Similar regions between promoters of phoA

sub CAACATAAAGGAAATAAATGAAAAACTTTCGGGGTCGGCTCATATATCGGAAAAATGAGT hal ............................................................ ste .......AAGGAAAAAAGAGAAA.........................GGAAAAAAGAG. -300 -290 -280 -270 -260 -250 sub GATAAAGTATATTCGAGGAGAGCTGTG----GTTATCCGCAGTTTTTTTATTTAAACAAA hal ...........................................................A ste ................GGAGAGCTGTCATCCGTTTTGTTCAACTGTTGAACTATTAGTAA -240 -230 -220 -210 -200 -190 sub C-ATATCATGCAAAGAC-AGAGAGGTAAA---GATTTTTCTGAAAAATGAATGCTTTACA hal C-ATATCAT..............GCTCAC---GGTTCTTTTGAAAA.............. ste CGATACCAAGGAAAAAAGAGAAAGTCAACAAGGAATGTTGCCAAAGGAGAAACCATTCTA -180 -170 -160 -150 -140 -130 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ sub TCAAATAAGGCAAGATAACGAAAAGCGTTTTTTCATTTCCTTACAAGGCTTTCATTATTG hal ......AAAGCTAGATAACGACA........TTAATTTCAATTAAATCCCTCCATT.... ste TCGTCCAAT-CTGAATAGAGAGGAAATTTTTTCAAAGCCATTACATTGCATTCACGAACG -120 -110 -100 -90 -80 -70 @@@@@@@@@@@@@@@@@@@@@@@@@@@@ sub TTTACATGATCAACAGCCGCATTTAACAAAGTTTCCCTAACATGATAAACGGAATACATT hal ..TACAT-ATCATTAGTCGCTCTT......GTTTCGCTTACCTG................ ste CTTA........................................................ -60 -50 -40 -30 -20 -10 sub AAAGGAGGC hal ......... ste ......... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...