Similar regions between promoters of comER

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GATGCTGAACAGCACCTTTGATGTCTATCACAATTGTTTCGTTTGACTCGTCGTTGTTTG hal ........................CTATATCAATTG........................ ste ..........................ACCACAGCGGTTTTTGGCGCCTCGTCCTTTTTTT -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub CTTCCTGCTTTACCACTGTATTTTCTGTCTCTGTTGGTACAGCTTGCTTCACCGGCTCTT hal ............................................................ ste CTTCC.................................ACAGCGGTTTTTGGCGCCTCGT -240 -230 -220 -210 -200 -190 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub TATTTTTCCCTGTGGCCAGAAAGATCATAATCGCTGTGAAAACAGCCGCAGAAGCCGCTA hal ................CAAATGGATCAAAAGCGA-GAGGAAGCGATCGAAAAAGCGGCTA ste CCTTTTTTTCT................................................. -180 -170 -160 -150 -140 -130 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub AAATAATTGCTTTCTTATGCTGATTCAACCAATTCATCGTGCATGTTCCCCGCTTTCGTC hal TATCAATTGCCTAC.....CAGTTTCAACAAATGGATC..................CATC ste ...............................................CCCCGCTTTC... -120 -110 -100 -90 -80 -70 sub ATATTTTATTTTCATAACACATATGGTTTAGAGGATAATAGCTCAAAGGAGGGGAAACCA hal ATATGTCAACTTGATATCATATGTCAACTTGATGGTAGCAGCGAGAAGGAGGCGACATC. ste ........TTTTTCTCATACATATCG....................AGGGGGGGACAACA -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...