Similar regions between promoters of spoIIGA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TATTAAAGCAAAAGGAGCAAAAGTAGAAGTGATCGTCCGAGATGATTATGGAAATGAAAC hal TCTTGATGGAAGAGGAGGAAGAG..................................... ste ......AACGAAAGGGCGAAAAAGAGAAG............................... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]]] sub AAGAAAAACTGCGAATGGAAAACTTAATATGAACACAGAAAATTAAGTGGAAAAAAAGCT hal ...................AACCTTTATAAAAAAACAG...................... ste ................................................GGACCAAAAACT -240 -230 -220 -210 -200 -190 ]]]]]]]]]]]]]]] sub GCCGTCATTGGCAGCTTTTTTTATATCCTCTCATTATACTTCCTCGACAAATTAAGCAGA hal ..............CTTTTATTTTTATTGGGCAATATTTCCCGCTGACAAAAAAACTGAA ste TCTCGCGTTGGCCGCTTTTGACAAAACCTCCCCTTTTTCA-CCGCCACCGATTGA-CAGA -180 -170 -160 -150 -140 -130 sub -TTTCCCTGAAAAATTGTATTTTCCTCTCAACATTAATTGACAGACTTTCCCACAGAGCT hal -AATCTCTCAAAATAACTAGCTTGTCCCCGTCATAAACTGACAGACTTTCCCTTCTCTCT ste CTTTCCCCGAAGAGATG...................ATTGACAGACTTTCCCCGAAGAGA -120 -110 -100 -90 -80 -70 sub TGCTTTATACTTATGAAGCAAGAAGGGGAACAGCGTGAGGCAAGAAAGAAAGGAGTCAGA hal TGTTTTATACT..TGATGGAAGAGGAGGAAGAG........................... ste TGCTATATACTTGT.............................................. -60 -50 -40 -30 -20 -10 sub T hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...