Similar regions between promoters of yubB

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGGAAAAAACCTTCACATCCATCCGATTACGATTATTTTTCTGCTGTTAACAGCCGGCAA hal ..............................GCTTATTTTCCTGACGTT............ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCTGTTTGGCGTTG-TTGGAATCATTCTTGCGATTCCCGGCTATGCGGTTGCCAAAGTCA hal ......TGACGTTGCTTCTACTCGTCTTCTCGAGAACACGCTACACGGTCGGAAAA.... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTACGACACATTTATTTGACTGGTTTAAAATGCAGTCACATTTATACGATGAAGAAAAAA hal .................................................TGATGAAAAAG -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATGAAAATACGCCGGGGCATAAAGTGTGATTTTCGTTTATAGTTATATAAGACGGGCTTT hal GGGAAGAT............AAGGCCTGATTCTCGCTTCCTTTTACAT.........TTC -120 -110 -100 -90 -80 -70 sub CCA-TTTATGGGAAGCTCCCGTTATGTAAAAAAATAAATGTCTAATGGGGAGAATCAAAA hal CCACTTTATGAGAATC.......ATGTCTAACTATTGATGAAAAAGGGGAAGATCGAAA. -60 -50 -40 -30 -20 -10 sub TC hal .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...