Similar regions between promoters of yngD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTTCAGAAATGATCATTGATGCTGTTATCCCAGCCAATTCGCTGCGTGATGAGCTGGCCA hal ............................................................ ste ..............................CGGCGAACCCGCCGCGTACGGATATGAACA -300 -290 -280 -270 -260 -250 >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AA-CGGCTCAAGGCATACATGACAAAGGAAATGACATTTACCAATCGAAAGCATCCGGTT hal ..........AAGCATTTATTAAAAAGG................................ ste AAACGGCATCATCGATAC..............GATATGAACAAAACGGCATCATC..... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>> sub TATCCGGTGTAAAAGCAAGAACTTAGGAGCGCAAAAAAAGC---GCTCCTTTATATATTT hal ..........AGAAGTAAAAACTGAAGAACAAAAAGAAGTCAAAGAGCAATTAGACAAAT ste ..............................GCACAAAAAGT---GCTGCT....ATATGA -180 -170 -160 -150 -140 -130 sub ACAATAACAACATTATGTCAACTAATTACCATTGCATAAAACGCTTGGTTTTTTAGAATA hal ACAAGGGCAAGCTTAAGCGA--GACGTCGTTTACCCTAAAAACTTAAACTATCAAAAATA ste ACAA-AACGGCATCAT...............TTGCAAAAAA................... -120 -110 -100 -90 -80 -70 sub GTAAATAAAGG---CTGCCGCACCTCTAGCGGCAATTGTCAGTTTATCATAAAAAGGGGC hal CCCAATGAAAGAATCTACTTCAGCTGTAGAAGCATTTATTAGTTTACCCTAAAAA..... ste .........GG---CTGTTGCCGCTCTTG...........AGTTTGTGACAAAAAGGTG. -60 -50 -40 -30 -20 -10 sub CTACATT hal ....... ste ....... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...