Similar regions between promoters of yktC

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGGAAGAGAAAAACAATCGTGTTGCTGTCTGGAGACTAGAGGTTGATTATGAATTGGCAA hal ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> sub CCCTATATGAAGCAATGCAGAAAGAAAATGAAGA---GCAGATTGAACAAAGCAAAAACA hal ........GAAGCATAACAAATAGGTTAGGAAAAAGCGCAAATTGA.......AAAAACA -240 -230 -220 -210 -200 -190 >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AA-------CTTGAGCGACTTAGAAAAGAATGGATTCGTCTTAACGGGTAAAAAAGCGAT hal AAGCGTCGCCTTGAAAAGCTTCGACTTGAACTGTTACAGCTGGAAGCATAACAAATAGGT -180 -170 -160 -150 -140 sub AGTGAAAACGAACCGCATGAATGGTTCGTTTTTACGTGAGAAGGGATATTTTTCATTTTC hal TAGGAAAAAGCGCAAATTGATTTTGCGCTTTTTTCGT..........ATTTTGCGCTTT- -130 -120 -110 -100 -90 -80 sub CTTGCTTTTTCATTGCCGTTATCAGTATCCT-ATAAAA-TAAAAGGTCTACATAGAAGAG hal -TTTCGTTTTCACTTTCATAAAGTTTCACTTCATAAAAGTAAAAG............... -70 -60 -50 -40 -30 -20 sub AGGTACGAACGA hal ............ -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...