Similar regions between promoters of yufT


                                                                      
                                                                      
sub       CTTTCCTTCAGCTTGATCAGGATTGATTTTAAATATACAAATAACCTCTTTTTTGTTAGA
hal       ...........................TTTAATAAATCATGAAACCTCTCT.........
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       CTTATTTTGAGGTCAAAAGAACTCATAAAAATCCATTACAGCAGTTCGAAGCGTGGCAGC
hal       ..................................ATTCCATCAATTTGAAGTG.......
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TTGCAGAAAAGTGCGATATAATTTGGACTAGGTCGTTTGACCGTATATTTTATACATAGC
hal       .......AAATTGCGTTATAATTTACGTTAGTTTG...........ATTAAAGAAATTGC
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       GCATTT--TTCAATTGAGAACGAGAAAAGGAGGTCTTATCTTTGCAGCTCTTACATCTTG
hal       CCAGTTGATTGATTTGATA-CTAGAA--GGAGGTTTTTT................TTTTG
       -120        -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       CTATTTTATCGCCTTTTT---TATTTGCTT--TTATCATTCCCTTCTTGGCAAAATACGC
hal       AAAAATAATCGCCTTTCTACATATTTAATAAATCATGAAACCTCTCTAAACCGAATAGCC
          -60       -50          -40         -30       -20       -10  


                 
                 
sub       AAAAAGA
hal       ACAAAG.
               -1


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

About alignment...