Similar regions between promoters of recA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TCGGCATTTCCGCAAATGGTAAAGAAGAGGTTCACGAGTTTCACTTTGCGGGCTCCAGAA hal .....................................................TCCAAAG -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGGGGATCAGAAAACGCGGCGCTAAATACGGCTGCCATTTAATCTTAAAGCTTTTAGAGC hal CGGGAATCACA...........................................TAGAGG -240 -230 -220 -210 -200 -190 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ >>>>>>>> sub AAAAATAATATTTTCAGCACATTATCCTCCTAAGAAAACATGATTTCTCTGATACATTAT hal AGAGATGATA....CAGCAAAACCTCGTCCAAAG.......................... -180 -170 -160 -150 -140 -130 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ sub GATATTTTGATAGGAATCACGCCAAGAAAAAATCCGAATATGCGTTCGCTTTTTTC-TTG hal ........................ATAAAAAAAGCGAATAAATGTTCGTAAAAATGGTTG -120 -110 -100 -90 -80 -70 sub GCAAATCCCTTCAAACAGGGTATAGTATATGTAGTGGTAACATAAAGGAGGAAAAAATAG hal GCAAATGGATCAAAACATTGTATGATAGA..............AAAGGAACGAAACATAG -60 -50 -40 -30 -20 -10 sub A hal A -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...