Similar regions between promoters of tsf

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CCCTATCATCGGTATCGTAGATACTAACTGTGATCCAGATGAAATCGATGTTGTTATCCC hal ............................................................ ste .......................CGAACTGCGATCCGGATGAAATTGACTATGTCATTCC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGCGAACGATGACGCTATCCGCGCTGTTAAACTTCTAACTTCTAAAATGGCAGATGCAAT hal ....AACGATGACGCGATTCGCGCGGTTAAACTTTTGACTGGAAAAATGGCAGATGCTGT ste GGCCAACGACGACTCCATCCGCGCTGTTAAGCTGTTGACTTCGAAAATCGCCGACGCCGT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTTAGAAGCGAAGCAAGGCGAAGAAGAAGCGGAAGTTGCTGAAGAAACTGCACCAGAAAC hal AGTAGAAGCAACTTCTGGTGCTGGCGAAGAGGCAG------AAGAAGTGGCGGAAGTGAC ste GCTTGAGGCGAAACAAGGCGAAGA---AGCGGCCGTCGCAGCAGA--------------- -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>> ]]]]]]]]]]]]] ]]]] ]]] sub AGAAACAACAACTGCGTAACCT----ATTC----AAAAGGTGATAAGAGGG-ACTG-CCT hal AGAAGAGACAACAGCTTAATGTCAAAACTCTCGGAAAGGGTGATAAAGGGG-AGTGACCC ste -GTAACGA----TGCACAA---------------GAAAGGTGATAAGAGGGGAAAG-CCT -120 -110 -100 -90 -80 ]]]]]]]]] sub TTTATCACCTTTTTTCAAGAAAAATGTGTAATATACATACTCTTGTTTAAACATATAAGG hal TTTATCGCCTTTTTT...................AGATCATCATACATAATCAT-TAAGG ste TTTATCACCTTTTTTTGAGACAGAAATG................................ -70 -60 -50 -40 -30 -20 sub AGGAATACAA hal AGGAAT.... ste .......... -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...