Similar regions between promoters of yqjV


                                                                      
                                                                      
sub       CAGCGTACATCTTGATCTCATAGCCGGTTTCACTGCCGATATGATCCACGTTCTGGCGGC
hal       ............................................................
       -300      -290      -280      -270      -260      -250         


                                                                      
                                                                      
sub       TTAAACTAACACACCCTCACTGACCAATCGCTTTGCTTTTCATCGGACATCCCGTCATTT
hal       .........................................ATCGTATATTCGATGATTT
       -240      -230      -220      -210      -200      -190         


                                                                      
                                                                      
sub       TCCTTCTTTCAAG--ATGTAAACTCCGTCAGCCACACGCATCCTCAACGCATAGTATATT
hal       TCGTTCTTTTTAGGTATGTAAA.....................TCATCCAATCGTATATT
       -180      -170        -160      -150      -140      -130       


                                                                      
                                                                      
sub       GCCATCCATACAATCAGGCATACTACATGTCAATAACGAAATATTTTGAACGATCTATTG
hal       ........................AAATGTCCATTACCACATA........GTTCAATTA
         -120      -110      -100       -90       -80       -70       


                                                                      
                                                                      
sub       GAGAAGGAAATTTTTTCATATATGATAGAGAA--AGATCATACATACAGGAGAGAATATA
hal       CAGGACGTTCTTTTTAGGTATGTAAAAGGGGACTAGCTCATGCGAATACGAAACA.....
          -60       -50       -40         -30       -20       -10     


              
              
sub       ATTC
hal       ....
            -1


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

About alignment...