Similar regions between promoters of appD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATACGCAGTTGGATTCAATATTGTAAAAAAATATTTAACCGCCAGCAAGGCAAGCACCGC hal .........................................................CGC ste ...................ATGGTAAAAAAAGGATTACC..................... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AGACGGGCTGTCCATTCCTGCTGAGACCTTTTTGGATGCAATGCTTTAAAAGGATAAAAT hal TGACGG...................................................... ste ............................................................ -240 -230 -220 -210 -200 -190 sub AATGGAATTTCATTAATAATATTACATTTATCCTAAAAAATTCTTGATTTTGCAAAATGA hal ......................TCCATTTATCGTCA..........ATATTGCGACAAGC ste .................................TAAAAAATCCTTTGTTTTGCAAAAAGT -180 -170 -160 -150 -140 -130 sub TTGTAATAATATACAACTATAAAATTTTTCGATAATTCAATATTATTTATTATTTCTGAA hal TGGT...................ATTTATCGTCATTTCTACGTTA...ATTATTTTAGA. ste TATTCTGAAAAACTAAATAAAAAATCCTTTGTT........................... -120 -110 -100 -90 -80 -70 sub TAAAGGGATTGCTTTCTCTTGAAAACGTTTGACAACAA--GAGGGGGGAAAGGGGAGCTA hal .....................................A--GAGGGGGGATAG........ ste ....................GCAAAAGTTTCATCAAAATCGAATGAGAGAAGGGGAGC.. -60 -50 -40 -30 -20 -10 sub GC hal .. ste .. -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...