -200      -190        


                                                                      
                                                                      
sub       GTATGGTCATCTGTCCTGATTTTTCACTTTTTTGATTTAATTTCAGTATTGCATTTATAC
hal       GGTTGGACGGATGCCCAGA..................TAATTACATGATTG.........
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       AGCACGGCTATTGCCAAATGTCCCCATGGATTCTATAGTAGAAATTGTCAAGATTGGGGG
hal       ............................GATTATGTGGGACAAGTTGT--ATAAGGGGGC
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       ATTTAACGTGAAAGACGCTATAAAACGGCGGCCTGGAATCAAGATCGGAGCTTTTTGTGC
hal       ATTCA.......................................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       C
hal       .
         -1


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

About alignment...