Similar regions between promoters of yfiD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTGCCCACAGGCTGAACACCATTCAAAGAGCGGACCAGATTGTGGTGCTAAAAAACGGTG hal .....................TTCAAATCGCGGAC......................... ste .........................AAAATCGGACCATACT..GGTGCGAAAA..CGGTC -300 -290 -280 -270 -260 -250 >>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAATGATTGAA-AAAGGCAGCCATGACGAGCTGATTCGGCAAAAAGGATTTTACAGTGAC hal ........................................AATTATGATTATATACTTAC ste GAATGGCTAACGAAAGGCA..........GCCGATATAGCAAAACGG............. -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>]]]]]]]]]]]]]]]]]]]]]]] sub TTATATGAAAGCCAATTTGAGAAATAGACCTTTGTCCTGCACAGAGGTCTTTTTTTGTTA hal TTACACAAA................................................... ste .......AATTCAAAGCTGCGAAATACAACCT..............GTCTCTTTTT.... -180 -170 -160 -150 -140 -130 sub CAGTTTTATAGTACTTTTATTTCATTTTCGTAAAATGTAACAAAAT-TACTTGACGTAAA hal ............ACTTTAATTTCAT.......AAATTTAACGAAATGTACTTGACGTCAT ste .............CTCTTTTTTCGCATTCGGA............................ -120 -110 -100 -90 -80 -70 sub CAAGTTATGTATATATACTAGCTTA-CATTAAGTAAGTGATAACATTTA---TCA-AGGA hal TTAATTATGATTATATACTTACTTA-CACAAAGTAATTAATTAACTTTAATTTCATAGGA ste ............AAATACAACCTCAACATCTTCTCGGTGCGAAAACTGT---TCA-AG.. -60 -50 -40 -30 -20 -10 sub GGATAAA hal GGA.... ste ....... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...