Similar regions between promoters of fer


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<                         
sub       TCGAGAACCATAATATCGAAGTAATTTAATGACAACCTATCCACCTACATTCTTCCTGAC
hal       .....AACCGTTATACGAAAAAAACTTAACG.............................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       AAAAATCGTTGATTTGCTCTT--TTTATTTTAACAGATTTCAAACAGAAATCGACGTTTA
hal       ...............GCTCTTCGTTTATTTTAACAGACAATGCTCTGAAAAAGAGGGGTA
       -240      -230      -220        -210      -200      -190       


                                                                      
                                                                      
sub       AAG-TCATCATTAAGGGGGATGTTATGTAGATAACCCCTTATGTGATAAGCATTCTCAAT
hal       ATGCTCACTCTCTCTGGACAAGTTA--AAGACAAACCGTTATACGAAAA--AAACTTAA-
         -180       -170      -160      -150      -140      -130      


                                                                      
                                                                      
sub       CATTTTTCTGTTGAAATGTGGCAGCAACATCATTACAATAAGTAAGAGGAATAGGTGTTA
hal       -------CGGTTGAAAACTGTCGTCATCACCGATACAATA-GTTACTGGAACGAACGAGC
          -120      -110      -100       -90       -80       -70      


                                                                      
                                                                      
sub       AATTGATTAAATATAAAGATTGATCCATTTGTTCCACCAAGAACAATCTGGGAGGTTTTA
hal       TGACCGTTAAAAATATATAAACATCCATTTCTT...........................
           -60       -50       -40       -30       -20       -10      


             
             
sub       TTC
hal       ...
           -1


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

About alignment...