Similar regions between promoters of yqcJ


                                                                      
                                                                      
sub       AAATCTGTGTGCTCTGACTAAATACGTATTATCTCGAATTATTATCGATTCTACATATTC
hal       ..............................................GATTTGATAAAGAC
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       ACAAAA-ATTATTTAATGTTTTTTTCTTGAAATTAGAAATTAGCGTTTATGATCTCCGTT
hal       ACAAAGGAATATTATATGAGTTT.....................................
       -240       -230      -220      -210      -200      -190        


                                                                      
                                                                      
sub       GCTGTAGTAGCAAAGTAGCGATGGAGGAAATAATAAAAATGGAAAACCTCTATCTGGTTA
hal       ......................GGAAAAAAAGATGAAAATAGGCTTAAACAATTT--TTA
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       CACAAGCTTTTAGCGGGTTTTACAATTAATCAAAATAAATTGATTTATTTGCTTGCATTA
hal       GACAAGTTTGGAGC.......AAAGTTAATCAAAAAAAATTGATTTAACA-CTTGCATAA
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TTTTAAAAATCAT-GAGTATAATAA--ATACATCAAAAAAAATTGATTAAAGAAGGCGAT
hal       ACT-AACAGGCATCGTGTAAACTAACAATAAATCAAAAAAAGTTGATAAAGGAGG.....
         -60       -50        -40         -30       -20       -10     


              
              
sub       ATGA
hal       ....
            -1


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

About alignment...