Similar regions between promoters of ydcD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAGTCACATTAATAGGCCGGCAGGGGGATGAATATATTTCCATGGATGAGATTGCAGGAA hal ...TGAGAATAATAGGGAGTTTTGCCGAAAAATATA...............TAGCAAAAC ste AGGTGACATTAATTGGCCGCCAAGGGGACGAAGTCATTTCCATCGATGATGTCGCCCGCC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGCTCGAAACCATTAACTATGAGGTGGCCTGTACAATAAGTTCCCGTGTTCCCCGTATGT hal GGCTGAACACCATTAACTATGAAATTCCTTGCGTGATTTCGTGGCGGGTACCGCGTATAT ste ATTTGGGCACAATCAATTATGAAGTGCCGTGCACGATCAGCTACCGGGTGCCCCGTATTT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >>>>>>>>>>>>>>>>>>> sub TTTTGGAAAATGGGAGTATAATGGAAGTAAGAAAT--CC--TTTATTGCAGGTAAATATA hal ATTTTCGAGATGGACAAATAATATCTGTTAAAAATAACC--TTTTGTG............ ste TTTTCCGAAATAAGCGTATAATGGAAGTGAGAAAC--GCCGTTGGCCGCGGATGAAGCGA -180 -170 -160 -150 -140 -130 >>>> >>>>> sub AGCA--ATTAACTTACCTAAATGGAGAATTCATAAAACAGCTTTGC--TTGAAGAG---- hal ........TATATTTTCGAGATGGACAAATAATA.................AAGTT---- ste TGCATAATCTGCTTCGGAAGACAAAGGATAGAAAATGGAGAAATGACTTTGCAGCGCCGT -120 -110 -100 -90 -80 sub TGAATAATGGTATCATTATCACTGGATGGATAAAAGAGTCGTATCCGTAAGTTTGGTGGA hal AGAATGATTGAATGACTA.......................................... ste TGTTTAATGGTATCATGA--AGTGGAAGCAATCAATGGCTGCAG--------TTCGTGGA -70 -60 -50 -40 -30 -20 sub GGTGTATGTTTT hal ............ ste GGTGTATATTT. -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...