Similar regions between promoters of ykwD

sub CATATACTGAGATTAATTGTAACACCTTTGTAATAGTTGTTACAGCGAAAAGGAGTAAAA hal ...............ATCGTAATATTTTCGTAAAATTTGCTAC.............AATA ste .............................................CCAAAAATATTACAA -300 -290 -280 -270 -260 -250 sub AAAGCTGTCAATATAAAAACACATTAAAATATAACTA-ACGGTTCAAAAAAAAGGAAGCT hal ATCGCTCACTTTATTACAAAATATCAATTTTTTATTACACCGGTCA.............. ste AAAACTCGTGTTATAA...........AATATCTCTG-AAACTTTCAAATAGAGGA.... -240 -230 -220 -210 -200 -190 sub ATGTAACGGTACGATAAAATCATATATACCGCTGATTCCCT-TATTCTTAGTGATTCAAC hal ....................CATCTTGCCCACCGATTCCCGCTATACTT........... ste ............................................................ -180 -170 -160 -150 -140 -130 sub GGATTTACTTTACGAAAATGACAATCTCTATTTGTCAAAGGAAAGTGCTGGAATCTTTAT hal .........................CTATACTTTTCAAACGTAA..........CTTTAT ste .........................................................TAT -120 -110 -100 -90 -80 -70 sub GACAAAAAAGCTATGTTATGATTTTCCTGTAAAAACAAACAACTCTAGGAGGTTACGAAC hal TACAAAATATCAATTTTTTATTACACCGGTCA............................ ste TACAAAAAACTCGTGTTATAAT............ACAAAAAACTC............... -60 -50 -40 -30 -20 -10 sub TA hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...