Similar regions between promoters of cotJA


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>
sub       GGTTTGCCCGCGGATTATGCCCATTTTATGGCGAAGCTTGATGA-GGCAATTAGCCATGG
ste       .......................TTTTATTCCTATAATTCGTCATGGCAAACAGGCATG.
       -300      -290      -280      -270      -260       -250        


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
sub       TGCGGAACATCGGGTAACGGATACAGTGAAGCGTGTGACGGGAAAAGAACCTCGTTCGCT
ste       ..........................................AAAACAGCAGCCATGGCT
        -240      -230      -220      -210      -200      -190        


                                                                      
          >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     
sub       GTCAGAGTTTGCGGCTGCTCATGCTGCATATTGGACCTCATTTTGGACTGAATAGTCTAG
ste       GTCATCGATA--GGCGGCCCAT......................................
        -180      -170      -160      -150      -140      -130        


                                                                      
                                                                      
sub       AAAGACCTTCGGCGCTTCCGAAGGTCTTCTTATTGAAAAAGCTAAGTCGTGTTTTAGTCA
ste       ..................................GCAAAAGC-AAGCCATGTT..AGGCA
        -120      -110      -100       -90       -80       -70        


                                                                      
                                                                      
sub       TAATCATGCCTCCTGCCTCATACCTATTAAGGTCATTGTTTTTGAGAAAGGAGGAGCCGG
ste       TGAACGATACCGCTCTATCATACATAT--AGACTGAACTTTGCCAAAAAGGAGGGG....
         -60       -50       -40       -30       -20       -10        


           
           
sub       A
ste       .
         -1


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

About alignment...