Similar regions between promoters of xkdD


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>           
sub       CAAAGGAGCAGCCTACGAGCTTAACCATAGATTGGAGGGCGTCAGATAATGTGTAAGCTT
ste       ........................CCATAAATCGGCG.......................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TGTCAAACAAAGAAAGTCATTGTGGAACATACCGGTATTGGAGTTGTTTTTCATCCATGT
ste       ...........................CACAGCGCGTTTGGCGTTG..............
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CCGAACTGCCGGTCCGGCACTGACTTAACGCCTGTCATTCAAAAGCTGGAGCAAATGCTG
ste       ........................TTAACGCCTG...TTCTAGCGCTGCAGCAGAAGCTC
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       -ACAGCGGGAAAAGCGAGGCTGAATATCTATGATTAAACAGCTGACTGCTCTAATCGCTT
ste       CACAGCGCG.................TCGATCCTTCAAAATATGATTACAATAACCG...
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TGCTGTTTCGGGCAAAGCGAACAGAAAAAAACATTGAACAATGGTATAAGGACGACGGGA
ste       ............................................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
ste       .
         -1


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

About alignment...