Similar regions between promoters of fus

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAAAGCACGCCGTGTAGGTGGTGCGAACTACCAAGTTCCTGTAGAAGTTCGTCCTGAACG hal ............TCTAGATGCTGCAAACAACACAGGTGCCG...............AGCG ste ................GGCGGCGCCATCTAC............................. -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCGTACGACTCTTGGACTTCGCTGGTTAGTTAACTACGCTCGTCTTCGTGGAGAAAAAAC hal CCGCACGACATTAGGACTTCGTTGGTTAGTGAACTACTCTCGCCTGCGTGGTGAAAAAAC ste ...................CGCTGGTAAG..................GCGGTGAAAAAAC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GATGGAAGAGCGTTTAGCTAACGAAATCCTTGACGCAGCTAACAACACTGGTGCTGCTGT hal GATGGAAGAGCGTTTAGCTAACGAAATTCTAGATGCTGCAAACAACACAGGTGCCGCTGT ste G......GAGCGCTTGGCAAATGAAATTATGGACGCTGCCAACAACACGGGTGCAGCGGT -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TAAGAAACGTGAAGACACTCATAAGATGGCTGAAGCAAACAAAGCATTTGCTCACTATCG hal GAAGAAGCGTGAGGATACTCACAAAATGGCGGAAGCGAACAAAGCGTTTGCACACTATCG ste GAAAAAACGCGAAGATACACATAAAATGGCTGAAGCGAACCGCGCGTTTGCCCATTACCG -120 -110 -100 -90 -80 -70 >>>>>>> sub CTGGTAGGATTTATAGATTAACAAAACACAATTTCCTAAT--AAGGAAGGAGAAATTACC hal TTGGTAGGAT.................................AGGAAGGAGAAATAAC. ste CTGGTAAG......................ATTTCATATTTGAAGGAAGGAGAAAATAAC -60 -50 -40 -30 -20 -10 sub CA hal .. ste CA -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...