Similar regions between promoters of spoVM

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CCCTCCTGGTGAATATGATATTGAGAAGGATGAAAATAAGCGATATATCTCCTTCATACC hal ......TGGCGCATATGATAGAGACA-GGAAGACAAGA...................... ste ......................................ACCGTTATGTGTCATACATCCC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GTTTTCCGAAGACATACATGAGCTGACCCTGACCGGTTTTAAATATCCTCTAAATAATTG hal ............................................................ ste GATTTCCGAAACGGTGGCAGAACTTACGCTGATGGGATTTAAATATCCGTTAACAAACTG -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCATATTACGCTCGGTTCAACACTATGTATTAGTAACGAACTCATTCATTCACGAGGTAC hal ........................................CTCTTTCGTTCACTAGATTG ste TCATATTTCTCGCGGTTCGACATTATGTATTAGTAATGAACTTATCCAATCTTCCGGTAC -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTTTCGTTTGCAAAAGGCATATTAATAATGATAAGAAGCACGGATTAAGCATGTGCTTT hal GATTTCTTTCAGTAAAGGAACATAAACAAAG....................ATTGGATTT ste TTTTTCGTTTTCAGAAGGCATATTAATGATGATAAGGAGCAGCGATTTTGC......... -120 -110 -100 -90 -80 -70 sub CATTCAATTGCTGAAAACAATGAACAAGGCGGTTACGGGACGTTATAGGAGGGGACAAAA hal CTTTCAGTAAAGGAACATAAACAA....................AAAAGAGGGGGCACAA ste ......ATGACGGAATATAATGGATAAGGAAATGGCGGGAAGCT................ -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...