Similar regions between promoters of cdd

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>> sub TGATAGGTGGTATGTTTTCGCTTGAACTTTTAAATACAGCCATTGAACAT-ACGGTTGAT hal .....GGTGGTGTGGTTGTGC.....................TTAAACATGACGGTCGA. ste ............................................................ -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TTAATAACTGACAAACATCACCCTCTTGCTAAAGCGGCCAAGGACGCTGCCGCCGGGGCT hal ............AAACATGACGGTCGAGCAA............................. ste ............................................................ -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GTTTGCGTTTTTGCCGTGATTTCGTGTATCATTGGTTTACTTATTTTTTTGCCAAAGCTG hal ...TGTGTTTTTACCG..........TGTCATTCATTTA....................G ste .......TTTTAACCAAGGAGTCGGGT-TCAT--GTCTCCTTTTTTGTTTGGATGTAAAT -180 -170 -160 -150 -140 -130 >>> sub TAATGGCTGAAAATT-CTTACATTTATTTTACATTTTTAGAAATGGGCGTGAAAAAAAGC hal TAACGTCAAAAGATTGCATCAATGTGTTTT.............................. ste TTATGTTAGTGAATT-TGCTCATCTACAGTAAAATAAAAGAAAGCAGCGT.......... -120 -110 -100 -90 -80 -70 sub GCGCGATTATGTAAAATATAAAGTGATAGC---GGTACCATTATAGGTAAGAGAGGAATG hal .....ATTATGATGAAAAGAAAATGATGGTTCGGGTGCGATCAAAAAGAGGAGATGAAT. ste ..........GTAAAATAAAAGAAAGCAGC---GTTTGC-TTGCAGGAAAGGAAG..... -60 -50 -40 -30 -20 -10 sub TACAC hal ..... ste ..... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...