Similar regions between promoters of yvbA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGGCTTGAACGAGCATTAAGCCCGATTAAAAAGAAAAAAGGAAATTTTATTATAGCTGAT hal .....................................AAGGAAATTTGTGTATCCTTTAT ste ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>> sub AGAAAAACCACCTCTATTTAAATACAACAGAGGTGGTTTTTTTAAATAAACAAC-----A hal TTAAGTAATTGCT-TAAATAATTAAATGAGGGGTGATTTCTTTTAATAA........... ste ...................................GTTTTTCTAAATATCTAACTATATA -240 -230 -220 -210 -200 -190 sub TGTGTTAGTATCTGTTAAACATATTTTCCAGCGTTGGGATTATCCGAGTATTTGAAAAAA hal .......................................TTATTTAAGTAATTGCTTAAA ste TGTATGAAAACCTGTTCA.......................................... -180 -170 -160 -150 -140 -130 sub TACAAAAATCAGATATTATAACCAATTTGAGGGTTGTTTTTAAAAAAA--TTCAAGT-TA hal TAATTAAATGAG.............TTTAATAATTATTTTTTAAAAAAGGTTCACAA-TC ste ................................GATGTTTTTCTAAATA--TCTAACTATA -120 -110 -100 -90 -80 -70 sub TA---ATGAAA-------ATAATACATTTATACAAATATCTAAATGTCTAAATGTTTTTT hal TA---AGGAAATTTGTGTATCCTTTATTTAAGTAATTGCTTAAATAATTAAATG...... ste TATGTATGAAA-------A....ACATTTAGATGTTTTTCTAAATATCTAACTATATATG -60 -50 -40 -30 -20 sub TGTAAAGGAGAAAACGCT hal .................. ste TATGAA............ -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...