Similar regions between promoters of cotX

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GAAAAAAGTATCAGACGAAGAAAAAGAAATGCTCTTAAATCTTGTAAAAGACTTACAAGC hal ..........................................TGTTGAAACCTTTTTGGC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TAAATCACAAGCGCTAATAGAAAACCAAAAGAAGAAAAAAGAAGAAGCAGCCGCACAAGA hal CAACCAACAAAAACGAATA---AATAAAACAAACGATAACGACCAAGCTCCAGAAAAATA -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub -GCAAAAGAACACAAAACCGTTAAGCCGCAGAGAGCAGCTCATTGAACAGATCAGACAAA hal AGCAAAACAGCTAAAA....................................CAGAAAAA -180 -170 -160 -150 -140 -130 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@ >>>>>>>>>>>>>>>>>>>>>>> sub GACGGAAAAACGATAACAATTAGCCAA-TCATAAAAAATAGGGTTCTTCATCAGGATATA hal TAAGCAAAACAGCTAAAATTCAACGAAATCATCA.......................... -120 -110 -100 -90 -80 -70 @@@@@@@@@@ sub TGACTCAGTCAAAATAAGAGGCTCGCTCATTTAATAACAGTAAAAGAA--AAGGAGGAAT hal ......................TCGTTCATACATTATCGTAGAAGGAAGAAAGGGGGAAT -60 -50 -40 -30 -20 -10 sub AGAT hal A... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...