Similar regions between promoters of yunC

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAATGGTGTATGCCGGCGTTGAGGTAGAAACGAAACGGCTCGATGACGGGATCACCCACG hal ............................AACGAGACGGAACGTTG............... ste AAATGGTGTACGACGGCGTGGACATCGAGGCCGGGCTCGAGGAGGACGGTCAATGGCATA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>> sub TCACTCGGATCACACTGAACGGGGAAGATATTGAAAAACATAAACAA-TACTCCGTTGCG hal ....................GGCGAACCTGTTGTCAAAGAGCAGCTT-TACGAGCTTGCC ste TCCGCCGCATTATGATCAACGGCGA-GCCGCTCAATCCCGAGCGCACGTATGAGGTGGCG -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GTGCTTGATATGTTTACGCTCGGCAAACTGTTTCCGTTGATTCGCGACGCTGCAGAAAAA hal ACCCTAGACATGTATACGTTCGGTTATTTGTTTCCGAAAATTGCAGAATCTCAGGAGAAG ste ACGACCGATATGTTTGCGATCGGCCACTTTTATCCGCAAATTCAGCGGGCGGCGGAAAAA -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAATATTTTATGCCGGAATTTTTGCGGGATCTGCTTGCTTGGAAGCTTGCACAATAAGGC hal CGGTATTTCATGCCGGAAATGCTTCGCGATGTGTTGGCGTGGCAGCT............. ste ACGTATTACATGCCGGAGTTTTTGCGCGATCTTCTCGCTTGGAAATTGGCCCAATA-GGC -120 -110 -100 -90 -80 -70 sub AGTCAGCCCACAACAAGCTGTGCCCTTCATCATAAAGTGATGA-ATG-AAG--GGAGTGG hal ...............................ATAAAGGGATGAGATG-AAGAAGGAGTG. ste AGGCA.............TTTTCCATGCTTCATACATTGGAGT-ATGGAAA--GGAGAG. -60 -50 -40 -30 -20 -10 sub TTGAC hal ..... ste ..... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...