Similar regions between promoters of yocC

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GGGCAATCTTCCATTCTCCCCCCTGCTGCTCTGGATCTCTCATGTCTGTATTGAGATACA hal ...................................TCTTTAATGTTTGTGGGGATTAATA -300 -290 -280 -270 -260 -250 <<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GAGAG-AGAATTTTATCCGGCGGTTCCAATTGGACATACTGTAATTTGTTAATCAATGAA hal GAAAGGAGTATTT................TTGTTCATCATCTATTTTTCTCTTAAATGTA -240 -230 -220 -210 -200 -190 <<<<<<<<<<< sub TCAATCGCCATTCCGATTCCTCCTTTT-TCACAGGTTAGTTTTCTTTTTCCTCTCTTAAA hal ...........TCACATTCCTTGTTTTCTTGCTTGTTCATCATCTATTTT-TCTCTTAAA -180 -170 -160 -150 -140 -130 sub AACGATCAAACCTGACTTTCCGCTAATTTCTAGTAATAATGGAATTGTTGTTTACAATAC hal ............................................................ -120 -110 -100 -90 -80 -70 sub GCCTCTCTTCTAATACAATTGGTAACTGTGTTTCTAAGCTGTTTTTTGAAAGGAGTTTGA hal ........TCTAGTAGAATGTAAAACTGTATGTTT......TTAATAGAAAGGAGTAT.. -60 -50 -40 -30 -20 -10 sub TC hal .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...