Similar regions between promoters of trpE

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCAGGATCAGATCAGACATGTATATTTAGAAAAAGTTGTCGTATTGAGGCCCGATTTATC hal ...............................................GACCAGATTTGCA ste .....................................GTCGTGTTGCGCCCGGATTTGTC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>> sub ATTGACAAAAAATACTGAATTGTAATACGAT---AAGAACAGCTTAGAAAT---ACACAA hal GTTGACAAAAGATTCCTAAT.....TAAGCT---ACGACCAGATTTGCAGT---TGACAA ste GTTGACAAAAAA-ACAGAAATGTAATATAGTTAAAATAACCTCTTTGCCCCCTGAGACAT -240 -230 -220 -210 -200 -190 @@@@@@@@@@ sub -GAGTGTGTATAAAGCAATTAGAATGAGTTGAGTTAGAGAATAGGGTAGCAGAGAATGAG hal -AAG.............ATGAGAATGAA--GAGTT-GAGGAGAGTCGAGCTGAGGA..AG ste CGGGGGCGTTAGAAGTG--GAGCGAGAGTGGAGAGCGAGCGTAGGGTAGATGAGAATGAG -180 -170 -160 -150 -140 -130 sub TTTAGTTGAGCTGAG----ACATTATGTTTATTCTAC--------CCAAAAGAAGTCTTT hal TTTAGTTGAGATGAG----A.......TTCATTCCTA--------CAAAAAGGAGT.... ste CG-AGTTTAGCTGAGGTTGAGCGTTTTTTCATTCGCCGACATCTGCCCAAAGACGGTCGT -120 -110 -100 -90 -80 sub CTTTTGGGTTTATTTGTTATATAGTATTTTATCCTCTCATGCCATCTTCTCATTCTCCTT hal .TTTTTAGATCACTTTTTA-AAACCCTCATTTCGAATGATTCC-TCGTTCCTTCATTCCT ste CTTTGGGCGTTTTATTTTCCCTC-TCTTTTTTCGCCTCAT---AAACCCTCATTCTCC.. -70 -60 -50 -40 -30 -20 sub GCCATAAGGAGTGAGAGCA hal ACAAAAAGGAGTGAGAG.. ste ................... -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...