# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWR1/seqs-shuffled # positives: 543 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWR1/seqs-centered (Sat Jan 18 21:44:06 PST 2020) # negatives: 543 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWR1/seqs-shuffled (Sat Jan 18 21:44:06 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:57:11 PST 2020 MEME version 4.12.0 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.303 C 0.199 G 0.197 T 0.302 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 81 2 1.7e-023 5.0e-019 # GGGTTCGA TCGAACCC 27 0 5.3e-009 1.6e-004 # CGGTTCGA TCGAACCG 30 1 1.0e-008 3.0e-004 # GAGTTCGA TCGAACTC 15 1 2.4e-004 7.2e+000 # CAGTTCGA TCGAACTG 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 5.0e-019 0.000000 0.481481 0.518519 0.000000 0.296296 0.000000 0.703704 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAWAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAW WTWTTTTT 139 51 8.6e-013 2.6e-008 # AAAAAAAT ATTTTTTT 73 18 5.5e-010 1.7e-005 # AAAAATAA TTATTTTT 45 13 9.2e-006 2.8e-001 # AAAAAAAA TTTTTTTT 59 23 2.3e-005 6.8e-001 # AAAAATAT ATATTTTT 26 9 2.6e-003 7.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 159 E= 2.6e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.616352 0.000000 0.000000 0.383648 1.000000 0.000000 0.000000 0.000000 0.540881 0.000000 0.000000 0.459119 MOTIF ACCDCT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCDCT AGHGGT 124 46 3.3e-011 9.9e-007 # ACCACT AGTGGT 74 26 2.6e-007 7.7e-003 # ACCTCT AGAGGT 35 12 4.2e-004 1.3e+001 # ACCGCT AGCGGT 22 8 7.4e-003 2.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 144 E= 9.9e-007 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.590278 0.000000 0.152778 0.256944 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ACCAACTK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCAACTK MAGTTGGT 38 2 4.1e-010 1.2e-005 # ACCAACTT AAGTTGGT 21 1 4.6e-006 1.3e-001 # ACCAACTG CAGTTGGT 17 1 6.5e-005 1.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.2e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.447368 0.552632 MOTIF CGCCTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 34 2 6.0e-009 1.8e-004 # CGCCTTA TAAGGCG 34 2 6.0e-009 1.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 25 1 3.1e-007 9.1e-003 # AGTCATAC GTATGACT 14 0 5.6e-005 1.6e+000 # AGTCAGAC GTCTGACT 11 1 3.0e-003 8.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.1e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.440000 0.560000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGGTTSAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GGGTTSAA TTSAACCC 21 0 3.9e-007 1.1e-002 # GGGTTCAA TTGAACCC 13 0 1.1e-004 3.3e+000 # GGGTTGAA TTCAACCC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.619048 0.380952 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTTATGGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTTATGGY RCCATAAC 20 0 8.0e-007 2.3e-002 # GTTATGGC GCCATAAC 11 0 4.6e-004 1.4e+001 # GTTATGGT ACCATAAC 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.550000 0.000000 0.450000 MOTIF AGCKCGC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGCKCGC GCGMGCT 26 2 1.2e-006 3.4e-002 # AGCGCGC GCGCGCT 13 1 8.6e-004 2.5e+001 # AGCTCGC GCGAGCT 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 19 0 1.6e-006 4.7e-002 # CGTGTTAA TTAACACG 10 0 9.4e-004 2.7e+001 # CGTGCTAA TTAGCACG 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.473684 0.000000 0.526316 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 39.18 seconds