Similar regions between promoters of ymfA


                                                                      
          >>>                                                         
sub       TAAGAAAATTTCATACAGTGAAACAAACGCGGTCATTCTCACATTCAGCTGAGTTTGACC
ste       .............................................CAAGTGACTTTGAGC
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       GTTTCTTTTACATATTGGTTTTCCCTAAACCTTCTGCTTTATCTTGTTTTCTAAATTTAC
ste       G...................TTCCCCAACGCTT-TGCTT.ATCTTGTGTTTTTCAGCATC
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TTTCAGTTATAATAGGAACAAGTGATGATGGACGGGT----ATGAGACTAGG-AGGATAT
ste       GATTCGTTATAATAAAAGCAAGTGACTTTGAGCGGGTTAGCATCACAATTGGGAGGACGC
       -180      -170      -160      -150          -140       -130    


                                                                      
                                                                      
sub       AGATTTTGAAAAAGAAAAATAC------AGAAAACGTTAGAATTATCGCCCTTGGCGGTG
ste       AGCCTT-GAAATCGAAAATAAAGCCGGTAGAGAAAATACGCATTTTTGCCCTTGGGGGAG
            -120      -110            -100       -90       -80        


                                                                      
                                                                      
sub       TCGGAGAGATTGGGAAGAACCTTTATGTCATTGAAATTGACTCAGACATATTTGTCGTTG
ste       TCGGAGAAATCGGCAAAAACATGTATGTTGTCGAATTGGACGAGGACATTTTTGTCATCG
         -70       -60       -50       -40       -30       -20        


                     
                     
sub       ATGCCGGCCTT
ste       ACGCCGG....
         -10       -1


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

About alignment...