Similar regions between promoters of clpX

>>>>>>>>>>>>>>>> >>>>>>>>>>>> sub AATTGATTTTCTTGTA-GAAAACCGTTAATATGGTGC-ATAATAATA---GTACTAATAA hal ....GCTTTTCGACTACGAGAAGCTTTAACAACGTGGTACAATACTA---GT........ ste AGTCGATTTTCTTGTA-GAGCACAGCAAGGTTGCGGC-ATAATAATAAATGTAAGGAAAG -300 -290 -280 -270 -260 -250 sub AACAGGGCGCGAATCATTCGTGCCTTGTTTTCGTACAATTATGAGTTATCTCTTTTTCTT hal .........................................................CGT ste AACAAGGCGCGAGACGTTCGTGCCTTGTTCT...........................TT -240 -230 -220 -210 -200 -190 sub GGGGCAATA-TAGTTAATGCAGGGCTGTTTTTTGTCATACATATAGAATGTGCAAGTCAG hal GGTACAATACTAGTTAAGG......................................... ste GCGGCATAA-TAATAAATGTAAGG.................................... -180 -170 -160 -150 -140 -130 sub AAACACATTGTTACCGTCTTTTTGGAAAGTATGGTAAAAT-GC-AATACATACT-CGTTC hal ...................TATTTGACAGTACATATGACT-TA-CATACCTATTTCGTTC ste .............................TATGGTAAAATAGCGAATACATAC....... -120 -110 -100 -90 -80 -70 sub GTTTCAAGAATCATTTTCTTTTGCTCTGCCGGTAAAAGAAAAAGTGAGACAAGATTAAG- hal GTCT..................................AAATAGCGAGGAAAGATTGAGC ste ................................TAATAATAAATGTAAGGAAAGAACAAG- -60 -50 -40 -30 -20 sub GGGTGAAAGA hal GGGTCAAA.. ste GCGCGAGA.. -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...