Similar regions between promoters of yomD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATTTAATTGTAACTGGAAACTCAGTTTATAGTGATGTTGAAGGAACAGCTTTCATTAGAA hal .......................................AAGGACAACCTTTTATCCGAA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTCCATCAGATATAGACAGAAGACGAGTGTCGGGTAACGTAGGTAATATACCTAGCTTGA hal ..........................................................GA -240 -230 -220 -210 -200 -190 >>>>> >>>>>> sub ACTTG-GATTAAGAATAAAGGAACAATAAAGGTG-GTGGTTACGTTCTAGATAAAATATA hal ACTTAAGATTTACTCATTAAGAAGAATGAAGCGGAGCGGTCAGGGGCTCGAGCAAGGACA -180 -170 -160 -150 -140 -130 sub GA-TTTTATTCAAAATACATACTTGAAAAACAGAGATAACAAGAGCATACGTGAGATAAA hal ACCTTTTATCCGAAAAA.....TTTAAAAACAAATCTA.....AACATAAGCGAGTGATA -120 -110 -100 -90 -80 -70 sub GAGAGATTGGGTTTAGTCCCCTTCTCTCTTTTTTGTGCTCAAATTTAATTATTAGGTGGA hal GGGCGTTGGCATCTA..CCCCTTCCCTTTTTATT....TAAGATTTACTCATTAAGAAGA -60 -50 -40 -30 -20 -10 sub TAG hal ... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...