Similar regions between promoters of yerN

                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       CGCTCGGCCTGCAAATCATCGGAAAACACTTTGATGAAAGCACTGTATACCGCGTTGCTC
hal       CGCTAGGCTTACAAATCATCGGAAAGCATTTTGATGAAGGTAGCGTGTACCGAGTGGCTC
ste       CGGTCGGCTTGCAAATCATCGGCAAGCACTTTGATGAAAGCACTGTCTACCGCGTCGCCC
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>          
sub       ATGCATTTGAACAAGCAACAGACCATCATAAAGCAAAACCTGAACTGTAAGGGGTGAAAA
hal       ATGCCTTTGAACAAGCAACGGACTATCATACGAAGCGACCAACGCTGTAAGGGGTGAAA.
ste       ACGCTTTTGAACAAGCGACCGACTACCATAAGCAAAAACCGGTGTTGTAAGGGGGGTTAG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       GAATTGAACTTTGAAACGGTAATCGGACTTGAAGTCCACGTTGAGTTAAAAACAAAATCA
hal       ........CTTTGAACAAGCAA-CGGACT...............................
ste       GTGATGAACTTTGAAACGGTCATCGGACTTGAGGTGCACGTCGAGCTGAAAACGAAATCG
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       AAAATTTTCTCAAGCTCTCCAACGCCATTCGGCGCGGAGGCGAATACGCAGACAAGCGTT
hal       ..................CCAACGCTGTAAGGGGTGAAAGC...TACGCAAACGACATTT
ste       AAAATTTTCTCCAGCAGCCCGAACGCGTTCGGCGCGCCCCCGAACACGCAAACGAACGTC
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       -ATTGACCTCGGATATCCGGGCGTCCTGCCTGTTCTGAACAAAGAAGCCGTTGAATTCGC
hal       TAACGATCCCGGTCAACCTTGC......................ATGCCTTTGAACAAGC
ste       -ATCGACTTAGGGTATCCGGGCGTGCTGCCGGTGTTGAACCGGCAGGCGGTCGAGTTTGC
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
hal       A
ste       .
         -1


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

About alignment...