Similar regions between promoters of yhdF

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGCTAGAAATCTACAAACCGGGACGAAAGCTGTACACAAATGTTGAATTTTACGCAGCTG hal ......AATTTGAGAAAAGGTGGGGAAAGTAGTTCATGAAGGAGAGATGTTTC....... ste .GCAAGAAACGAAAAAACAGAAGAGAAA.........AAGTGTGGAGTAATACG...... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAGTGATGAGGGCCATCGATTTTGACGATGAATTGTTTACTCCGACCTTTTCAGCAAGCC hal ......................TGACGAAGAA............................ ste ....................TGTGAGGATGGCTTCATTAC.................... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAATGGTAGGGTGGTGCGCCCATGTACTGGAACAGGCAGAAAACAACATGATTTTCCGGC hal .........................................AAGAAAATGATTT...... ste .............................GAAAAAACAGAAGAGAAAAACTTGTTCC... -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGTCAGCGCAATATACCGGTGCCATTCCCGAGGAAGTTCTTTCATAACATATTTTGGCGT hal .............................GAGGAGCTTCGTCCA.......TTTTGGCGA ste .....................................TCTTTACTAAC-TATTTTATC-T -120 -110 -100 -90 -80 -70 sub TTATTCATTTCTGTCGTGTGGTAACGTTCAGTATC-AACCACATGTCTAGGAGTGATGAA hal GTA.TTATTTTTGGCGAGT...AACGGTGAAAATCTAATCATTGATGGAGGAATGACGAA ste TTACTCAAT................................................... -60 -50 -40 -30 -20 -10 sub T hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...