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Table 3 Novel predicted regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

From: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Sequence Rank DATG WATG Orientation U/C Experiment Comments
CTGCGTCT 1 635.5 - → (p < 10-10) 2.70 - Unknown site
CGACACTCC 4 234 [0;1500] - 2.49 - Unknown site, positive regulation of growth (p < 10-7)
CTCCGCCC 14 440 [0;900] - 3.51 2(2/0) Unknown site, similar to Sp1
CGAGACC 20 738 [0;1900] - 1.34 30(7/23) Unknown site, embryonic development (p < 10-7)
CGCGACGC 23 457 [0;1900] - 2.34 - Unknown site
ATTTCGCAA 29 641 [0;1900] - 2.50 1(0/1) Unknown site
CGTAAATC 31 514 [0;600] - 2.78 - Unknown site
TTGCGGAC 39 253 [0;1700] - 1.43 - Unknown site
ATGATGCAA 44 600 [0;1600] - 0.88 - Unknown site
CGCGCTC 46 576 [0;900] - 2.73 2(0/2) Unknown site
TGGCGCC 49 770.5 [0;1800] - 1.01 - Unknown palindromic site
AACCGGTT 50 651 [0;1900] - 1.41 - Unknown palindromic site
TAAAGGCGC 61 524 [0;700] - 8.67 27(12/15) Unknown site
CGCGCGC 120 455 [0;600] - 5.40 11(3/8) Unknown site
CTAATCC 228 934 - → (p < 10-7) 1.20 - Unknown homeodomain site, similar to Bicoid
TACCGTA 242 975 [0;500] - 2.23 20(18/2) Unknown site
  1. k-mers shown here were selected from the list of 437 highest scoring k-mers based on their short median distance to ATG, short optimal window, significant orientation bias, strong over-representation ratio (U/C), presence in upstream regions of over/underexpressed genes in several microarray conditions, palindromicity or resemblance to known sites in other species.
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Genome Biology

ISSN: 1474-760X

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