Similar regions between promoters of yvaK

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGTTTTGCTTCAATCCAGTAAAAGTGCCGGATTATCTGGTGCGATTTCAGGCGGAGCGGA hal .....................AAGTGCCGGATTATCTGGCGCCATTTCCGGGGGAGCAGA ste .GTCTTGCTGCAGTCGGGCCGCAGCGCCGGGCTGTCGGGGGCGATCACCGGCGGCGCCGA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCAGCTCTTCGGGAAACAAAAAGCAAGAGGTCTTGATTTAATTTTGCACCGCATTACGGT hal GCAATTAGTAGGGAAACAGAAGGCACGCGGGATTGATGCATTTCTTGCTCGTGCTACGGT ste GCAATTGTTCGGGAAGCAGAAAGCCCGTGGGCTCGATGCGGTGTTTCAGCGCGTCACGGT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGTGCTGGCAGTCTTGTTTTTCGTGTTAACGATTGCGCTTGCTTATATCCTATAGGGCAA hal CGTGCTAGCGGTGTTGTTTTTCGTGCTAACCATTGCAGTTGCATA............... ste CGTGTTGGCCGTCTTGTTTTTCGTATTGACGATCTTGGTTACGTA............... -180 -170 -160 -150 -140 -130 sub TGTTTGTATAAGGTCTGATGTGAAGTCAGGCCTTTTTCACGTTTCTGGATGATATTCAAA hal ............................................................ ste ....................TGCAGTCGGGCC............................ -120 -110 -100 -90 -80 -70 sub ACGTTTTTTTCTGATTAAACTGTGGAAAACTAA-----AATGA--TC-GTGCAGATAGAA hal ....................TGTGGAAACCTAATAAACAATGACATCTGAGAATAGAGAA ste .CTTGTTTTTCGTATTGA.......................GA--TC-GCGCTGATCGCA -60 -50 -40 -30 -20 -10 sub AGGGAGAC hal AGGAAGA. ste ........ -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...