Similar regions between promoters of pheB

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACGATGGAAAATGAAGAAGTGCCATTTAACATTACACGCGATCCAGACGGTGTATTTGT- hal ............................................AGACGGTGACCTTGTT ste ......GAAAAAGAGGAGCCGCCGTTTACGATCACCCGCGCCAGCGACGGAGCATTCAT- -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub -GCTTTCAGGAGACAGCCTTGAGCGGTTATTCAAGATGACTGATTTCTCACGTGATGAAT hal CGCTTACTCGAG.........AACGTTTATTTTAGATGGCT................... ste -TTTGGCGGGCGACAAAATTGAAAAGTTGTTTAAGATGACGGATTTCTCGCGCGAAGAAT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGGTTAAACGGTTTGCAAGACAGATGCGCGGAATGGGTGTTGATGAAGCACTCAGAGAAC hal .........................................................AGC ste CGGTGCGCCGCTTCGCCCGCCAGCTTAAGGCGATGGGGGTGGATGATGCGCTGCGCGAGC -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCGGAGCCAAGGATGGAGATATAATCAGGCTTCTGGAATTTGAATTTGAATTTATTGATT hal GTGGAGCCAAAGACGGTGACCTTGTTCGCTTACTCGAGTTTGAATTTGAATTTATTGAAT ste GCGGCGCGAAAGACGGAGACACGATCCGGTTGCTTGATTACGAGTTCGAGTTTGTCGA.. -120 -110 -100 -90 -80 -70 >> ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] sub AATCAATGTTGGCTGAAAAGAGAGCCTGGTGCCAGGCTCTCTATTTTAAAGGGGGGATGC hal AAT..........TAAGATGACAGTGTTTTGTCAAAACGTTTATTTTAGATGG....... ste ........TGGGATGAATAGAGCG.................................... -60 -50 -40 -30 -20 -10 sub AA hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...