Similar regions between promoters of ygaD

>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCAATTAAATATATTGATTATGACTTAGATGTTAAGGTTTTTCCTGACATGACCTACAAT hal ...........TAGTGTCGATGAATTAG...............................T -300 -290 -280 -270 -260 -250 sub ATTCTCGATGAAGACGAAT-ATG-ATG-ATCATCGGAAAGCCATGAATTATCCAAAAGAA hal AGTGTCGATGAATTAGTATCATGGATCCATCAACGAAAAG.CATGAAGTATC........ -240 -230 -220 -210 -200 -190 sub ATCGACAGTATTTTAAGAGACTACTTAAATACGCTGCTCCATTGGATTCACCAGCGTCAG hal ..........................................TGGATCCATCAACGAAAA -180 -170 -160 -150 -140 -130 sub GGACCGTATGCGCCCGAGTTTGTCGATATGTGGTATGAACGGTATTTGCGCTATACAAAA hal GGGCCTTTTGCGCCGCAGTTTGTGGAAAGCTGGTATGAACGATTTTTGCAATA....... -120 -110 -100 -90 -80 -70 sub TAATGGTTACGTAAAAACCTGTTGCGGGGTACAACAGGTTTTTCACATGGGCTCACACAC hal ................................AGCAGGCTTTTC................ -60 -50 -40 -30 -20 -10 sub ATC hal ... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...