Similar regions between promoters of yvyC

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGGCTTCTCAAGCTATGCTTGCTCAAGCAAACCAACAGCCGCAAAACGTACTTCAATTAT hal AAGCGTCTCAAGCGATGCTTGCTCAAGCAAACCAACAGCCACAAGCTGTATTACAATTAC -300 -290 -280 -270 -260 -250 >>>>>>>> ]]]]]]]]]]] ]]]]]]]]]] sub TACGTTAATTT---TAAA---AAAGACCTTGGCGT-TGCCAGGGTCTTTTAATTTAAATT hal TTCGTTAATTTGCTTCCATTTAAAGATCTGGATTTATTCCAGGTCTTTTTTATTT..... -240 -230 -220 -210 -200 -190 sub TCTATCTCCTAATCATTCCTCATCCTGTCACTAACTCATGATATAATAACCGGATTCTCC hal .......................................GATATAATA............ -180 -170 -160 -150 -140 -130 sub ACTAACTTTTTATAAATGTATTTCC-ATACAAGAAATCTAAAACAGAAGATTTTTTTCCA hal ........TTTAGGAATGAGATACCGATATAATAGATATGAAA................. -120 -110 -100 -90 -80 -70 sub AAAATATGTGTAATCTTATCTCGACTTAGTCGATATAAACGATAGATTGGGGCATAGGGG hal .AAAGTTTAGGAATGAGATACCGATATAATAGATATGAA..................... -60 -50 -40 -30 -20 -10 sub ATGATCAA hal ........ -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...