Similar regions between promoters of queA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAAAGAACGCCGCGTGGAAGGATCGTGACACCGGCCGTTTATCATCATTTCCAAATGGAG hal ....................GATCATGAC----GTCGATTATCATTAGT........... ste CAGCGTACGCCGCGCGGGCGCGTCGTCACGCCGGCTGCGTACACCCATTTAGGAATGGAG -300 -290 -280 -270 -260 -250 >>>>>>> >>>>>>>>>>> sub GCTCCCC-GATATGACTGAATTTCCTAAGATCATT-ATGATTCTTGGTGCTGTTTTGCTT hal .........AAATAAATGAACATCCCAAAAATATTCATTACCCTTGGCATTGTTCTCATT ste GTTCCGAAGCGGTGAACAGCTTGCCAAAGTTGATC-ATGACGATCGGCGTTGTGCTCATC -240 -230 -220 -210 -200 -190 sub ATTATCGGAGCAGTTTTGCATTTTG------------------TC------GGCAAGATG hal ATCATCGGCATTCTTTGGCAAATCGGTGGTCGGTTTCTACCGCTC------GGAAAATTA ste ATTGTCGGGTTTGTCATGCAGTTTG------------------TCAAACTCGGCCGCTTG -180 -170 -160 -150 sub CCGGGAGATATTTTTGTAAAAAAAGGAAATGTTACGTTTTTCTTCCCGGTTGTCACTTGT hal CCAGGAGATATTTTAATTAAACGAGAAAATGCCACGTTTTATTTTCCGATCATGACGTCG ste CCGGGGGATATCGTCATCCGCAAAGGGAATATGACGTTTTATTTTCCCGTTGTGACATCC -140 -130 -120 -110 -100 -90 sub ATTATTATAAGTGTGGTATTATCA---ATTTTGCTTAATCTTTTTGGCAGAATGAAATAA hal ATTATCATTAGTATCGTCCTATCGCTCATTTTGTTTTTGCTT.................. ste ATCTTGCTGAGCGTTGTGTTATC........TGCTCGGACGATTTCGCTGAAGGAA.... -80 -70 -60 -50 -40 -30 sub CAAAAGACTAGAATAAAGGTGAAATCATC hal ............................. ste ............................. -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...