Similar regions between promoters of yrvM

                                                                      
                                                                      
sub       ATACGAATGTGGAGTGAGGTTCTTGTTACACCAGTTTTCACGCAATGAATTAGCTATCGG
hal       ..............TGAGGTCTTTGTT........TTTCACACACTGTATT.........
ste       ...................TTCTTGCTTCAGCTCTTCGAACGC.................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       AAAAGAAGGCCTTGAAACGCTGAAAAACAGCACAGTTGCTGTGCTTGGAGTCGGGGGAGT
hal       ..........................ACGGCACATTTG......................
ste       ..................................................TTGGGCGGAT
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       CGGGTCGTTCGCGGCGGAACGTCTCGCGCGGTCAGGCGTCGGCGCATTCTGCTTGTCGA-
hal       ...............................TCAAGCGTTGAGGTCTTTGTTTTTTCGAT
ste       CGAGGAGAT-GCGTCACAACGGATGACGCCTTCTTGCTTCAGCTCTT.............
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       CAAAGATGATGTCGACATTACAAATGTAAATCGTCAGCTTCACGCGCTGCTTTCAACTGT
hal       CTGTTATGATATAGTCATTTC.........TCCCCAGAATCAAGCGTTG...........
ste       .....ATGAGGCCGATCGTTCCAATCGTGATCGT..........................
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       CGGACAGCCGAAAGTTGATTTAATGAAGGCGCGGATCGCAGACATTAACCCGGAGTGTGA
hal       ...ACACCCTTAGGTTTTTTTA......................................
ste       ............................GGGCGGATCGAGGAGAT...............
         -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...