# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RPB2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RPB2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RPB2/seqs-shuffled # positives: 1741 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RPB2/seqs-centered (Sat Jan 18 05:20:33 PST 2020) # negatives: 1741 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RPB2/seqs-shuffled (Sat Jan 18 05:20:33 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:29:32 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 0.301 C 0.202 G 0.199 T 0.299 MOTIF TACCR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TACCR YGGTA 659 334 8.9e-035 3.2e-030 # TACCA TGGTA 497 243 2.2e-026 7.9e-022 # TACCG CGGTA 261 105 1.9e-018 6.9e-014 letter-probability matrix: alength= 4 w= 5 nsites= 867 E= 3.2e-030 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.663206 0.000000 0.336794 0.000000 MOTIF AMGAAGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AMGAAGR YCTTCKT 336 116 1.2e-029 4.2e-025 # AAGAAGG CCTTCTT 155 42 1.5e-017 5.1e-013 # AAGAAGA TCTTCTT 137 54 2.9e-010 1.0e-005 # ACGAAGA TCTTCGT 40 14 2.4e-004 8.6e+000 # ACGAAGG CCTTCGT 30 12 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 379 E= 4.2e-025 1.000000 0.000000 0.000000 0.000000 0.812665 0.187335 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.496042 0.000000 0.503958 0.000000 MOTIF AHTGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AHTGG CCADT 1007 747 7.2e-019 2.5e-014 # AATGG CCATT 514 332 3.7e-013 1.3e-008 # ATTGG CCAAT 471 322 1.0e-009 3.6e-005 # ACTGG CCAGT 308 226 6.8e-005 2.4e+000 letter-probability matrix: alength= 4 w= 5 nsites= 1420 E= 2.5e-014 1.000000 0.000000 0.000000 0.000000 0.409155 0.232394 0.000000 0.358451 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF SAAGR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST SAAGR YCTTS 1284 1049 1.4e-017 4.7e-013 # CAAGA TCTTG 638 420 5.4e-016 1.8e-011 # GAAGA TCTTC 528 414 8.0e-006 2.7e-001 # CAAGG CCTTG 397 309 1.2e-004 4.1e+000 # GAAGG CCTTC 351 283 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 5 nsites= 2238 E= 4.7e-013 0.000000 0.535746 0.464254 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 0.643432 0.000000 0.356568 0.000000 MOTIF CGAYG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGAYG CRTCG 383 230 5.5e-012 1.7e-007 # CGACG CGTCG 136 65 1.4e-007 4.4e-003 # CGATG CATCG 273 173 2.4e-007 7.4e-003 letter-probability matrix: alength= 4 w= 5 nsites= 423 E= 1.7e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.309693 0.000000 0.690307 0.000000 0.000000 1.000000 0.000000 MOTIF TGBTCAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TGBTCAA TTGAVCA 173 75 4.9e-011 1.5e-006 # TGTTCAA TTGAACA 90 40 4.7e-006 1.4e-001 # TGGTCAA TTGACCA 43 11 6.0e-006 1.9e-001 # TGCTCAA TTGAGCA 48 25 4.4e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 183 E= 1.5e-006 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.262295 0.234973 0.502732 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTCTARC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTCTARC GYTAGAG 73 17 6.2e-010 1.9e-005 # CTCTAAC GTTAGAG 43 9 8.6e-007 2.6e-002 # CTCTAGC GCTAGAG 30 8 2.2e-004 6.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 1.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.573333 0.000000 0.426667 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRGCACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRGCACC GGTGCYG 47 6 2.3e-009 6.9e-005 # CGGCACC GGTGCCG 16 0 1.5e-005 4.5e-001 # CAGCACC GGTGCTG 31 6 1.9e-005 5.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 6.9e-005 0.000000 1.000000 0.000000 0.000000 0.659574 0.000000 0.340426 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 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 0.000000 MOTIF GTAAGCAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTAAGCAC GTGCTTAC 27 0 6.7e-009 2.0e-004 # GTAAGCAC GTGCTTAC 27 0 6.7e-009 2.0e-004 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.0e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTKTGAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTKTGAC GTCAMAG 86 27 7.0e-009 2.1e-004 # CTGTGAC GTCACAG 46 11 1.4e-006 4.2e-002 # CTTTGAC GTCAAAG 40 16 8.5e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 2.1e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.534884 0.465116 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCAAAGM DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCAAAGM KCTTTGG 