Similar regions between promoters of smc

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGCAGCGGGACGGCAAAGGCTCTCTGGAGTATAAAATCTCCAACGAAAAAGGACCTGCGC hal ....................TCGCTCTATGATAAAAT....................... ste .......GGAGAGCAAACGCT......................CGAAAAAGGA....... -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> sub ACAACCGTGAATTTGAAGCCATCGTATCTCTAAAAGGT-GAACCACTCGGAGTCGGAAAC hal ...................CATCGTATC................................ ste ....................ATGGTAGGATGAAAAGATCGAACGTCTCGGTTTCCCAAAA -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GGCCGTTCAAAGAAAGAAGCCGAACAGCACGCTGCTCAGGAAGCTTTAGCTAAATTGCAA hal ............................................................ ste GGGC..TCGAAAAAGGAAGCTGAACAGCATGCGGCGCAAATGGCGCTCGAAACGTTGC.. -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>]]]]]]]]]]]]]]]]]]]]]]]]]]]] sub AAACACCATACGAAACAATAAAATCCCCCTTATGACTCAGGGGGATTTCAGTATGTATGC hal ........TATGATAAAATAAA...................................... ste .......................TTCCCAAAAGGGCTCCGGGGTGTTTGTGT........ -120 -110 -100 -90 -80 -70 sub CGTCTTATTTGACCAATGTTTATGATAGAATTGAAATACTTATTACATAAGGAGGATCGC hal .GTCTTATT.........TCTATGATAAAAT--AAATAGGCTGTAGAAAGTGAGGTTTG. ste ....................TATGGTAGGATGAAAAGA...................... -60 -50 -40 -30 -20 -10 sub T hal . ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...