Similar regions between promoters of yhaA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCCATCGCAAAGCTCTTTTCGTCCGCTCTCCATGCCGATCCCGCTATTCTGACCGCGCTC hal ............................................................ ste ...............TTTTTGTCCGCTCCCAAGACGGA...................... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>> sub GGACAAATCTCTGCCATCTGGGTGGGCGGAGGAACACTGGTCCCATGGGCT----TTGAT hal ...................................ACTCGCCCCTTGTGCGCACATTGAT ste .....................GCGCGCGGCGGAGGCGGCGTGCCAAAAACT----TGGCT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sub TCCCGCCGCGGCCATTTGCAAAGTTGATCCTTTTGAGCTTGCCAGAAAAAACTTCATT-C hal TCCTTCGGGGG...........GGTGAACTTTATGAGATT.................... ste GCCCGTCG......................................AAAAACTTGGCTGC -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CCGTCGCGATTGGCCTTTTGGTGACAACCCTCGCAGCTGTGATGATGCTTTAAAACAGCA hal ........................................GATTATGCTCCAGATCGGAA ste CCGTCG.........TTTGGCTGCCGAGCGGCGCAGC....................... -120 -110 -100 -90 -80 -70 sub TGAGTTGAAATATTCAGACTTTTTCTATACAATCATGGAAAAG-CATA-GAAAAGGGGGA hal TCA.....AATAAACAGACTTTTCTTTTA..................A-GAAAAAGATGG ste ..............................AATAACGAAAAAGACAAACGAACAGGGGGA -60 -50 -40 -30 -20 -10 sub AGCGGCT hal AGGGGAT ste ....... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...