Similar regions between promoters of rpsD


                                                                      
          <<<<<<                                                      
sub       TACCATGTTTTTATCACCTAAAAGTTTACCACTAATTTTTGTTTATTATATCATAAACGG
hal       ................................................TATCGAAAAACC
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TGAAGCAATAATGGAGGAATGGTTGACTTCAAAACAAA-TAAATTATATAATGACCTTTG
hal       TTAAGTAGCCAGGGATATCTCCTTGACTTCAATTGTTTGTGGAGGTTATAATGGACTCTG
       -240      -230      -220      -210       -200      -190        


                                                                      
                                                                      
sub       TGTGAAATATTGCAGCCTTTTTGTTC--AGCTTCTATGTTTT----CATTTTGTTCCTTA
hal       TGTGAAATAAGACAGCCAAGGTGAACTTAACATGTACACCCTTCGGCATTTTGTTCCTCA
        -180      -170      -160        -150          -140      -130  


                                                                      
                                                                      
sub       ----------TCAA-------TAAGGTGTATCGTGTAACTCTCT-GCTGCTGGAGCGAGG
hal       AACCAGCGGCTGAACTTGTTTTGAGGTGTACCACGTAAC-CTCTAGCTGTCGAGGCGAAG
                               -120      -110       -100       -90    


                                                                      
                                                                      
sub       ATACATGAAAACAAAATGTGCATGGTCGAATAGAGC-AGACGGTTTTTATTTTCCA-CAA
hal       GTACAGAACAACAAAATGAGCATGTTAAAGGATTGCCAAACTGTTGTTATTTTGCATCAT
             -80       -70       -60       -50        -40        -30  


                                     
                                     
sub       AAATAAAACCAAAGGAGGAGTCACATT
hal       TCAAAATAACAAAGGAGGAGTC.....
               -20       -10       -1


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

About alignment...