Similar regions between promoters of yugJ


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
sub       AATCCGATCAGTCCCCAGTTAATGGCGCCAATGATGGTTAATACAAGACAAATTCTTTGA
hal       AATCCGATTAGTCCCCAGTTAATTGCACCAATGATCGCTAGGACAAGGGCAGTACGTTGA
       -300      -290      -280      -270      -260      -250         


                                                                      
          <<<<<<<<<<<                                                 
sub       ATGGTACTCATGTTTTGCAACCTCCTCCATGAATTATTAAAACAGTTATAGATTGTGAC-
hal       ATACCGCTCA....................................TTTAGATTGAGAAG
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       ATATTGGAGAATCTATACATGCATTCTCCATATGAGGGAAGCTGGCCTGCCCTCGCTTAT
hal       AGAGCGGCTGAATTATACATGAA..........................CGCTCACACCT
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       ATCAGCTTCTTTCCCAGCACCTTGCAAAATAAAACCATCTGGTATGCTGATCGGTGAGAG
hal       ATCACCTCCGTTCTCTGGA.......................................AG
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       CTGATTGCTTTACATGTGGTGAGGACATTCTGCATAATAAAAAATCTAAGGAGGAGATGT
hal       CAGATTGATTTACAAATTGATTTTCCATCGTTCATACTGAAAGA................
         -60       -50       -40       -30       -20       -10        


           
           
sub       C
hal       .
         -1


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

About alignment...