Similar regions between promoters of dps

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCAATCAGTCAGAAGAGGAGCATTCACATCATCATTGATTGTGTGAATCAGAGTGATTTT hal GAAAACAG-CAAAGGAGGACGAAACAAATC.............TGACTCAAAGCGAACTG ste ............ATGAGGAGGAGTGAGAT............................... -300 -290 -280 -270 -260 -250 sub CTTGTGGTGGATCAATGGTATGCTTTACATTATAGGCTTTTACAGTCGTCCAAATGGTTA hal CT......................................TACGTTCGGGTAAATG--TA ste ..................TTTTCTTTCCATTATA...............CCAGCTGGGTA -240 -230 -220 -210 -200 -190 sub CAAGCAAAACAGCCAGCACAATCAAAATACTTATCGTAATGAGAAGCGTCATGACATTCC hal AAATGAAAACAGCAA..............CATACCGTGATTAGAA............... ste CAAGAA...................................................... -180 -170 -160 -150 -140 -130 sub ACCTCCCGTTTTT-TAACAATTGTAGCATAATAGAAGAAATCGTGACAGATAAGGGTAAA hal ...........................................TCACCGATCAAGACACG ste ACCCCCCTTTTTTCTTTCCATTATAACATACAAAAAG....................... -120 -110 -100 -90 -80 -70 sub AAAGAGGTTTTAGCGTACGATATTAAGGGTATACATAGTCATATAACAAGGAGGAGATAC hal GAAAAGCTTTTAAC.................................AAGGAGGA..... ste ........................AAAGCTATCCATCGGCA.AGAACCATGAGGAG.... -60 -50 -40 -30 -20 -10 sub C hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...