Similar regions between promoters of yhdE

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAGCTGGGTGTCGCTGCGACAATCGTCAATTCCGCGTTCATCATCGTTCTTAGCGGCTTC hal ............................................................ ste ..........................CAATTCTTCGTTC..................... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>> sub GCACTTGCTTTTGGTTTATCCTTCGGCCTTGGCGGTAAGGATTTTGCATC---ACGTTAT hal ........TCTTCCTTTTTTCTGTTTACCTGACGCTAAAGCTTGCACCCCCATACGTTAA ste ...................................TAAAGGTTGTGAATC---ACG.... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTGTCTACATTTGAACGCAAAATGCAAAACACAGAAATCGAAAAAAACCGTAAAAACCAA hal C-GTATCCATT-GAATGGAAATAGGATAAAA...........................AA ste .............AAAGCAATATTTCAAATACA........................... -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>]]]]]]]]]]]]]]]]]]]]]]]]]]] ]]]]]]]] sub AATCCGCCGAATGACATGTAAGCAAAAAACACCCAGCTGGGTGCATGT-TTTTTAATTCC hal AATCCCCCCACTGA.........AAAAATCCCCCCACTGAATGAAGTT-T......TTCC ste ...........................................CATGTATTTTTAATACA -120 -110 -100 -90 -80 -70 sub TTTTTTTTCATTTTTCAATCGATTATGATAAGATATAGAAAATGTCTTATTCTGAGGTCT hal TTTTTTCTGTTT................................................ ste TCTTTTAT.........................TGTAAAACATGTATTTTTAATACATCT -60 -50 -40 -30 -20 -10 sub TATT hal .... ste TTT. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...