119 48 8.9e-009 2.7e-004 # CCAAAGC GCTTTGG 48 15 1.6e-005 4.9e-001 # CCAAAGA TCTTTGG 73 34 8.2e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 119 E= 2.7e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.596639 0.403361 0.000000 0.000000 MOTIF ACSATCTG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACSATCTG CAGATSGT 26 0 1.4e-008 4.1e-004 # ACGATCTG CAGATCGT 15 0 3.0e-005 8.9e-001 # ACCATCTG CAGATGGT 11 0 4.8e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.423077 0.576923 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGCAKCAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGCAKCAG CTGMTGCT 41 5 1.8e-008 5.5e-004 # AGCAGCAG CTGCTGCT 23 3 4.2e-005 1.3e+000 # AGCATCAG CTGATGCT 18 2 1.9e-004 5.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 5.5e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGKAGATA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGKAGATA TATCTMCT 36 4 8.0e-008 2.4e-003 # AGGAGATA TATCTCCT 20 1 1.0e-005 3.0e-001 # AGTAGATA TATCTACT 16 3 2.2e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.555556 0.444444 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GSTAAGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GSTAAGA TCTTASC 68 20 9.9e-008 3.0e-003 # GGTAAGA TCTTACC 32 8 8.4e-005 2.5e+000 # GCTAAGA TCTTAGC 36 12 3.3e-004 9.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 3.0e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.529412 0.470588 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AACATSTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AACATSTA TASATGTT 51 11 1.1e-007 3.3e-003 # AACATCTA TAGATGTT 27 6 1.5e-004 4.6e+000 # AACATGTA TACATGTT 24 5 2.6e-004 7.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 3.3e-003 1.000000 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.529412 0.470588 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAAGCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACCAAGCC GGCTTGGT 23 0 1.1e-007 3.3e-003 # ACCAAGCC GGCTTGGT 23 0 1.1e-007 3.3e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.3e-003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCRGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACCRGC GCYGGT 118 52 1.2e-007 3.5e-003 # ACCAGC GCTGGT 84 38 1.4e-005 4.1e-001 # ACCGGC GCCGGT 36 15 2.2e-003 6.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 122 E= 3.5e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.704918 0.000000 0.295082 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TAGAAAKA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TAGAAAKA TMTTTCTA 58 15 1.6e-007 4.7e-003 # TAGAAATA TATTTCTA 30 8 2.2e-004 6.6e+000 # TAGAAAGA TCTTTCTA 28 8 5.6e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 4.7e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.482759 0.517241 1.000000 0.000000 0.000000 0.000000 MOTIF GAACTYTA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GAACTYTA TARAGTTC 46 9 1.8e-007 5.3e-003 # GAACTCTA TAGAGTTC 25 2 2.6e-006 7.8e-002 # GAACTTTA TAAAGTTC 21 7 6.1e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 5.3e-003 0.000000 0.000000 1.000000 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 0.543478 0.000000 0.456522 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTTCTCY DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CGTTCTCY RGAGAACG 25 1 3.7e-007 1.1e-002 # CGTTCTCC GGAGAACG 18 1 3.7e-005 1.1e+000 # CGTTCTCT AGAGAACG 7 0 7.8e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.720000 0.000000 0.280000 MOTIF GCCATRAC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GCCATRAC GTYATGGC 25 1 3.7e-007 1.1e-002 # GCCATAAC GTTATGGC 15 1 2.5e-004 7.5e+000 # GCCATGAC GTCATGGC 10 0 9.6e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 0.000000 0.000000 1.000000 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 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RGAATCCA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST RGAATCCA TGGATTCY 30 3 6.3e-007 1.9e-002 # GGAATCCA TGGATTCC 15 1 2.5e-004 7.5e+000 # AGAATCCA TGGATTCT 15 2 1.1e-003 3.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.9e-002 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGYACTTG DREME-24 # Word RC Word Pos Neg P-value E-value # BEST AGYACTTG CAAGTRCT 29 3 1.2e-006 3.4e-002 # AGCACTTG CAAGTGCT 15 1 2.5e-004 7.5e+000 # AGTACTTG CAAGTACT 14 2 2.1e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.517241 0.000000 0.482759 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 211.76 seconds