Similar regions between promoters of ydhM


                                                                      
          <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<
sub       AATAAAAAAAATCCTGATTACAAAAAATGTCAT-AAACAAATTTTGTAATCAGGATTTTA
hal       ................AGTTCATATTATATCGTCAAACAACTCCTATTCTCATGATGTTA
       -300      -290      -280      -270       -260      -250        


                                                                      
          <<<<<<<<  <<<<<<<<<  <<<<<<                                 
sub       CGGTTCCT--GGTAGACAC--CCTCAAACCATATTATTGAGGTTATACA---AGTGATAA
hal       GGATGCAAAAGATACAAACATCATTAAATAAAAGTATAGACATTTAAAATTAATTGATTA
        -240        -230        -220      -210      -200         -190 


                                                                      
                                                                      
sub       TAGCTATTTAATTGATTCGTTTCCGTTGATGAGTGTACCACATTATGAATGAATCTTCCA
hal       TAATTAT............................................AAACATCAT
               -180      -170      -160      -150      -140      -130 


                                                                      
                                                                      
sub       TAGAAAAATTTATAAAACGGTGAACCGGAAAAAAATATGATTATATTTATTTTATAAAAG
hal       TAAATAAAAGTATAGA-CATTTAAAATTAATTGATTATAATTATA.TCATTAAATAAAAG
               -120      -110      -100       -90       -80       -70 


                                                                      
                                                                      
sub       TATAGACATTTAAAATTAAATGACTATAATAATC----AATGTAAGCGTTT-TAATAACA
hal       TATAGACATTTAAAATTAATTGATTATAATTATAGGAGAGTGAAAGCGCTTATCATAAAA
                -60       -50       -40           -30        -20      


                       
                       
sub       GGGGGGATAGCAG
hal       AAGGAGCT.....
           -10       -1


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

About alignment...