Similar regions between promoters of flhO

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGGCCTTGACCAGCTGCTTGCTGAAGAGCTGAAGGTACCGGGTCCTCGTTGCTGGAAAAT hal CGGAATCGATCAACTCTTATCGGAAGAATTAAGAGTTCCTG-TCCTTGTGGCAG-AAGAC ste ........ATCTGCCGCTGCCCAAAGAGCGG............................. -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>> sub CCTATGGATTGCGTAGCCATCGGGCACAGGTGTCATGCT-GATAATATGGACAAGCTTCC hal CCGATGGATTGTGTAGCGAAAGGG-ACAGGCATTATTCTTGAAAACTTGGA......... ste ..........GCTTGACCATAGGGAACA.......TTCT-GATCGATCGGACAAGC.... -240 -230 -220 -210 -200 -190 ]]]]]]]]]]]]]]]]]]]]]]] sub TAAACGCAAACTAAGCTGATTTCACAAACCTCATTCTGAAAAAGAATGAGGTTTTTTTAT hal .......................ACAGGCATTATTCTTGAAAA................. ste ...........................................GAAGGACGTTTTTCT.. -180 -170 -160 -150 -140 -130 sub GAAAAAGCCTTCACGAAAAGATGTTAAATGACGATAATAGGATAAAATACTGAGTTTTTA hal ..........................AACGACGATTGTAG.................... ste ......................................................TTTTTC -120 -110 -100 -90 -80 -70 sub TTATAGAACGAACGTTCCTATATGACAACTGGAAAAAATGCCATTTTTAGAGGTGGGAAA hal ....AGTAAGAAAGTTCGTATATAATCATGGCGAAATTTGTC.................. ste TGATCGATCGGAC............................................... -60 -50 -40 -30 -20 -10 sub T hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...