Similar regions between promoters of yrpB


                                                                      
                                                                      
sub       TCTTCTAAGCTTTATTTTACATGATGTTCTCCTATATATCATTCAATATTAAGATGCAAG
hal       ..TTCAAAGTTTTCTTGT.......................TTCTACGGTGACAAGCAAG
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       ACATC-TCAAAATCAGATATCAACTATGACGGACTACATGAATATTCAGTTTTTTGTAGA
hal       ACGTGATCAAGATCGCGTACGAGAAATGA........AAGAAACTTAATTGTATTATAGA
       -240       -230      -220      -210      -200      -190        


                                                                      
                                                                      
sub       GCCGCCATGGGACGACACTATCTTTGACACACTTTAATCCCCCCTGCTTTATCGACATGT
hal       ............................................................
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       TAACTGGTATGAGAGATTGACAAAAAGAAGGAAAACGATATATTTAAGCGAATACGAGTT
hal       ..............GATTCATAAAAAGTCGGAATTCAAAGTTTT................
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TTTGAGTAAATTTTAAAATGACACTTTTTTCAAAAATCATGTCTTAACGGGAGGATTCGG
hal       ............................................................
         -60       -50       -40       -30       -20       -10        


           
           
sub       T
hal       .
         -1


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

About alignment...