Similar regions between promoters of yfhD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTCGTTTTACATATTCGGATCTTGAATTTGCACTCTCACAGCTGATAGCGGACCGAAAG ste ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>> sub ACTGTATAAAAACAGCAGGAAGCGTCAACCTTAAGAATAACATGGTTGAAGGAGGTCCTT ste ...GCATAAAAACGGCTG.....................................TCTTT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTATGGAAAAAAAGAGGGAGAAGCACCAGCAAGGCGCCAACCTGAAAAAAATGCAGGAA ste TTTACGCATAAAAA............................CTGACAAGCGCCCAAGAA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sub GTTCTTTATTCAGGCGAATTTAAAAAAGCGGAAAAAGCTGCTAAGCGGAAGTA-GGAATA ste GTAAGCTATGCCCGCGATTTTAAAATGGCGGACCAAGCGG----GCGGCTATACGGCCAA -120 -110 -100 -90 -80 -70 sub CATAGC---CCCTTAAAACCAAATACTATATTTGTTTGATATCACTTTTTAGGGGGAATT ste AAAAGCGCGCCATTAGAAACGATTGCTATTTAT........................... -60 -50 -40 -30 -20 -10 sub TGAT ste .... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...