Similar regions between promoters of dnaD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>> sub CGATATGGAACTTTTGGAATCGCGTCTTAAAGAACATGGACTGGATT-CTGACGCTTATA hal ................................ACCGTCGGCTGGATTTCCGGCGCT.... ste CGATTATGAGCTGCTCAAGCGCCGCCTTGAAGAGCACCATTTGCCGC-TTGAAGCGTATG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AATGGTATGCTGAACTTAGAAAATATGGATCAGTTCCTCATTCCGGCTTCGGCCTTGGAT hal ....GTATTTAGATTTGCGTAAATACGGGTCAGTACCGCACTCTGGCTTCGGTTTAGGTC ste AATGGTATTTGGATTTGCGCAAATACGGTTCTGTGCCGCATTCAGGGTTCGGGCTCGGCT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TAGAGCGGACAGTAGCTTGGATCAGCGGAGCGCCTCACGTTCGTGAAACGATTCCGTTCC hal TTGAGCGAACCGTCGGCTGGATTTCCGGCGCTGGACACGTACGAGAAACGATCCCGTTCC ste TGGAGCGCACCGTCGCTTGGATTTGCGGCGTCGAACATGTGCGCGAGACGATTCCGTTCC -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]]]]]]] sub CAAGACTGTTAAACCGTCTGTATCCGTAATACATTCAAATGAAACAAAAAAGAGTCTCCT hal CTCGTCTTTTAAACCGCTTGTATCCGTAA............................... ste CGCGGCTGCTCAACCGGCTTTATCCGTAAAAAA............AAAAAACCCCCTGCA -120 -110 -100 -90 -80 -70 ]]]]]]]]]]] sub GCAAGGGAGACTTTTTACAGTAAAGGGGCAATCACAATCCTTTACAGTAAGAGGTGTGAC hal ..........CTTTTTCCA-TAAATGAT-AATCAATTTCCATTA....AAGAGGTGTTTC ste AAAAGGGGGTTTTTT............................................. -60 -50 -40 -30 -20 -10 sub G hal G ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...