Similar regions between promoters of yjzC

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGCCTTATCAGGTGAATGCGGCGCTGGTCAGCCATGCCAAGCCTGACTATACATTTTTAC hal .GCCGTATCAAGTGAATGACCAGCTTTTAACATTAGCCAAAAAGGACGTTAGTTTCTTAC ste ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATTGTCTCCCTGCGCATCGCGAGGAAGAAGTGACTGCGGAGATTATTGACGGGCCGAACT hal ATTGCTTACCAGCTCACCGCGGAGAAGAAGTAACAGCTTCTGTCATTGACGGTCCTCATT ste .......................GAAGAAGTGACGGCCGGCGTCATGGACGGCCCGAACT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTGCAGTGTTCCAGCAGGCGGAAAACCGTCTTCATGTGCAAAAAGCACTGCTGAAGGCCA hal CGGCTATTTATGATCAAGCCGAAAACCGTCTCCATGCACAAAAGGCTGTCCTAACAGCTC ste CGGTCGTATTTGAGCAGGCCGGCAACCGGCTTCATGCCCAAAAAGCGATTTTAGTGTCGA -180 -170 -160 -150 -140 -130 >>>>>>>> >>>>>>>>>>>>>>>>>>>>]]]]]]]]]]]]]]]]]]]]] sub TTTTATAT-AAAGGGGAATCATCAAAAAACTGCTGAGCCAAACTCAGCAGTTTTTTTGAT hal TTTTA----ATAGGTGAATGAA-ACATAATTGCTCA........................ ste TCCTATAGGAAAAAGGAAT..................CCGAACTCGGTCGTATTTGAGCA -120 -110 -100 -90 -80 -70 sub GGCAACATATTCACAGCCGCTTAGGCGCATACTACAGCAAAAAGGAAAAGGAGGAAAAAC hal .....................................CAAAAAGGA.............. ste GGC.........................ATCCTATAGGAAAAAGGAA............. -60 -50 -40 -30 -20 -10 sub A hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...