Similar regions between promoters of yyxA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCACGTGTCAAATGAAGATGCTGCCTTGGCGATGACGGATGTCATTGGCGATGAGACGTC hal ......................................ATGTTGTTGGCAAT........ ste ...................................CTGACGTGATCGGCGACCGGACAAA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCGTATTTACCTGGCGCATTTGAGCCAGGACAACAACATGAAGGAGCTGGCAAGAATGTC hal ............................................................ ste GCAAATTTATTTGGCCCATTTGAGCCAAGATAACAATATGAAAGAGCTGGCGCGCATGAC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGTGCAGCAGACATTGGCTTCTAAAGGATTTGTGACGGGTGAGACATTTGACTTATACGA hal .....................................................TCTACGA ste CGTGACGCAAGTGTTGGAACAGAAAGGCTTAGCGGTCGGCGCCCGCTTTCGTTTGTATGA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>> sub CACCGATCCGAAGAAGGCCACTCCGCTTTGGC-TGTATAATTTTTCTATG-TAAATCATG hal TACCGATCCCTATAAGCCGACGCCCCT................TTCCATGATTAAGCGTC ste TACCGATCCGCGTCGGGCGACAGCGCTGGCGTATGTATAA.................... -120 -110 -100 -90 -80 -70 sub ACTATTCTAGGAGTTTCTAACCCACAATATAACCATATTAACGTTCTTGGAAAGGATGGA hal AATGTTGTTGGCAATTCTA..................TCAATGTTGTTGGCAA....... ste ........................CAAGATAACAATATGAAAGAGCTGG........... -60 -50 -40 -30 -20 -10 sub AT hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...