Similar regions between promoters of yrvE

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GATTACCTGTTTGGAAGATCAGAATGGCCGCTCATTCTTGTTATTTTGGGCTCAGTTTTA hal .ACTATTTGTTTGGGACAGCCGAATGGCCGCTCATTTTAGTCATCTTAGGGTCTGTGCTC ste ..............................CTCCTTTTTGT-ATAATAAGGAGAGTTGAG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> sub ATGGGAGCACTGATCGTA------TTTTCTGTCG---GCATTTTTCAGGTAATGAAATTG hal ATGGGAAGTTTAATGGCAGGAGGCTTGTCGATCGTACGAATCTATCAGCTTCAGCACGAG ste GTGGGAG..........................G---TCATGGTTCACATCAACCCGTAC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAGCGGGAAATAAAAACCTTGCGGAAAGAAAATAGAACAGCAATACATAAACAAGAGGAT hal GTGCGTCGTCTAAAA-------GGAACGGC--TCGCACAAAGCAGCCTCAACAAACGGGC ste AATCCGGAAAAAAAACCGT..CGGAAAGAAAGTGAAAGAAAAA................. -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACTCATCTTGCTGATCAGACTGAC-ACACAGGATGCATCAGCCATGATTGAGAAAAAAGA hal GCTGATCAACAAGA---GAGAGACGACAAAGG-TCCCTCTACG--GACTCTGATAAA--- ste ............................................................ -120 -110 -100 -90 -80 >>>> sub CTAGTTTTCGAATATTATTTGAAACCCCTCAGCCTGCTCTAGTATAATAGGGTG-GTTGA hal -TCGTAAAAGAACATCATTGTCACCCCTTAATCC--CTCTAGTATAATAGGATG-GTCAA ste .....................................TTTTGTATAATAAGGAGAGTTGA -70 -60 -50 -40 -30 -20 sub GGGGTGAATTT hal GGGGTG..... ste GGTGGGA.... -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...