Similar regions between promoters of acoR

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCGAAATCGTGGGTGTCTCGATGATTGGCCCGGATGTAACCGAGCTCATCGGCCAAGCGG hal .................................ATGCCACGGAATTAATTGCTCAAGGAA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAGCGATCATGAATGGTGAGATGACGGCAGATATGGCGGAGCATTTTATCGCCGCCCATC hal CGCTCATGGTACACAATGAATTAACGCTTGATAGTTTAGAGTCGTTTATCGCTGCTCACC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGACTTTATCGGAAACATTGCATGAGGCGCTGTTAAGCACGATCGGCCTTGCGGTACATG hal CAACCGTATCGGAAGCTGTACATGAAGCTGTGCTGCAAGCATTAGGCCAGGCGGTTCATG -180 -170 -160 -150 -140 -130 >>>>> ]]]]]]]]]]]]]]]]]]]]]]]]]] sub CATAATAAAGGAAAAAGCAGGCGCATGGATATAAGGCGCCTGCTTTTTTATTGTTGAAAG hal TCTAAT................................CCTTGATTGATCTCATTGTTAG -120 -110 -100 -90 -80 -70 sub CGCTTTATTTTTCCCCTACAATAGATGAAAACGGCGTGTAAGGGAGGAGCGATCAAGGAA hal CGCTTTCTTTT.................................AGGAACGCTCATGGTA -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...