Similar regions between promoters of dnaJ

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CACAGCAAGCTCAAGGCGGAGCAAACGCTGAAGGCAAAGCGGATGACAACGTTGTCGACG hal ............................................................ ste ..........................................AAGACAACGTGGTGGACG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTGAATACGAAGAAGTAAACGACGACCAAAACAAAAAATAAGTTCTTTTTAGTGTCAGCC hal ............................AACCAAAAAAT..................... ste CCGAGTTTGAAGAAGTGAACGACGATAAATA..AAAATTAAATTTATGTGAGTG...... -240 -230 -220 -210 -200 -190 ] sub CCGCTTCCGGAGCTGACCGAAAAGAACACATTTCATA-ATCTGATTCAATGATTAGAAAG hal .............................ATTACATC-ATCA-ATTCAAACATCAGACAT ste ...........GCAGAGGGAAATGATAAAATTAAATTTATGTGAGTGAAT.....GAAAG -180 -170 -160 -150 -140 -130 ]]]]]]]]]]]]]]]]]]]]]]]]]]]] sub TCAAAGTCAGGCATCTCTTGGCTTTGACTTTTTTTCTTGCCCGGGATAAAAGGAATTGAA hal TC...................................................AATTCAA ste TCAAAGTCAGGCCTGCCTTGGCTTTGACTTTTTTTCTAGCATTG-ACATATTGCCTTGC- -120 -110 -100 -90 -80 -70 sub AAATCATAATTCAAAATGATACAATCTAATTTATGTGAGAAATTCGGGAGAGTGAAGCGA hal ACATCAGA....AAAATGGTATGATGAACGTTATGTGATA.................... ste ----CGCAGAGGGAAATGATAAAATTAAATTTATGTGAGTGAATCGGGAGTG........ -60 -50 -40 -30 -20 -10 sub G hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...