Similar regions between promoters of rnpA

>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGGAGGTGTCATAAATG---AAAAGAACATTCCAACCGAATAACCGTAAACGCAGCAAAG hal GGGAGGTGTTATAAATGGGAAAACCAACATTCCAACCAAATAACCGCAAACGTAAAAAAG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTCATGGCTTCAGAAGCCGTATGAGTTCAAAAAACGGTCGTCTAGTTTTAGCACGCCGTC hal TACACGGTTTTCGTGCGCGTATGAGCACTAAAAATGGCCGTAAAGTATTAGCTCGTCGTC -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >]]]]]]]]]]]]]]]]]]]]]]] sub GCCGCAAAGGCAGAAAAGTATTATCAGCTTA-GGCCACTGAATAATGTCAGTGGTCTTTT hal GGAAAAAAGGAAGAAAAGTGCTATCTGCATAAGGCCACTG----ATGTCAGTGGTCTTTT -180 -170 -160 -150 -140 -130 sub TTCACGTTATGGGAAAAGATAGATGTGATGCGTAATGAACCGGGGCATGCTTCCTGGTTC hal T---CTTCAGGGGAAAAGATGG...................................... -120 -110 -100 -90 -80 -70 sub AGATGCATCTCATGTTCATAATAAATTTTAAAAGTTTCTGCCAGCCAGTATCGGAGTGAG hal ............................................................ -60 -50 -40 -30 -20 -10 sub TCAT hal .... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...