Similar regions between promoters of hag

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCGGTTGAAGGGGATCAAGTGAAGCTTGGAATTGACGCCCCAAAGCATATTGATATTCAC hal ......................................CACCAACCACAAGGATGTGGGC ste ................AAGTGTATCTTGCCATCCAAGCGGAAAA..............AC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGGAAAGAAATTTACTTGACCATTCAGGAAGAAAATAACCGTGCAGCAGCGTTATCCAGC hal GGAAAACACATTT.....ACATTTCAAGGAGGAAAT........................ ste CGCAAAGAAGTGTATCTTGCCATCCAAGCGGAAAACAACGCCGCCTCCGAAGCGTCCGAA -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GATGTGATCTCCGCATTATCCTCACAAAAAAAGTGAGGATTTTTTTATTTTTGTATTAAC hal ...........................AAATCGTGTCGATATTATTAATGT.......AA ste GCCTCGCTCGCCGCACTGACCGCATATAAAAAGTGAG....TTTTCATTTCCCTATTAAA -180 -170 -160 -150 -140 -130 sub AAAATCAGAGACAATCCGATATTAATGATGTAGCCGGGAGGAGGCGCAAAAGACTCAGCC hal AAAATCATAAAAAAT.CGATATTATTAATGTACCGG........................ ste CTTCCAAAAAACGCGCCGATATAAAAAGTGAGCGCGGCTGGCGGCG-AAAGGCGGCCGAC -120 -110 -100 -90 -80 -70 sub AGTTACAAAATAAGGGC------ACAAGGACGTGCCTTAACAACATATT-CAGGGAGGAA hal ................C------ACAAGGATGTGGGCGGAAAACACATTTCAAGGAGGAA ste TTTCGCCCCAGCCCCGCCGTTCCACAAGGACGTGGAA-AACATCAT-TT-CAAGGAGGAA -60 -50 -40 -30 -20 -10 sub CAAAACA hal ....... ste GAGAAC. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...