Similar regions between promoters of yrvI

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGACCGCCGCGGATTGCTGAACGAGGTACTCCAGGCAGTGAATGAAACGAAAACCAATAT hal TGATCGGAATGGCTTATTGAACGAAGTCCTTCAGGCGGTGACGGAAAGCAAAACACTGAT ste ..................GAATGAGGTGCTGCAGGCGGTCAATGAAACGCGAACAGACAT -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTCATCTGTCTCTGGCAAATCGGATC---GCAATAAAGTGGCAACCATCCATATGGCGAT hal CAATGCTGTCTCAGGTCGTTCGGATCATCGAAATCGAGTGGCGACGATTCATATGACGAT ste TTCCGCCGTCTCGGGACGCTCCGATCACCGCCATAAAATCGCGACGATCCATATGACGAT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTTTATCCAGAATATCAATCACTTGCATAAAGTCGTCGAGCGTATTAAACAGATTAGAGA hal CTCTATTCACAACATCGACCACCTTCATAAAGTGGTTGAGAAAATTAAGCAGCTGAAGGA ste CGCCATTCATAATTTGAGCCACTTGCAAAAAGTGGTCGATCGAATCAAGCAAATTCCCGA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sub TATCTATTCTGTGCGCCGCGTCATGAACTA--AAGGGGTTAGAAAAGAG----------- hal CATTTATTCGGTCCGACGAGTGATGAATTA--GA.......................... ste CATTTATTCCGTCCAGCGCTTGATGAACAACTAAGGGCGGCGAAAGGAGGAAGGCGAGTG -120 -110 -100 -90 -80 sub --ATTAGTTGTTCAGCGAGTAACAGAAGCAAGCGTTACAGTGGACGAAGAGGTCGTCGGC hal .....AGTCCTTCAGGCGGTGACGGA---AAGCAAAACACTGATCAATGCTGTC...... ste AGAGCGGTCATCCAGCGGGCGAAAGAGGCCAAAGTCACCGTCGACGGCGAAGTTGTTGGT -70 -60 -50 -40 -30 -20 sub CAAATTGGACAAGGCCTT hal .................. ste GCCATTG........... -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...