Similar regions between promoters of yddR


                                                                      
                                                                      
sub       TTGATTTACTTTAATGTTAGATCCCTCAATAACTCCATTCTCTTCTAATTTCTCTACTCT
hal       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       AGCTGTAGCTGCTGGGCATGTTAAATGTACTCTCTCCCAGATCTTTCATTGAATTCGGCT
hal       ........................................................GGAT
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       ATTATACATAATTTCTCTATAATTTTTTATCTGTTTGATCTATTTGAACGTTAATTCCTT
hal       ATTAAACAGAATTAGTTTATAAGTTTTCCCGTGTTTTAACTATATTAA............
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       TCGAAAATAAAGTCAAAGAGTTAAAACACTTTTTTTTATCTATGTATTCGAACACTGCTG
hal       .....AATAGTGGCAAAAAGTTTTTTTCCTTCACCT-ATCTTTTTATTC...........
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       ATATTATACACTTAACTCTGTCGATCTAAGACAAATAAAAAAAGAAAGTGAGTTGTAAAT
hal       ............................AGAAAAATTCAAAAGGGAAG............
        -60       -50       -40       -30       -20       -10       -1


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

About alignment...