Similar regions between promoters of sms

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AATTGACAGATGCTGCAAAAGCGAAAGTCGCGGAAGAGGGCGTTGACCTGGAATACGGTG hal ........................AAAACGGCGAATTGGTCGTACATTCGAAAGAAGGGG ste ...TGACGGAGGCCGCCATTGAGAAAATCGCCGCCGAAGGGTTCGATCCAGAATACGGTG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CCCGTCCGTTAAGAAGAGCGATCCAAAAACATGTCGAGGATCGTTTATCTGAAGAACTCC hal CCACACTGTAAGGATGAACCAT........AAGTGGAAGATCGCTTGTCCGAGGAACTTC ste CCCGCCCGTTGCGCCGCGCCTTGCAAAAGCATGTTGAAGACCGTTTGTCCGAAGAATTGT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCAGAGGAAATATTCATAAAGGACAGCATATTGTTCTTGATGTAGAAGATGGCGAATTTG hal TCAAAGGAACAATTCAAAAAGGACAGCGGGCCATTATCGATGTAGAAAACGGCGAATTGG ste TAAAAGGCACGATCGCCAAAGGGCAAAAAGTCGTCGTGGATGTCAAAGACGGGGAGTTTG -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCGTAAAAACGACTGCTAAAACGAATTAATATAGAAGACGGAA-ATGAGGCATACAGCAT hal TCGTACATTCGA................................................ ste TCGTA...............................GAGGGAAGAAAAGGCATGCGGCAG -120 -110 -100 -90 -80 -70 sub GTAAGTGT--ATGCCTCACTTTCATATCAAGAAATAGAACAAGGGAGAGGTCTTACACTA hal ........................TATCGATGTAGAAAACGGCGAATTGGTCGTACATT. ste CTTCCTGCCCATGCCTTTTTTTCGTTGGAAAACGTTACAGAAAGG............... -60 -50 -40 -30 -20 -10 sub TAT hal ... ste ... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...