Three Bioprospector runs Command used (your file names will vary): BioProspector -W 13 -i All_enriched_fragments.txt -f yeast_all -c 2 -t 1 -o 2001_all_rslt2 -e All_Fragments.txt & Top-scoring Motif Matrix Revised Motif: Width (13, 0); Score 934.902; Significance 24.93; Pvalue 1.652275e-137; Segments 443 Blk1 A G C T Con rCon Deg rDeg 1 59.7 20.3 11.4 8.6 A T A T 2 24.0 7.6 67.6 0.8 C G C G 3 88.7 4.7 5.4 1.3 A T A T 4 1.0 2.7 73.8 22.5 C G C G 5 12.4 0.9 86.3 0.4 C G C G 6 1.5 0.4 92.1 5.9 C G C G 7 67.7 27.7 0.4 4.2 A T R Y 8 9.5 6.0 33.0 51.4 T A Y R 9 80.2 12.3 0.4 7.1 A T A T 10 1.3 0.9 97.0 0.8 C G C G 11 80.2 0.2 19.2 0.4 A T A T 12 4.6 0.4 50.2 44.8 C G Y R 13 29.8 2.0 44.4 23.8 C G M K Second-scoring Motif Matrix Revised Motif: Width (13, 0); Score 931.327; Significance 24.76; Pvalue 1.238373e-135; Segments 442 Blk1 A G C T Con rCon Deg rDeg 1 22.7 43.6 2.5 31.2 G C K M 2 47.1 48.3 0.4 4.2 G C R Y 3 0.4 17.9 0.2 81.5 T A T A 4 0.8 97.0 0.9 1.3 G C G C 5 7.1 0.4 12.1 80.4 T A T A 6 50.2 30.9 6.5 12.4 A T R Y 7 3.9 1.3 25.7 69.0 T A Y R 8 8.4 89.6 0.2 1.7 G C G C 9 0.6 87.0 0.9 11.5 G C G C 10 21.4 75.8 1.8 1.0 G C G C 11 1.3 3.4 4.7 90.7 T A T A 12 0.6 69.3 7.4 22.7 G C G C 13 11.1 9.4 19.9 59.6 T A T A Third-scoring Motif Matrix Revised Motif: Width (13, 0); Score 926.475; Significance 24.52; Pvalue 4.137159e-133; Segments 438 Blk1 A G C T Con rCon Deg rDeg 1 24.1 44.0 2.0 29.9 G C K M 2 44.8 50.8 0.5 4.0 G C R Y 3 0.4 18.0 0.2 81.4 T A T A 4 1.1 96.8 0.9 1.3 G C G C 5 6.9 0.5 12.6 80.0 T A T A 6 51.8 33.2 5.9 9.2 A T R Y 7 3.8 0.5 28.0 67.8 T A Y R 8 5.8 91.8 0.2 2.2 G C G C 9 0.4 86.8 0.9 11.9 G C G C 10 22.7 73.5 2.7 1.1 G C G C 11 1.3 5.4 4.5 88.8 T A T A 12 0.8 67.2 7.4 24.5 G C G C 13 8.7 11.1 19.4 60.8 T A T A