Similar regions between promoters of yveM

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AACAAAAAGAAAATGAAAAAATCGGAACACTATTCCTACTAGTTTTTGTAAAGGTGATGT hal ..CATAGAGAGAAAGAAAAAA.................CAAGTTTTTCTGAA........ -300 -290 -280 -270 -260 -250 sub CTCCTGACCTGTATCAATGGAGGCACTCGGCTCTGCTGTGGGCAGCTGAAGTTGC--TG- hal ................ACGGAGGCACTCGGCCATGTTGTGGGTCG-TCAATCAGCGATGA -240 -230 -220 -210 -200 -190 sub CCTTAGATGCTG--GTCGTCGCTGGCGGGGCGTGAGGATGGGTTAAATGCC-CACTTATC hal CCTTAGACGCGTCCGTTGTCATTGATGTGGCGTGAGGTGAGGTTCAATGCCTCATGTTTA -180 -170 -160 -150 -140 -130 sub TCATATATACATAGGACGTATTGTCGGTTTAGCTGCTGCCGATTTTTTGGAGAGACGAAA hal TTTTATTTTCATAG.............................................. -120 -110 -100 -90 -80 -70 sub ACCGCCGCAGCTAAACCGATAAAAGAATTAGGGGG-GAAAAGGTTGAGTTACCGGAGAAG hal ..................AAAAAAGATTGAGGGTAAGAAAAACTTGGCTT.......... -60 -50 -40 -30 -20 -10 sub ACTGTCA hal ....... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...