Similar regions between promoters of yuiD

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub ACATCACCCTCTTTTAAAAGCTGTGTCAGATGGCCTTCGAGCATTTCATCAATTTCCAAC hal ACTTCACACCATTTTA...........AGATCGCCTTC...................... ste ............................................................ -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GCTTTTCCTGTCAGCTGGCTTTTTTGAAAAAGCCCGACAACAAGGGTTTCTGTATGCTCT hal .....................TTTTGAAAA......ACCACAATGGTTTC.......... ste ............AGCTTGCTTTTTGGA................................. -240 -230 -220 -210 -200 -190 <<<<<<<<<<<<<<<<<<<<<<< sub GATTGTTGAACCGCATAAAACATGAGGCTTACACTCCTAACGTAATGGGTATTTGTAATG hal ..................AAAATACAGCATACGCTCCT...................... ste ............................................................ -180 -170 -160 -150 -140 -130 sub AACAATGGTATAATAGGAAAAACATTCTTTCCACTATACTTATTTTAACAAACAACAGTC hal ....ATGGTATAATTG-ACAAGCAT-CTTTACACAAT....................... ste ..........................................................TC -120 -110 -100 -90 -80 -70 sub TAAGACTTGCTTTTTTCTTTTGAAACACGAAGG-ATTTTTCAAATAGAAAGGATGTCGCC hal ...............TCTTTACACAATCGAACG-ATGATT.....AGAAAGGACGTTG.. ste TCAAGCTTGCTTTTT..........CACGGCGGCATTTTGCAAATGG............. -60 -50 -40 -30 -20 -10 sub G hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...