Similar regions between promoters of yxiO

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub AGTCTGCGAACATCTGAGCCTCACCTTCACTTTCGCATGCGCTCATCACAAGAACTGTGA hal ............................................................ -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub CCAGCAGGCTTATACACAAGCCTATTCGCCTCATGCTCTGTCTCCTCTCTGCTGAATCCC hal ......................TTTTCGCCTCTT.......................... -240 -230 -220 -210 -200 -190 sub TTCTGGAAAATACCATAAAATATAGTTAAATGGTACCAGATGCACCTAACCCCAGCAATA hal ........AATAAAATGTAAAAACCTTTAAGTCTTCCCTATGAATCTA............ -180 -170 -160 -150 -140 -130 sub AATCAAAAGTATGATTTGAAGCGAAAAAACATAAATATTTTGTAAAAATTGACGTGCATT hal ...CAAAAGGATGA............AAATGTTAATAAAATGTAAAAA...AGGTGGATT -120 -110 -100 -90 -80 -70 sub CCATTCTTTTCAGGCCCATTTCTCGTACAATAGAAGTATCGTTACCGGAGAGGGGCTCTG hal TCATTATTTT.................................................. -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...