Similar regions between promoters of spoIVB

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTCTCTAAGCAGGAAAAGGTAGCGGAAATCGAGCGCAGTATTGCAGGTGTCGAAGTAACC hal ..........AAGAAAAGGTGGAAGAGATCGCGCGAATGATCGCTGGCGTTGAAATGACA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>> sub GACTTAACGAAACGCCATGCGAAAGAACTTTTAAAACAAGCGG-----ATCAAGTCAAAA hal GAGCTGACAAAGGAGCACGCAAAGGAGCTTCTGGACCTAGCGACAAGCATCAAATGTAAC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>]]]]]]]]]]]]]]]] ]]] sub CAACTGGGTAAGCTGCGCGAGAAGCGC-AGCTTATTTTTTTCGTGCACATCCATTCGTTC hal CA--TTGAAAAGCTAACCAATAAAGGTTAGCTTTTTT....................... -180 -170 -160 -150 -140 -130 sub ATCAGTATATCCAATGTTTTTCTTCATATGACAGTTATAAATAAGCCGTCAGAAGGCAAA hal ................TTTTTCATCCCGAAACAGTTATAAACGTGAGCTCGAAAGGCAAC -120 -110 -100 -90 -80 -70 sub ATTAAATGATGTAGCAGCAAGTCATAAAGAAGGTGTGGGATAGGAGCGAGGAGAGTGAAG hal ATTA---GATATAG-AGCCAAACCAATCGGGTGTGTGGGCTAGGAGCTAGGAGAGTGAAG -60 -50 -40 -30 -20 -10 sub TAGTGA hal GA.... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...