Similar regions between promoters of pyrR

>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTTCACGCGGCGAGTTTTAGGTTTTGACCATCCACGAACAGGAGAATATGTCGAATTTGA hal .....................................ACCGGTGAATTTATGCGCTTTAA -300 -290 -280 -270 -260 -250 sub AGCGCCGCTTCCCGAGGATATGGCAGAATTAATCGAAAACCTCAGAAAAAACGGTTGACA hal AGTAGAAATGCCAGAAGAGATGAAAAAACTCATCAGACAATTGCAAAATAACCGTTGACA -240 -230 -220 -210 -200 -190 @@@@@@@@@@@@ sub -GAGGGTTTCTTTTCTGAAATAATAA-ACGAAGC------TGAATA-GATTCTTTAAAAC hal CGATCGTCGCATTT-TGTCATAATTGCACCAAGCGAGAATTGAATAAGCTCCTTTAATGT -180 -170 -160 -150 -140 -130 @@@@@@@@@@@@@@@@@@@@@@ @ sub -AGTCCAGAGAGGCTGAGAAGGA-TAACGGATAGACGGGATG-CGTGTATAGGCGCGCAC hal TAGTCCAGTGAGGCTAAGAAGGAATCACGAAAACGCCGCTCGTCGTTTTCATGACTTTAG -120 -110 -100 -90 -80 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ ]]]]]]]]]]]]]]]]]]]]]]]]]] sub CTTGTCCTAAAACCCCTCTATGCTCTGGCAGGAGGGGTTTTTTCTTCTATATGAACTGTG hal GTAA--CGTATACCCTTCTGCCCTTTGGACAGAAGGGTTTTT............ACTTGG -70 -60 -50 -40 -30 -20 sub AGGTGTCACACA hal AGGTGTCACA.. -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...