Similar regions between promoters of glyA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTCTCAAAACAGCCTCGGTTCAGCTCATGTGACATTGGCGCGTACACGGCCGAAACTAAT hal ......................GCCCATGTAACCATGGCTTACTCTCGACCGAAGCTGAT ste ............CATTGGATCGGCGTGCGTGACGCTGGCGAAAACGCGGCCGAAGCTGAT -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>]]]]]]]]]]]]]]]]]]]]]]]]]] sub CGGCGGAGTGCGGGCGGTTTATGAGTGCGAATGAAAGGACTGCATAGCCAGTCTTTTCTT hal TGGCGGTGTGCGCGCCAATTATGAA--CGAACAGAAGAAC---AT-GAAAGTTTTCGCTG ste CGGCGGCGCCCGAGCGGTCTACTCGTTGGAA.................CATTTTTTTCTT -240 -230 -220 -210 -200 -190 ]] sub TTATTTTAAGATAGTGAAATAAATTCCGAACTTTAAATTAAATTTAAGTTATTAATATTC hal TTAATTTCAAA...................................AGGCATTGATATTG ste TGAATTT..................................................... -180 -170 -160 -150 -140 -130 sub GTTTTTACCAATAAAAATTTAGATTTTTTAAAAATAATCTTTTACATCGGCCTTAAAAAC hal GT........................TTTCAAAATTAT...................... ste .........AATAAAAACGAATATT.............CATTGACATCGGCCATA..... -120 -110 -100 -90 -80 -70 sub CATGTACAATAGTGATGGTAAAAACAAAGAACAGGATACGGATAGGAGAGGATCTCGCTG hal ..........................AAGAACATGAAA...AGAGGAGAGGA........ ste ..................TAAAAACGAATA.........GGATCGGCGTGCGTGACGCTG -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...