# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HIR1/seqs-shuffled # positives: 711 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HIR1/seqs-centered (Sat Jan 18 00:20:18 PST 2020) # negatives: 711 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HIR1/seqs-shuffled (Sat Jan 18 00:20:18 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:35:58 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 0.206 G 0.202 T 0.296 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 87 5 8.6e-022 2.8e-017 # TGTATGGG CCCATACA 37 1 9.0e-011 2.9e-006 # TGTACGGA TCCGTACA 34 1 7.2e-010 2.3e-005 # TGTACGGG CCCGTACA 12 0 2.3e-004 7.6e+000 # TGTATGGA TCCATACA 14 3 6.1e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 2.8e-017 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.470588 0.000000 0.529412 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF GGWTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 99 11 2.0e-020 6.4e-016 # GGTTCGA TCGAACC 85 8 1.2e-018 4.0e-014 # GGATCGA TCGATCC 21 3 1.2e-004 4.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 6.4e-016 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.191919 0.000000 0.000000 0.808081 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 BTAAGGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 61 2 6.2e-017 2.0e-012 # TTAAGGCG CGCCTTAA 34 1 7.2e-010 2.3e-005 # CTAAGGCG CGCCTTAG 16 0 1.4e-005 4.5e-001 # GTAAGGCG CGCCTTAC 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 61 E= 2.0e-012 0.000000 0.262295 0.180328 0.557377 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 65 5 3.0e-015 9.6e-011 # CTCGGCCA TGGCCGAG 35 2 3.5e-009 1.1e-004 # CTTGGCCA TGGCCAAG 18 2 1.8e-004 5.9e+000 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 9.6e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.538462 0.184615 0.276923 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 1 5.6e-012 1.8e-007 # GCGCTACC GGTAGCGC 26 1 1.7e-007 5.4e-003 # GCTCTACC GGTAGAGC 15 0 2.8e-005 9.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.8e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.634146 0.365854 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 GTGATAGY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 38 1 4.5e-011 1.4e-006 # GTGATAGC GCTATCAC 20 0 8.3e-007 2.7e-002 # GTGATAGT ACTATCAC 19 1 1.8e-005 5.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 1.4e-006 0.000000 0.000000 1.000000 0.000000 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.512821 0.000000 0.487179 MOTIF ACCCANAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 47 4 6.2e-011 2.0e-006 # ACCCAGAC GTCTGGGT 14 0 5.7e-005 1.8e+000 # ACCCAAAC GTTTGGGT 15 1 2.4e-004 7.8e+000 # ACCCATAC GTATGGGT 9 0 1.9e-003 6.1e+001 # ACCCACAC GTGTGGGT 14 3 6.1e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 2.0e-006 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.272727 0.290909 0.254545 0.181818 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAAC GTTGCCAT 32 0 1.6e-010 5.2e-006 # ATGGCAAC GTTGCCAT 32 0 1.6e-010 5.2e-006 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.2e-006 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 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 MOTIF TAGTGGTW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 42 3 2.5e-010 8.0e-006 # TAGTGGTA TACCACTA 25 2 2.4e-006 7.5e-002 # TAGTGGTT AACCACTA 17 1 6.7e-005 2.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 8.0e-006 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.595238 0.000000 0.000000 0.404762 MOTIF ATGGGHG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATGGGHG CDCCCAT 60 13 5.1e-009 1.6e-004 # ATGGGTG CACCCAT 26 5 8.2e-005 2.6e+000 # ATGGGCG CGCCCAT 22 6 1.7e-003 5.4e+001 # ATGGGAG CTCCCAT 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 1.6e-004 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 0.000000 1.000000 0.000000 0.213115 0.360656 0.000000 0.426230 0.000000 0.000000 1.000000 0.000000 MOTIF CACGGYG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 40 4 5.4e-009 1.7e-004 # CACGGTG CACCGTG 28 3 1.9e-006 5.9e-002 # CACGGCG CGCCGTG 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 1.7e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 0.000000 1.000000 0.000000 MOTIF ARAAAAW DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAW WTTTTYT 225 131 5.4e-009 1.7e-004 # AGAAAAA TTTTTCT 74 33 2.4e-005 7.6e-001 # AAAAAAT ATTTTTT 105 63 3.6e-004 1.1e+001 # AAAAAAA TTTTTTT 113 74 1.4e-003 4.4e+001 # AGAAAAT ATTTTCT 35 16 4.8e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 290 E= 1.7e-004 1.000000 0.000000 0.000000 0.000000 0.651724 0.000000 0.348276 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 0.562069 0.000000 0.000000 0.437931 MOTIF ACGCSAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACGCSAC GTSGCGT 32 2 2.5e-008 8.0e-004 # ACGCCAC GTGGCGT 20 0 8.3e-007 2.6e-002 # ACGCGAC GTCGCGT 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 8.0e-004 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 0.000000 0.625000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGCGCMAG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGCGCMAG CTKGCGCT 24 0 4.9e-008 1.5e-003 # AGCGCAAG CTTGCGCT 12 0 2.3e-004 7.3e+000 # AGCGCCAG CTGGCGCT 12 0 2.3e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAGCGWGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 27 1 8.6e-008 2.7e-003 # AAGCGTGA TCACGCTT 16 1 1.3e-004 4.0e+000 # AAGCGAGA TCTCGCTT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.7e-003 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 0.000000 1.000000 0.000000 0.407407 0.000000 0.000000 0.592593 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 1 1.7e-007 5.3e-003 # AGTCATAC GTATGACT 14 0 5.7e-005 1.8e+000 # AGTCAGAC GTCTGACT 12 1 1.6e-003 5.1e+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 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 0.461538 0.538462 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTWGACC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 42 8 3.8e-007 1.2e-002 # CTAGACC GGTCTAG 21 3 1.2e-004 3.9e+000 # CTTGACC GGTCAAG 21 5 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 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 1.000000 0.000000 0.000000 MOTIF GACTMCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GACTMCA TGKAGTC 27 2 6.5e-007 2.0e-002 # GACTCCA TGGAGTC 19 2 1.0e-004 3.1e+000 # GACTACA TGTAGTC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.0e-002 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 0.000000 0.000000 1.000000 0.296296 0.703704 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 23 1 1.3e-006 3.9e-002 # AGATCGGG CCCGATCT 15 1 2.4e-004 7.6e+000 # AGATCGTG CACGATCT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.9e-002 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 0.652174 0.347826 0.000000 0.000000 1.000000 0.000000 MOTIF GAATTGAA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GAATTGAA TTCAATTC 23 1 1.3e-006 3.9e-002 # GAATTGAA TTCAATTC 23 1 1.3e-006 3.9e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.9e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 93.25 seconds