Similar regions between promoters of yozD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATGATGTTTGTTTTGGAAAGTTTAAAAGAGCATTTCAGTTAATTTGTGAACATACGGATC ste .........GTTGTAAAACGTTTGCG-GACAATCTCCGATCACCAGGATAGAAATTGATA -300 -290 -280 -270 -260 -250 sub AAGACATATAA-AAAATATGGCAGACAGCCCCAAATCATCACACGCGTC-ATTCCTTTGA ste AAGAATAAAAAGAAAATAAGGAATGCCGGCGAAAATGA-CGATCGCGCCCAATCCATTGA -240 -230 -220 -210 -200 -190 sub GCGTTTTTTCCATTATGATATCAAATCTTTCTCCGTCCAGTGCTTCCATCATTTTAGCAA ste CAACTGTTTCCATCATTTTATCGA..........GACAACTGTTTCCATCATTTTATCGA -180 -170 -160 -150 -140 -130 sub TCATAGCGTCAGCCTCCCATGGCTCGTTTTTTATTCAATATATGACTGAAAGAATTGTTT ste TCGCAGTG...................................GACTGAAAAAATAGT.. -120 -110 -100 -90 -80 -70 sub AGAACACCGGGTATAATTCAGCCTGTTTTTTCATAAAACATAAAAAAGGAGGCGGTACGG ste ...............................CATACAACATTACAAAGGGGGCG...... -60 -50 -40 -30 -20 -10 sub AG ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...