Similar regions between promoters of ysgA

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub TTCAGCATTTCGTTTTTCTCACTTTCGGATGCGTGCTGCCAAATGACTTCGAATAAAACG hal ...AGCATTTTTTCTTCACCACTTT.......GTTTTTCCAATATACTTCGAATAAGACA ste ..........................................................CG -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub CCGAGCCCTGGAAGCATTTTTTCTTCACCGCTTTGAATCGCATCTACGATTGTATGCTCA hal CCGAGACCTGGGAGCATTTTTTCTTCACCACTTTGAATGGCGTCAACAATCGTTGCTTCA ste CCGAGCAGTCAAAGC............................................. -240 -230 -220 -210 -200 -190 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub AGCTGCTCCTGATTATTGCCGGTGACATTGGCAATGACGGCATGACGTAAATTAAGATCC hal ACCTCTTGTTCGTTACTTCCTTGAATGTTTGCCATGATTGCTTGACGTAAATTAAAATTC ste ...........AATTTTGCCGGCGAC.....CGATGACGGC.TGACGAAAATT....... -180 -170 -160 -150 -140 -130 << sub ATGTAAAACGC-TCCTTTTTCTAAAATGTAATACGTATATTCTAACCCTGCACCTGGTTT hal ATTTTGATCACCTCAGCTTTATAAATGGTCGTTCG...............CAACTGGTCT ste ...............TTTTACCATAACGAAAAAC.......................... -120 -110 -100 -90 -80 -70 sub ATTATGTGCTGTTCTTGCGATATAATAACATCATGTTAAAAAAAGGAGCGCCACATAGAC hal TTTTGCTGCT............................AAAAAAGGAG............ ste ................GCGATTTTTTACCATAACG-----AAAAACAGCGCCA....... -60 -50 -40 -30 -20 -10 sub A hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...