Similar regions between promoters of yuiA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTGTTTATGGCAGAAAGCTGAAAGGCACGCCCGCTTCGTTTATGAAAAAAGTCATTGATA hal ........................................TATAAATGAAATGATTGCTA ste ...........................................GACGAAAATGGGGGAGA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACCGCTCACTGTTTATGATTGGCGGACTCGGACTGACATTGAAAAAAGGCAAGTTCAAGT hal ........................GAACCGGAAAAACATTGAA................. ste ATCGCTGTTTGTTTTT............................................ -240 -230 -220 -210 -200 -190 >>>>>>>> ]]]]]]]]]]]]]] sub TTTTCTAAAAACCCGCGGAAGCGGGTTTTCTTTATTAAAAAACGCCAAAATAAAAAGAGA hal .........................TTGTATCGATGAAAACGTTAGAAAATTCAAAGAAT ste ......................................................AAGAAA -180 -170 -160 -150 -140 -130 sub ACG-AGAGGAAAACAAGTATGTTTCCGCTTACATCAAAAGATTTGTCACATGATCTGACT hal TCGTAGATAGAGTCAATT--GATTACGCTTACATGTGAGAATACCTCGCA-------ATT ste ATA-AAAGCGATCGAAAGATGTATCCGCTTACACGGACGAAAATGGGGGAGAATCGCTGT -120 -110 -100 -90 -80 -70 sub TTATTGTTGACAGCTTGATATGGTATATTATCAGAAAATTAAGAAAAAGGGTGATGATTA hal GTCATGTTTA----TTTGTATTGAAAATTCTGATAATATAAATGAAATGATTGCT..... ste TTGTTTTT-ACAGAAAATTTTGATATATTAACAAAAAAAGAA.................. -60 -50 -40 -30 -20 -10 sub G hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...