Similar regions between promoters of ispA

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub CATCGTTTCAATCCATTCCTCGGCCATTTGTTCCACATGCTCTGAAAAAAATGCATATAA hal ................................................AAAAAGAGAAAA -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<< sub TTTTTCATTCAGTTTCATGACACTGCTCCTTTCCCCAACACTATTATAACTTGACTTACA hal CGTTTCATTAGGCCTAAAAACAG-GCGACTTTTTGCCTTCCAATCGTCACAATATTTGTC -240 -230 -220 -210 -200 -190 sub GTTGAATCCCAGTCATACATGTTGAAGCCATCCAATATTTTGAAGATTACTAATTCTTTG hal GAAGGAGCGGAGAATTATATGCTAAAAATACTGAATATTCTG..........ATTATTTG -180 -170 -160 -150 -140 -130 sub GTGTGTATC----CTATTTTTTCAAAATGCTTCAAATGGCTCTGTCCGAGCGCTTGCTTT hal GAACGAATCTTTACTATCGTATCATAATTCGACAAAAGTGTCT................. -120 -110 -100 -90 -80 -70 sub TTTCATATAATATGAGGCAACACCCTTGAATCCACTTGCAAGCATAAAAAAGGAGGGCTT hal .......................................AGGCCTAAAAACAGGCGACTT -60 -50 -40 -30 -20 -10 sub TTTT hal TTT. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...