Similar regions between promoters of ygaJ

sub CCCCTTTTTTAACAGAAGATTTGACAGTTCATCATGGAGATAAACAGCTGTATTTAATTG hal ..........................................AACACTTTTTATTAATTG -300 -290 -280 -270 -260 -250 sub ATCATGCAATGCTCTTCTGATGTGGGGATTTTCGGTTGCTGTTGTTGCGACAGTGTATTT hal ..............................TTCGCTTGCGATTGGCGCGC---TGTTACT -240 -230 -220 -210 -200 -190 sub GTTAATGCTGGTTTTTATTGTTGTTAACAAATCAAGAATATCTTTGGGACAAAGACTTTG hal GTTGATAG-GATTTGTACTTTTACGA--AAATCAAAAAGA.................... -180 -170 -160 -150 -140 -130 sub TTCAATGGGAAACCACCTCCTTTGTTTTTTTAGCAGCTCCTGATAAGAAAGTATTTGACT hal ....................................CTCATTTTAAGAAAG......... -120 -110 -100 -90 -80 -70 sub TTGTTTCTTGCTTCTATACAAAATGCTATAATAAGCAACAAGTTTTGCTTGGCGGGTGTG hal .................................AGCAACACTTTTT.............. -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...