Similar regions between promoters of hmp

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGAACCGCAAGAGACACAGCCAGGCGCTTGCAAATGCGCTCGGAACTGATAAGCCTTGGT hal ..................................................AAGCTTTAGC ste ............................................................ -300 -290 -280 -270 -260 -250 >> ]]]]]]]]]]]]]]]]]]]]]]] sub GAACGTTAAACCCAAAACATAAGTTGTTTTGGGTTTTTTTGTACTT---TTCAATGGTGA hal GTCAGGTAAACAGAAAAAA...........GGATTTTATCCTATTTCCATTCAATGGATA ste ................................GCTTTTTCGCAGTG---CTCATGGTTGA -240 -230 -220 -210 -200 -190 sub TTATTACAATGGTTAG---TCC--GT-TTTTGCTAGGGGATTCTATAAAAAAGCAACAAA hal CGTTAACGTATGGGGG---TGCAAGC-TTTAGCGTCAGGTAAACAGAAAAAAGGAAGACG ste ATAAAAGATGTATTAAAAATAC--ATGTTTTACAAGGGGAT................... -180 -170 -160 -150 -140 -130 sub TGTCATGTTAAATTGATAATTTTGTGACAACTTTATTAAAGATTCATTTTAGATATATCT hal AGGACTCATTTGTGGCGAAAATT-TAACAA-TGGTTTAAATATGTATTTTAAATAT-TGA ste .....................TTGTGAACAATTTATTAAAGATGTATTTGAAATATTGCT -120 -110 -100 -90 -80 -70 sub TTTATTCGTA-A-GATCATGTATT--TTAAAGATATATTTTAAATACATCTTTTCGAAAG hal TTAATGAACATA-GGTGGTGTACT--TTAAATATGTATACAAAATACTTATTTATAAAAG ste TT--TTCGCA-GTGCTCATGGTTGAATAAAAGATGTATTAAAAATACATGTTTTACAAGG -60 -50 -40 -30 -20 sub GATTGTTTATAAA hal ............. ste GGATG........ -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...