Similar regions between promoters of prfA

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< << sub AGAACAGCTCAATGACATACGAGCCGTTAAGCGACAAATCAAGCTTATAGGAGCCGC-GC hal .........CAACGACATAAG....................................... ste .............GACATACGAG.........................AGGAGCGGCAGC -300 -290 -280 -270 -260 -250 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub TCTTCGCGGTACGTTTCTTGAATCACCTGAAAACCAAGCTTATGTACGTAGAAAGCTTTC hal ......................................................GCTTTC ste GCGAGGCGCAACGCATTGACAAGCTGCTGACAA........................... -240 -230 -220 -210 -200 -190 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GACTTTTCGTAATCTGAACATATGATTGCAATATGATGTATGGATTTCAGCAACATCATC hal -ACCTCTTGTTTACAGAACAT-TACTTGTACTAT..................ATAACATA ste .........TAATCTAAAAATA...................................... -180 -170 -160 -150 -140 -130 sub CCTCCTCGAATTCCAGTATAGCAGAGGGAGCTTTTCCAGCTGGGATTGAAATGCTTTTGA hal CTTCATCGCTTTC...........................................TTGA ste .......................................................TTTGG -120 -110 -100 -90 -80 -70 sub CTGGGGTTAAT-CACTATACTATAATGAGAATGTTACGCACAGGAAAACAGAGGTGAAGA hal CCGGGAACTTC-CCGTATACTATAATGACAATGTTATGAAAATGAAAAATGAGGTGAA.. ste CTTCATTTCATGCTATAATCTAAAAATAGACTGTGTGG----GAAAAACAGAGGTGAA.. -60 -50 -40 -30 -20 -10 sub CC hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...