Similar regions between promoters of yrvD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAAGCAGAGGCGGGAGCGCCTGCCATTCATCAGACGATTGGTGATTTGAATGTGGGTCAG hal .....................GCGATTCATAATACACTTGATCATGTG............ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAATATCATGTGACGGTCATTGCAATTGTTAAAAAGAATCAGGATAAACAACTGAATCCG hal GGAAATCAAGCGATTCATAATACACTTGATCATGTGCTTCATGATGAAGA.......... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGCTCTGAAACAGTCATTGACGAAGGCGATACACTTGTGATTTCCGGTGAGGGAACCGGA hal ............................ATACACTTG.......CGGTGAAAGAACGG.. -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTGAAGAGGCTGATCCGGGAAAAATTAACAGCAAAGGGAGCTTAACCTAGTGTTAAGCCA hal ...................AAAAATTGCCGTCAACCCTCGCATGACC............. -120 -110 -100 -90 -80 -70 sub TGTTTAAAACCAGTCTTGATTGGGAAAGTTACCTCAATAAGAAGTTTGGG-GGAAAAGAG hal .............................TGCTTCATGATGAAGATACTGTGGAAATGAG -60 -50 -40 -30 -20 -10 sub A hal A -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...