Similar regions between promoters of spoVE

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GTCAAAGCAGTGCTTACATTTGGCCAGACGGCGCCAAAACTCGAGAAACTCGGCAATGAA hal .........GTGCATACAGTTTGGTAGAGGG............................. ste ...AAGGCGGTCGTACTGTTCGGCCAGACGGCGGATAAAATCGGCCGCATCGCCCAAAAA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTGGGAATACAACATGTCAAACGTGTCGATAATGTTGAACAAGCAGTATCTGCGGCGTTT hal .................................GTAGAAGATGCAGTACGTAAGGCATTA ste GCGGGAATAGAAACGATCCGATATGTCGATAATGTGGAAAAAGCCGTCCCGGTTGCTTTC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCGCTCTCAAATGAAGGAGATGTCATCCTGCTGTCACCCGCGTGTGCGAGCTGGGATCAA hal GACGTATCTGCGAATGGGGATGTCATCCTTTTATCGCCTGCATGTGCGAGCTGGGATCAA ste GAGCTTTCCGAGCCGGGCGACGTCATTTTGCTCTCTCCAGCATGCGCCAGCTGGGATCAA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTCAAAACATTTGAAGAACGCGGTGACATGTTTATAGATGCCGTGCATATGCTTAAGTAA hal TACCGTACGTTTGAAGAGCGCGGTGAGGCGTTTGTAGATGCAGTACGTAAG......... ste TACAAAACTTTCGAGGAGAGAGGGGACATTTTTATCAATGCCGTGCATAAGTTGAAATAG -120 -110 -100 -90 -80 -70 ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] sub GGGCTTGTCTTGAAGTAAATCGGCAGCCCTAATGACTTTAAGCTTGGGGTGTCGATTGCT hal ............................................................ ste AGG......TAGAGGGAAAGGGACAGCCCT.............................. -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...