# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/seqs-shuffled # positives: 504 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/seqs-centered (Sat Jan 18 14:19:51 PST 2020) # negatives: 504 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/seqs-shuffled (Sat Jan 18 14:19:51 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:32:21 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 0.304 C 0.195 G 0.192 T 0.309 MOTIF TBGGCCA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TBGGCCA TGGCCVA 72 3 1.5e-019 4.1e-015 # TCGGCCA TGGCCGA 37 1 7.4e-011 2.0e-006 # TGGGCCA TGGCCCA 15 0 2.7e-005 7.5e-001 # TTGGCCA TGGCCAA 20 2 5.2e-005 1.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 4.1e-015 0.000000 0.000000 0.000000 1.000000 0.000000 0.513889 0.208333 0.277778 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 CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 75 6 1.2e-017 3.1e-013 # CGCCTTA TAAGGCG 61 5 2.6e-014 6.9e-010 # CGCGTTA TAACGCG 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 3.1e-013 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 0.813333 0.186667 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 GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 83 10 5.2e-017 1.4e-012 # GGTTCGA TCGAACC 63 4 8.9e-016 2.4e-011 # GGTTCAA TTGAACC 21 7 5.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 1.4e-012 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 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 50 1 6.8e-015 1.8e-010 # ATGTATGG CCATACAT 26 0 1.1e-008 2.9e-004 # ATGTACGG CCGTACAT 26 1 1.5e-007 4.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 56 E= 1.8e-010 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TGGCGYA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 44 2 6.3e-012 1.7e-007 # TGGCGTA TACGCCA 20 0 7.9e-007 2.1e-002 # TGGCGCA TGCGCCA 24 2 4.1e-006 1.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 1.7e-007 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 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 1.000000 0.000000 0.000000 0.000000 MOTIF AGCGCV DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGCGCV BGCGCT 87 22 1.2e-011 3.2e-007 # AGCGCG CGCGCT 32 7 2.6e-005 6.8e-001 # AGCGCA TGCGCT 31 8 1.1e-004 3.0e+000 # AGCGCC GGCGCT 28 8 4.9e-004 1.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 91 E= 3.2e-007 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 0.340659 0.307692 0.351648 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 39 2 2.0e-010 5.1e-006 # ATGGCAAC GTTGCCAT 29 1 2.0e-008 5.1e-004 # ATGGCATC GATGCCAT 10 1 5.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 5.1e-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 0.743590 0.000000 0.000000 0.256410 0.000000 1.000000 0.000000 0.000000 MOTIF CTARACCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 34 1 6.1e-010 1.6e-005 # CTAGACCA TGGTCTAG 20 0 7.9e-007 2.1e-002 # CTAAACCA TGGTTTAG 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.6e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.411765 0.000000 0.588235 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATAGTKTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 43 4 6.4e-010 1.7e-005 # ATAGTGTA TACACTAT 28 1 3.9e-008 1.0e-003 # ATAGTTTA TAAACTAT 15 3 3.5e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.7e-005 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 0.651163 0.348837 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGA TCCGTG 37 3 5.4e-009 1.4e-004 # CACGGA TCCGTG 37 3 5.4e-009 1.4e-004 letter-probability matrix: alength= 4 w= 6 nsites= 37 E= 1.4e-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 1.000000 0.000000 0.000000 0.000000 MOTIF TAGCTCR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TAGCTCR YGAGCTA 34 2 5.8e-009 1.5e-004 # TAGCTCA TGAGCTA 23 1 1.2e-006 3.1e-002 # TAGCTCG CGAGCTA 11 1 3.0e-003 7.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.5e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.676471 0.000000 0.323529 0.000000 MOTIF TCTCCACR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 24 0 4.5e-008 1.2e-003 # TCTCCACA TGTGGAGA 13 0 1.1e-004 2.9e+000 # TCTCCACG CGTGGAGA 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.2e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.000000 0.458333 0.000000 MOTIF GTTGGK DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTTGGK MCCAAC 96 39 7.8e-008 2.0e-003 # GTTGGT ACCAAC 59 23 2.2e-005 5.6e-001 # GTTGGG CCCAAC 38 16 1.5e-003 3.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 97 E= 2.0e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.391753 0.608247 MOTIF ARAAARAA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ARAAARAA TTYTTTYT 94 38 9.9e-008 2.5e-003 # AAAAAAAA TTTTTTTT 53 22 1.3e-004 3.4e+000 # AGAAAAAA TTTTTTCT 31 10 5.8e-004 1.5e+001 # AAAAAGAA TTCTTTTT 27 11 6.1e-003 1.6e+002 # AGAAAGAA TTCTTTCT 7 0 7.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 115 E= 2.5e-003 1.000000 0.000000 0.000000 0.000000 0.747826 0.000000 0.252174 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 0.713043 0.000000 0.286957 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATTAASAG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 28 2 3.1e-007 7.9e-003 # ATTAAGAG CTCTTAAT 15 1 2.4e-004 6.0e+000 # ATTAACAG CTGTTAAT 13 1 8.6e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 7.9e-003 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.464286 0.535714 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TAATCWGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TAATCWGA TCWGATTA 21 0 3.9e-007 9.8e-003 # TAATCAGA TCTGATTA 14 0 5.6e-005 1.4e+000 # TAATCTGA TCAGATTA 7 0 7.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.8e-003 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGCGWGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGCGWGA TCWCGCT 23 1 1.2e-006 3.0e-002 # AGCGTGA TCACGCT 14 1 4.5e-004 1.1e+001 # AGCGAGA TCTCGCT 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.0e-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 1.000000 0.000000 0.391304 0.000000 0.000000 0.608696 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RCACCCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 41 9 1.7e-006 4.2e-002 # ACACCCA TGGGTGT 30 7 7.3e-005 1.9e+000 # GCACCCA TGGGTGC 13 2 3.5e-003 8.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 4.2e-002 0.659574 0.000000 0.340426 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 136.20 seconds