Similar regions between promoters of yrkF

                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>
sub       GACAATGGATCTTCTTGGTTTACAGGAAAAAGAACTATTA-GATGATATTGACTATGCTG
hal       ........................GGAAAAAG..CGATTACGATTATTTTCATTCTCCTT
ste       .....................AGAGGTAGAAGAAC.........................
       -300      -290      -280      -270       -260      -250        


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    
sub       GTGTAGCAGCTTATTTGGCAGATGCTGAGGAAGGCAGTGTCAACTTATTTATCTAATGTT
hal       GTG--GCAGGCCGCTTTGCAG...........GGCCGTTCCAACTTA.............
ste       ............................................................
        -240      -230      -220      -210      -200      -190        


                                                                      
                                                                      
sub       ACTCATTTACTCATTGCTAAGCGGAATGAGAAGTTTAAAGGCAAGTAAAAATATTGAAGA
hal       ....ATCGACTCACCGCTCACCG.....................................
ste       ...............................................ACAAAAATGAAGA
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       AACAAGGATTTAAAAACATCACAAATATAAAAGGGGGTATGAATACATGGTGTTAACTTA
hal       ...................................GGTATGATAACA.............
ste       A..........ACAAAAATGAAGAATATA...............................
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       CAGTGAGAAACTTTTTGTATATTTGTATACCCCCACCCCTATATAAGAAAAGGAGGAAAA
hal       ............................................................
ste       ....GAGAATCTCTTCATAT.............................AAGGAGGGAA.
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
hal       .
ste       .
         -1


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

About alignment...