Similar regions between promoters of ytcQ

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATATGACAGCGATCTTGTACTTAAATGATTCAGCAAAATGGCCAATTCAGGTGCTTCTGC hal ..ATGCAAGCGATTTTGTACTTGAATGATTCGAGCATGTGGCCTATTCAAGTGTTATTGC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>> sub GCCAAATCGTCATTGTATCAAGCGGTATGCAGGGGGATATGTCTGAAATGGG-GTCGGG- hal GACAAATTGTCATTATGTCTAGTGGTATGCAAGGGGATTTAACCGAGCTCGGTGCCGGGT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub -CAGCCCGCCGCCTGAGCAAACCATTAAAATGGCGGTCATAGTGGTGGCGACCATCCCTG hal TCGTCATGCCACCAGAACAAACAATTAAAATGGCCGTTATCGTTGTTGCTACCATTCCTG -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTCTGCTTGTCTATCCGTTTATACAAAAGCATTTTGCAAAAGGAGCTTTGCTGGGATCTG hal TGTTAATCGTCTATCCGTTTATTCAAAAGCATTTTGCAAAAGGAGCTTTACTAGGTTCAG -120 -110 -100 -90 -80 -70 >>>>>>>>>>> sub TCAAAGGATAAAGAAATATGAAACGGAGGGGTACGATGGGAAACAAATGGAGGGTGCTTT hal TGAAAGGGTAA--AAATAAAAAATGGGGAGGTATGTT....................... -60 -50 -40 -30 -20 -10 sub TGA hal ... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...