Similar regions between promoters of rpsJ


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       CGCATATTGAGGAGCCATCATTATTCGCGAACACATTAAGTCGGCATGCACGCAACCATT
hal       ......................................................AGCATT
       -300      -290      -280      -270      -260      -250         


                                                                      
          >>>>>                                                       
sub       TATGATAGATCCTTGATAAATAAGAAAAACCCCTGTATAATAAAAAAAGTGTGCAAATGA
hal       TATAATAGA......................CATTTATAATAGAAAAAGTGTGACCA--A
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TGCATATTTTAAATAAGTCTTGCAACATGCGCCTATTTTCTGTATAATGGTGTATGTTGG
hal       CGCATATTTACACTTGCTTTGGTTTTTTTCG------TTGTGTATAATATTGAATGTTGG
       -180      -170      -160      -150      -140      -130         


                                                                      
                                                                      
sub       TCTTTGACTGCGATGAAGTGAGAGGTTGCTGACACACCCGGCCGCTTTGCCATGGCAAGG
hal       TCATTGACAGCGATGATGTGGAAGGTTGCTGACACACCCGGCCCCTTTGCCATGGCAGGG
       -120      -110      -100       -90       -80       -70         


                                                                      
                                                                      
sub       TGTTCAGGTTTTTCTCACGGAGACTGTCTAACGTGATGTAGG-CGA-AAAGGAGGGAAAA
hal       TGTGG-GGAAATTTTCACGGAGTATGTCTATTTTCAAAATGGACGATAAAGGAGGGGCAA
        -60       -50       -40       -30       -20         -10       


            
            
sub       TA
hal       TA
          -1


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

About alignment...