Similar regions between promoters of cotA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTATTGATTCCATGAGAGACGAGCTGCTGCTGACAGGCGTCATCACGGGAATCGTTCTGA hal ...........................TGTAGTCAAGCTATATCAAGGGA.......... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTCTTACCTTGTGTTCAGAAAACGCAAGGTGAGCGAGAAAGCGGCTGCCAACCCAGTCA hal ............................................................ -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]]]]]]]]]]]]]]]]]]]] sub CACAGCAGCAACCCGATATCCTGCCTTAATGCTGATCAAATCCTAAACGGCCTGCCGTTT hal .......................CCTTAGTCCTCATC....................... -180 -170 -160 -150 -140 -130 ]]]] sub AGGATTTTGTTATTTTCTTCTTCGGGCGGGCTGCAGCACGAAGATTTTTTGTAACCATCA hal ....TCTTCATATTTTCT.............TCCCGGACTAAGGTTTTTTGATATGAAGA -120 -110 -100 -90 -80 -70 sub CGTC---CTTATTGTCATTAACTATAGTACCAATTTGGAAAATTTAGATAAGGACAGATG hal AATCAAACTTCTTCATATTTTCTATA................TTTTGATATGAAGAAATC -60 -50 -40 -30 -20 -10 sub AAA hal AAA -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...