Similar regions between promoters of hrcA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGAGGAAGAAATGTTTTTAGGTTTGAGAAAAACAGCCGGTGTCAGCAAAAAACGATTCGC hal ........AAGTGTCTTTATGT........AACAGTGGAAGGCATGAAAAA....TACGT ste ....GAGGAAATGTTTTTAGGGCTGCGCAAAACGGAAGGGGTGTCCAAAGCCTGCTTTCG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGAAAAATACGGCCGTTCCCTGGATGGACTTTTCCCAAGCGTGTTAAAAGACCTCGCT-- hal TGACAAATAGGGACCTT........................................... ste GCAAAAGTTCGGCCGCGACCTCCACGACATATTTG---GCGCGGCGATCCGCCGGGAAAT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sub -GAAAAAGGGCTGATTCACAATTCGGAGTCTGCCGTTTATTTGACTCATCAAGGAAAT-T hal ....................................................GGCTAT-T ste CGAAAACGGACGCCTCGAGGAAACGGAGACTCACATCCGCTTGACAAAACGGGGCAAGCT -180 -170 -160 -150 -140 -130 >>>>> sub ATTAGGCAATGAAGTTTTTGGCGCTTTTTTTGGGTGA--GTTATAATTGACATTTTTCTT hal ATTAGGAAATGAAGTATTCG.......TTTTTGATAA--GTTA................. ste GCTCGGCAATGAAGTGTTTGCCGCGTTCCTCGGTGAAATGTAAACATTGACATTTGCCGG -120 -110 -100 -90 -80 -70 @@@@@@@@@@@@@@@@@@@@@@@@@@@ sub GTGGTTTGATACTTTTGTTATAGAATTAGCACTCGCTTATTGAGAGTGCTAACAGAGGTG hal ....TTTGATAAGTTAGCAATAGATTTAGCACTCGAACTATGAGAGTGCTAACAGTGG.. ste GCGATTTGCTACCCTAGTAGTAGATTTAGCACTCGAATTGTTCGAGTGCTAACAGAGGTG -60 -50 -40 -30 -20 -10 sub ATGATG hal ...... ste A..... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...