Similar regions between promoters of secA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGAAGAAGCGATCTTGCAAATGAATATGCTCGGCCATAATTTCTTTGTTTTCACAAATGC hal ................................GACATGAATTTATTGTTAACGCGAATG. ste ...................ATGAATAAGTGAGTCCATGA..................... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> sub GGAAACAAACCTTACAAATGTCGTGTACCGCAGAAATGACGGG-AAATATGGCTTAATTG hal .................................AAATGAAGGG-TAAGTTTGTATTATTC ste .GAAACGCAGCTTGTGGATGACGTGCA........ATGACGTGCAAATATTGCTT..... -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>> ]]]]]]]]]]]]]]]]]]]]]]] sub AACCGACTGAATAATGAAGAGAAGCCTTCCGTGATGTCCGCGGAAGGTTTTTGTTTTTCT hal ATCGT--TTAATAATAACGA............................TTTGGACTTGGT ste ............................................................ -180 -170 -160 -150 -140 -130 sub TATTTGCAAATTCTTTGGAAATAACAAAAGGTATGATATGATAATGAGAGGTATACATGG hal GACTGGCCAAGTTTTTGTAAGGAG-AAAAGAAAAGTGAGGCGAATG.......TACATAA ste ................................ATGATATGATGAATAAGTGAGTCCATGA -120 -110 -100 -90 -80 -70 sub ACTAGTAAATTATTTATACATGCCTCTAAAATAGGCGTGTGATGATAGAGGAGCGTTATA hal AATGGAAGATCCTATAGCCTTGTCTTGTTATTAGG......................... ste A...........TTTGGACATGCCCCT.....................AGGAGCGTT... -60 -50 -40 -30 -20 -10 sub A hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...