# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SWI1/seqs-shuffled # positives: 685 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SWI1/seqs-centered (Sat Jan 18 01:06:21 PST 2020) # negatives: 685 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SWI1/seqs-shuffled (Sat Jan 18 01:06:21 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 01:22:49 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 0.298 C 0.202 G 0.202 T 0.298 MOTIF GTTCGANY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGANY RNTCGAAC 106 7 8.3e-026 2.9e-021 # GTTCGATC GATCGAAC 26 2 1.2e-006 4.2e-002 # GTTCGATT AATCGAAC 19 2 1.0e-004 3.4e+000 # GTTCGAAT ATTCGAAC 12 0 2.3e-004 8.0e+000 # GTTCGACT AGTCGAAC 13 1 8.7e-004 3.0e+001 # GTTCGAGT ACTCGAAC 9 0 1.9e-003 6.5e+001 # GTTCGAAC GTTCGAAC 10 1 5.7e-003 2.0e+002 # GTTCGAGC GCTCGAAC 10 1 5.7e-003 2.0e+002 # GTTCGACC GGTCGAAC 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 106 E= 2.9e-021 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 0.207547 0.188679 0.179245 0.424528 0.000000 0.500000 0.000000 0.500000 MOTIF AAAAAAKA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAKA TMTTTTTT 102 34 3.4e-010 1.1e-005 # AAAAAATA TATTTTTT 57 15 1.7e-007 5.7e-003 # AAAAAAGA TCTTTTTT 48 19 1.9e-004 6.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 106 E= 1.1e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.462264 0.537736 1.000000 0.000000 0.000000 0.000000 MOTIF CCYTAACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCYTAACC GGTTARGG 29 1 2.2e-008 7.4e-004 # CCTTAACC GGTTAAGG 21 1 4.8e-006 1.6e-001 # CCCTAACC GGTTAGGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.4e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.275862 0.000000 0.724138 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACGRTG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CACGRTG CAYCGTG 28 2 3.4e-007 1.2e-002 # CACGGTG CACCGTG 18 1 3.4e-005 1.2e+000 # CACGATG CATCGTG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 1.2e-002 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 0.000000 1.000000 0.000000 0.357143 0.000000 0.642857 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCGGRGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCGGRGA TCYCCGC 32 4 7.3e-007 2.5e-002 # GCGGAGA TCTCCGC 14 1 4.6e-004 1.6e+001 # GCGGGGA TCCCCGC 18 3 6.9e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 2.5e-002 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 0.454545 0.000000 0.545455 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 34 5 8.9e-007 3.0e-002 # CCGTACA TGTACGG 17 2 3.4e-004 1.1e+001 # CCATACA TGTATGG 18 3 6.9e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 3.0e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.513514 0.000000 0.486486 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCACTW WAGTGGT 46 11 1.0e-006 3.5e-002 # ACCACTA TAGTGGT 28 4 7.8e-006 2.6e-001 # ACCACTT AAGTGGT 23 7 2.4e-003 8.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 3.5e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.549020 0.000000 0.000000 0.450980 # Stopping reason: E-value threshold exceeded # Running time: 35.51 seconds