Similar regions between promoters of yusI

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGTTCAAGAGGCCTTTAACGAAATCGAAGCGCATGCAAAGGAATCCCTTATCGCAATGGA hal ....................................................GGAATGAA ste ...TCAAGAGGCGTTCAATGAAATTGAAGCCCATGCGAAAGAAACGCTCGTCGCCGTCGA -300 -290 -280 -270 -260 -250 >>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGAAGG--AGATTCACTCCGCATGATGCTTTCCGCTCTGCGCAAGCTGACACGCGTAACG hal AGGAGGGAAGATT........................TACGTAAGCTTACGCGCCATACA ste ACAAGG--CGACACGCTGCGGATGATGCTCGCCGCGCTCCGCCGGCTGACGCGCCATACG -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CCTAAAAACGTGATTCAGAAAAAACGCGAGGCGGCGGCAGGCATTTTTGAGGCTGAGAAA hal CCAATCAATGTGATTGCGAAAAAGCGGGAAATTGCAGGGCGTATTTTAGAAGCTGAGCGT ste CCGATCAATGTGATCGCGAAAAAACGCGAAGCGGCCGCCGCGCTCATTGAAGCCGAACGG -180 -170 -160 -150 -140 -130 >>>>>>>>>>>> ]]]]]]]]]]]]]]]]]]]]]] sub TATACTGTCTGATTGGCCATGAGCTCCGCATGCGCGGAGCTCTTTTTTAAGAAGCACTGT hal TACGTTGTGTAA.......................GCAGGGCGTATTTTAGAAGCTGAGC ste TATATTGTGTGAT.....................CGCCGCGCTCATTGAAGCCGAACGGT -120 -110 -100 -90 -80 -70 sub TTTAGGTTTTTAAAACAAACTGTGTTAAAATAACCTCGATTATTTTATTGAGGGGGAAGA hal GTTACGTTGTGTAAAC........................TTTTTCAATTTGGGAGGAGA ste AT.......................................................... -60 -50 -40 -30 -20 -10 sub AG hal A. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...