Similar regions between promoters of ybaS

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>> sub TTGCGAAGTTTAAGGAACAAGGCATTGAAGCTGAGTTAAAAGGTTTGAATAAAG--CGAG hal ..............GGACAACGGGTTGATGCT.AGAGAAATGAGTTGATAAAAGGACGAG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>> ]]]]]]]]]]]]]]]]]]]]]]] sub TAAATCTCTAATGAAACAGATGGCATAAAATAGAGAAGCCCAGATGAATGAGATCTGGGC hal T.............................................AATGACTGCTGGGA -240 -230 -220 -210 -200 -190 sub TTTTTTATATAACATACACTTAAGCAGCATTGATATAATAGAGAGAAGAGAAATTTTAAA hal TGTT.....................AGAAATGAGTTGATAAAAGGACGAG.......... -180 -170 -160 -150 -140 -130 sub TAGGGGGACTTGCATATGATGCTTCAGAAGCTGAACCGTGTATTGGGGAGAGTGATGCCG hal TAGGAGGATTTACATCT................AACCGTGTGTT.....GAGTGACGCGA -120 -110 -100 -90 -80 -70 sub CTGTTAACGCCGACTAGTGTGGTGCTGGGCGTGCTGCTGTCTCAGTTTTTAAATGGGTAT hal CTGATTATG.........................TGTTCTCTCATCTTAAAAAGAGGAGT -60 -50 -40 -30 -20 -10 sub GA hal GA -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...