Similar regions between promoters of yaaD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATGTAGAAAAAGCAAACTGGTTTGTTTTGACAATGCGCAGTATCGGCGGATTTTTTGCCG hal ATGTTGAGCGAGCAGGTTGGTTCTCCCTCCTCATGCGAGGCATCGGTGGCTTTTTCTCCA ste AAGTCGAAAAAGCCAATTGGTTTGTTCTTTCGATGCGCGCGGTCGGCGGACTGTTTGTTG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAATTTGGGGAAGCATTGTTGATACGGTAACCGGCTGGTTTTAATCAATTGAAAGAGCTC hal ACGTTTGGAGTGCAGCGGCTGATACCGTTCGCGGTTGGTTCTCATAATAGGTCAAAGGTG ste ATTTATGGACAAGCGTCGCCAAAACAGTGAAAGGCTGGCTGTA................. -240 -230 -220 -210 -200 -190 sub TGATGGATGTTAGGGCTCTTTCGCGTAATATACTGAAAAAACCCAATTTTTAATAAAAAA hal TCAT........................................AATTTATGATAA.... ste ...............................................TTTTTGTAAAAAT -180 -170 -160 -150 -140 -130 sub TGATTTTCAAAGCGCTAAAAACCGAA-TAAAATAGTATATATGCATATGAATTATTGGAT hal .......................................................TGGAT ste TGA............TAAAAATTGAGGTAAAATAAAACAG-TGGAATCGTCCTTTTGCAT -120 -110 -100 -90 -80 -70 sub TTCTAG-GATACAATAAGGATTAGAAATCATATAACTATACCTTGATTAGGGGGACCAAG hal GACTTGAGATACTATGTGAATGAGTAGTGA.............................. ste GCCTCG-CAAAGCATAAGGATTAGGAAT................GAATAGGGGGA..... -60 -50 -40 -30 -20 -10 sub AA hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...