Similar regions between promoters of yutM

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CATTTCCGCGTCTGGGAACGGGGATCAGGGATTACTCAGGCATGCGGGACAGGAGCATG- hal ..........................................TGCGGGAGAAGATGATGG ste ....................GGGATCATGGATGGCAGAGGCA.................. -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub -TGCAGCGGCAGTCGCATCTGTATTAAACGGCGTATCAAAGCGAAATCAAGACATCACGG hal ATGCAGC..................................................... ste ..GCAGAGGCAGT..............................................G -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGCATTTAGCAGGCGGGGATTTGGTGATAAACTGGAAAGATAACGGCCATGTAATGATGA hal .....................................AGACCACGCCCATAACATTATGT ste TCCATTTGGCCGGCGGCGATTTAACGATCGTATGGGGGCACGACGGGCGCGTGCGCATGA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAGGGCCGGCTGAAACCGTTTGTGAGGGTGTCTATTTCTTGTAAAACACCTTGTTTGAGA hal TACGACTTGATGGAA.........AGAGGGTATACTGGCTGTGATGCAACTTCATTGA.. ste CTGGTCCGGCGGAGACCGTGTGCGCCGGCGTTTATTACT..................... -120 -110 -100 -90 -80 -70 sub ATTGGAACGATCATGTTTATAATAAAAGACAGCAACCGGTTTTTAAAAGGAGGTTCATAA hal .........................................TTTATGAGCAGGTT..... ste ............................................................ -60 -50 -40 -30 -20 -10 sub TG hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...