Similar regions between promoters of yyaF

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATGAAGGGCAAGGTGAAAGTGATGAAGCAGGCTCATGCGAAGACGATTAATATAGATGAA hal ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> sub GGCATGTGGGCGGCTTTTGGAGGGTCAGTCAATGCACTGACAAA-TGATACAAATTCTGA hal ................................TGCACTTAAAAACTGTTGGAAATTCTAT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TAATGGAATGGGAAGTACGCTTTTTGACTGTTTAGTAGGCTTGAAAAAAGCATAATCAAA hal AATTGGAATGG................................AAAAAAGCTAAAGCGA- -180 -170 -160 -150 -140 -130 sub GGGATTGGCAAGCTGAAAATGCTTTTTTGTCAGCTTGTCTTTTCCAGTGAACCTCCTTAT hal -GTATTGGCTAGTCGACATTGCCTTTTTTGCA..TTGTTTTTCTCAAGGGTTGTCTCTAT -120 -110 -100 -90 -80 -70 sub AATTGCTCTAGGTTCAAAATACGTTCATACAATGACGGTTTTATATAGAGGAGATGAAAG hal AATTGGAAT-GGATGTCAATATGGAGAT-CAAGCAATTTTTTAAATAAAGGAAGTGA... -60 -50 -40 -30 -20 -10 sub A hal . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...