Similar regions between promoters of yfiB

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>> sub AACATCACTGAAGTCACAAACTGCGCCACCCGCCTCAGAGTCAGTGTCAAGG-ATGAAAC hal ............................................TGCCAAGCCATGATTC ste ...............................................CAACG-ATGAACG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAAGGTTGAACCCGACAGCGTATTCCGCGCGCTTGGCGCACACGGCGTTGTCAGGAACGG hal GCGGCTTGCTCCCG-CAACGTAT..................................... ste GCGGCTGGGCCCCGCGATCGGAAT.................................... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAAGGCGTTTCAGGTAATTATCGGATTAAGCGTGCCGCAGATGCGGGAGCGTGTGGAAAA hal .......................................GCTCCCGCAACGTATGGTAAA ste ............................AGAGTGGCGCAGA..........TGTCAAATA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>> ]]]]]]]]]]]]]]]]]] sub AATATTGAATCAATAAAGACTGCCCTCCTTTTCGGGAGGGTTTTCGTTTGCCGTCAAAAA hal A............TAAAGAATGGCTTC.......GGAGGGTGTT................ ste AATATT.................CCTCTTGGCCGGGAGCATCTCCGCTT--CTGCAAATG -120 -110 -100 -90 -80 -70 sub GACCGCCATAGTAAAGTAAAGAAAGAGACAATCGAGTAAAAAGGGGTTTGGAGGCTTTTA hal ...............................................TTGGAGGGTGTT. ste CATTCTCATTGTCAAATAAATATTTCGGGTTTAGAATAAAAATGGGTCTGGAAGC..... -60 -50 -40 -30 -20 -10 sub C hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...