Similar regions between promoters of ycdI

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCGCAGCCAGCTTGGCAAAGCTGAAAACATATGCCAAAGAACATAATGTAAAAGTTATTT hal .........................AATATATACCTAATAA.....TATAAACGTTAT.. ste .........GCTCGGCAAAGGCGG----ATATACGGACGAGCAAAAGGAAA---TTATTT -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACTTTGAAGAAATTGCATCCTCAAAGGTCGCAGATACGCTCGCCAGTGAAATCGGCGCGA hal .....GATGGAATTGGAACC........................................ ste A....GACGAAATTGC-TCGGCAAAGG-CGGATATACGGACG..........CCGCGGGA -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGACAGAAGTGCTGAATACACTGGAAGGCTTGAGCAAAGAAGAACAGGATAAAGGTTTAG hal ........GTGATAAATAAATCGGAATGATTCTT--AATATATACCTAATAAAGGATTA. ste CGACGAAATTGCT.................TTAGCAAGGGAGAACCG..........TGG -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGTATATCGACATTATGAAACAAAACCTCGATGCCCTGAAAGATTCACTATTGGTTAAAT hal ..TTTATCGAAAAAATAAA.....................AGATTCTCCTTTATCGAAAA ste GGTATACTTGCATAGTGAAGCAAATC.................................. -120 -110 -100 -90 -80 -70 >>>>> ]]]]]]]]]]]]]]]]]]]]]]]]] sub CATAAGATAGTGTGCGCCGGAGGGGTGCACACTATTTCTTTGTGAGAAAGGAAGATTAAC hal AATAA.....................................TAATAAAGGATTATTCA. ste ...................................TTCTGAATTAGCAAGGGAGA..... -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...