Similar regions between promoters of ylxA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTACCCGCTTCTTCTTTTCAGGGGCGACTGAATGCGAACTGGATAAGCAAGGCAGGGTA hal TTTACCCGTTTCTTTTTCTCGGGGGCTACGGAATGTGAACTAGACAAACAGGGAAGAGTA ste ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AATATCGCATCATCTCTAT-TGAATTACGCCAAACTGGAAAAAGAATGTGTTGTTATCGG hal AATATTGCCTCCCCATTGCGTGAATTT-GCCCAGTTGAAAAAAGAATGTGTCGTCATCGG ste ......................................AAAAAGGACGTTTTTTTA.... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGTTTCTAATCGAATTGAATTGTGGAGTAAAGTAATTTGGGAACAATACACAGAAGAGCA hal TGTTTCTAACCGAGTGGAGATTTGGAGCAAAGAGCTTTGGGAAGAGTACTTTGCAGAGTC ste .........................................AAAAAGAAACAAAA----A -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGAAGATTCATTTGCTGAAATTGCTGAAAACATGATTGGGTTTGATATATAATGATTCTT hal CGAAGAATCATTTAGTGAGATTGCTGAAAACATCGTTGATTTTGATTTGTAA........ ste AGGACGTTTTTTTACAAAAAAAGCTAAAATTTTGTCCATCTTTGCGATATAATAA..... -120 -110 -100 -90 -80 -70 sub CGTGTATAACACTCTAAAAACAAT-TTCAATTCATCCTGATAAAAGGTGGGACCAACACA hal .............CTGAAAACATC-GTTGATTTTGATTTGTAAACGGTCGG......... ste ...............AAAAACAATATTCACGAAATGGAAATAAAAG.............. -60 -50 -40 -30 -20 -10 sub AT hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...