Similar regions between promoters of rocR


                                                                      
          <<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
sub       GTTGGCTCCGTAATGAGACG-TCTGATCAATAATTTCTTTGGATTTAGATAAAGCTGTCA
hal       .TTTGCTCATTATTTTGGCGATATGAGCGAAAAACTTTTTGG.............TTTCA
       -300      -290       -280      -270      -260      -250        


                                                                      
          <                                                           
sub       TATTTGAATTCCCCCTTGTTTTCTGTTTCAACATGTTATCCTGCTTTCCCTTTATATAAA
hal       TGTTCAATCTCCCCCTT......................................ATCAA
        -240      -230      -220      -210      -200      -190        


                                                                      
                                                                      
sub       TGCAAGTTCTGTGCCAAATCAAGAATTCGTGTGTTTTCTACAATTTTCGAGGACAAGGTG
hal       TGCAAATCCTGTGCCAACTTTATAAACCACGATGTTTC......................
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       CAAAAACATTCTGATATTTCGAGCGAAAATTTCAGCAAGTGCAAAATTCTTTTGCATATC
hal       .............................................AGTCTTCGAAAAATT
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       CTCTCCGTTTTTTTATAAAATAGAAGCAATATTAAGAAAATAATTGAGGGAGGTTCATAC
hal       ATTTTTCTTTATTTCTTAATCATAACCTATAAAACGAAAAAA..................
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
hal       .
         -1


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

About alignment...