Similar regions between promoters of polA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> sub GGACGGGGAACTGTCTTTACCGTGACGCTGAAAC-GGGCCGCTGAAAAGTCCGCCTAATG hal ..........................................................TG ste ................TTACCGTAGCGAGCAAAGTGGGGCGCGGCACCGT.......... -300 -290 -280 -270 -260 -250 sub TTTACAAAGGTTTAACAATATCTTCATGCACTGTTAAACCTATGCTGGTAGGATGTAGTA hal GTTACACAGG.......AAAACTTCATTCAGTG........ATGCTGGTTGCA....... ste .............................ATTGTGAAACATTTGGTTG............ -240 -230 -220 -210 -200 -190 ]]]]]]]]]]]]]]]]]]]]]]]] ]] sub GAACCCCTTCATCCAAGGAGCCAATTTTGACGGCGGGAACCTATTTGTGTTCCCG-TCCT hal ................................GCGGGAGCCT..TTGTTGTCCCC-TCAC ste .........CATCCGAGGAG..........................GTGTTCACGATCCA -180 -170 -160 -150 -140 -130 sub TTTTTGTGTCTTCTCTTATAGTTCACGTATTTTCCTTTCAAATTGAACTT-TGTTAAAAT hal TAAATGTGAC...................TTTTTCTTTCAAATCCTTCATGTGATAAAAT ste TTTT........................................................ -120 -110 -100 -90 -80 -70 sub AAGAGGAGCTAATGACTATGTAAGAGATGAATGGAAGCCTGAGGCTTCTTAGGAGGAAAT hal AAGGTGA........................TTGAAGCGGGAGCCTT............. ste ................TAAGCAGGGGATGAATCGGCGCCT..GGCTTCTTTTGA...... -60 -50 -40 -30 -20 -10 sub TGA hal ... ste ... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...