# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--STE12/seqs-shuffled # positives: 656 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--STE12/seqs-centered (Sat Jan 18 00:09:19 PST 2020) # negatives: 656 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--STE12/seqs-shuffled (Sat Jan 18 00:09:19 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:28:24 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 0.295 C 0.209 G 0.203 T 0.293 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 108 5 1.8e-028 5.7e-024 # GGTTCGA TCGAACC 86 2 7.3e-025 2.4e-020 # GGATCGA TCGATCC 31 3 2.8e-007 9.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 5.7e-024 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 86 16 6.1e-014 2.0e-009 # AGTGGTT AACCACT 61 8 5.3e-012 1.7e-007 # AGTGGTA TACCACT 36 8 9.4e-006 3.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 2.0e-009 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.363636 0.000000 0.000000 0.636364 MOTIF ARAAAAAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAAW WTTTTTYT 135 46 3.6e-013 1.2e-008 # AAAAAAAT ATTTTTTT 67 22 4.2e-007 1.3e-002 # AGAAAAAA TTTTTTCT 42 11 7.7e-006 2.5e-001 # AAAAAAAA TTTTTTTT 57 23 5.7e-005 1.9e+000 # AGAAAAAT ATTTTTCT 18 5 5.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 153 E= 1.2e-008 1.000000 0.000000 0.000000 0.000000 0.679739 0.000000 0.320261 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 1.000000 0.000000 0.000000 0.000000 0.529412 0.000000 0.000000 0.470588 MOTIF CWTGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CWTGGCC GGCCAWG 47 6 1.5e-009 4.9e-005 # CTTGGCC GGCCAAG 36 4 6.3e-008 2.0e-003 # CATGGCC GGCCATG 19 2 9.9e-005 3.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 4.9e-005 0.000000 1.000000 0.000000 0.000000 0.361702 0.000000 0.000000 0.638298 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 26 0 1.2e-008 3.7e-004 # AGATCGGG CCCGATCT 16 0 1.4e-005 4.5e-001 # AGATCGTG CACGATCT 10 0 9.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.7e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.615385 0.384615 0.000000 0.000000 1.000000 0.000000 MOTIF CGCCTTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 35 3 2.3e-008 7.3e-004 # CGCCTTA TAAGGCG 35 3 2.3e-008 7.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 7.3e-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 GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 25 0 2.4e-008 7.6e-004 # GCGCTACC GGTAGCGC 18 0 3.4e-006 1.1e-001 # GCTCTACC GGTAGAGC 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.6e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.720000 0.280000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AMGATGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AMGATGG CCATCKT 46 8 3.9e-008 1.3e-003 # ACGATGG CCATCGT 24 2 4.4e-006 1.4e-001 # AAGATGG CCATCTT 22 6 1.7e-003 5.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 1.3e-003 1.000000 0.000000 0.000000 0.000000 0.478261 0.521739 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATAGTKTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 26 1 1.7e-007 5.3e-003 # ATAGTGTA TACACTAT 14 0 5.7e-005 1.8e+000 # ATAGTTTA TAAACTAT 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.538462 0.461538 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 22 0 2.0e-007 6.4e-003 # CGTGTTAA TTAACACG 14 0 5.7e-005 1.8e+000 # CGTGCTAA TTAGCACG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.4e-003 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 0.363636 0.000000 0.636364 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTCTYCC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTCTYCC GGRAGAG 28 2 3.4e-007 1.1e-002 # CTCTTCC GGAAGAG 12 0 2.3e-004 7.4e+000 # CTCTCCC GGGAGAG 16 2 6.1e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 1.1e-002 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 0.000000 0.571429 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 106 48 3.9e-007 1.2e-002 # CGCCCA TGGGCG 45 17 1.8e-004 5.8e+000 # CACCCA TGGGTG 64 31 2.9e-004 9.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 125 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.640000 0.000000 0.360000 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCTTCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCTTCCA TGGAAGC 21 0 4.1e-007 1.3e-002 # GCTTCCA TGGAAGC 21 0 4.1e-007 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 22 E= 1.3e-002 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 57.28 seconds