Similar regions between promoters of gapB


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       CTTGGGGAGCGAATCATATTAACAGAGTGTACGGGGATACATTTTCTGTGCTAGAAGAAA
hal       .............TCATAATAAGAGAGGGGA.................TGCAACAA-AAA
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]]]]]]]]]]]]]]]]
sub       GTGTGCTCAATGATAAGTTAAAACAGGAATCATAAAGCATGAGGGCAGTCAGTGCGGAGC
hal       GGCAGCTTATTGACATTTTAAAAC....................................
       -240      -230      -220      -210      -200      -190         


                                                                      
          ]]]]]]]]]                                                   
sub       GCTGGCTGCTTTTTGGTTCTTACGCCTGATATTCTGTGCAAGAAAACATAAGATGCATCA
hal       .............................................ACATTGGATGCAACA
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       TAAATTAGCGTTATAATCGTTGATTTTTATCAATATGTACTGGCGAATTTGTTTTAATGT
hal       AAAA...........................................TTCGAATAAAAGT
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       GTTATACTAATTTTAGATAGTAACAAATTAGGATGGCATAATT-GATAAGGGGTGTCCAA
hal       GATATACTATTTATTATAAATGAATTATTAGTATGTCATAATAAGAGAGGGGATTTCCA.
        -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...