Similar regions between promoters of cheR

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CATTTTCTTTAAGAATGAAGAATTAGTATCATATCAGCAGCTTATGGCAGGCTGGATCTA hal .ATTTTCTTTGATTCTTCAGAGCTTAATGAATATGACAAGGTCGTCAATCGCTGGGTATA ste CTTGTTCTTTAAAGAAGAAGAGCTCGTCAGCTATTCGAAACAGATCAATGCATGGCTGTA -300 -290 -280 -270 -260 -250 >>>> sub ------TTAATCATTGTGAAAATAAGCAACAGAGCCGGCAACATATAACGCCGCCGGTTT hal ACATGTTTAATTATTTTGTTTATAA................................... ste ------CTGAT.......................................CGGCCGGTTT -240 -230 -220 -210 -200 -190 sub TTGTTCTGTTTTGTAAAGGTTTACATTAAAGTGAATAAAGGGTTGAATGGCAGTGTGCAT hal ............................................................ ste TTGC-CGTTTTTGTACA........................................... -180 -170 -160 -150 -140 -130 ]]]]]]]]]]]]]]]] sub CAGACCTCTGCCTTTCCCAACGATCTAAAATCAGCTGAAAAGCTGATTTTTTTATTGA-A hal ...........................................TAATTATTTTGTTTATA ste ................................AGAAGAAGAGCTCGTCAGCTATTCGA-A -120 -110 -100 -90 -80 -70 sub ACAATACAATTTCCTGATAAAACAAGCTATACTAGGACAAAAAGACAGCGAGACTGGGAG hal ACAAGGCTGTCTCATGATCAGAGA....ATAAAAGAAAAAACAACCACTGAAAAAAAGGG ste ACAGATCAAT.................................................. -60 -50 -40 -30 -20 -10 sub AGTAGAG hal AGTCGA. ste ....... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...