Similar regions between promoters of yrbA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACAAATCGAATCACTCAACCCTGACATGTGCCCTTGCCTGACAATGAACCGAATTGATTT hal ............................................................ ste ...AATCGCATCAC.............................ATGAATCGAATTGATTT -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> sub GCCGCATTTGTTGTGGTCGCTGGAACAAATTGAAAAAGGAGA-ACCTTCAGGCGTC---- hal ................................AAAAAATCGA-ACCTTGACACATATTTT ste GCCGCATTTCGTCTGGGCGCTCGAATCGCTTGAGCAAGGAGCGATCGTCAATCG-C---- -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub --ATCAAGGTGCCAAAAGCCATTCAGGAAGATGCACTCCTTGCCCTGAATCGAATGCTTT hal TGATCAAGGCGACATAA........................................... ste --ATCACCGTTCCGAAAGACATCGCCGCAGAGGCAAAAGAGGCGCTCGACCGCATGCTTT -180 -170 -160 -150 -140 -130 >>>>>>>>>>> sub CGATCACGTAGATCAGAAATATTTTCCCTTCCTTTACTCATAA----CTTCTTTTGTTCA hal ...............GAACTTTTTTCATTTCATTT--TCAAGA----GAAACGTTCGTAA ste CGCTTGCCTAGCT--------TTTTCCCTGGCTTGACGAGGAGGGATCCTCGTTCGGTCA -120 -110 -100 -90 -80 sub GGCATATGTTGTGAAGAAACATATTGTAATCACAGCTGAACTGTTCACGTTTTGCATAGG hal GCTGTGTTTTCCGAAGAAAAAGTTAGAAA....AGATGAAAAGTTCACGAT.TGCATAGG ste GGGATTTTTT..........ATTTTTTTATCATAAATCAACGATCATCGTCATACATTGT -70 -60 -50 -40 -30 -20 sub AGGGGAAAACG hal ATG........ ste GTTGAAAGACG -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...