# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SRB8/seqs-shuffled # positives: 462 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SRB8/seqs-centered (Sat Jan 18 09:47:18 PST 2020) # negatives: 462 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SRB8/seqs-shuffled (Sat Jan 18 09:47:18 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 09:55:57 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 0.290 C 0.213 G 0.213 T 0.285 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 119 12 9.8e-027 2.6e-022 # GGTTCGA TCGAACC 89 5 4.4e-023 1.1e-018 # GGTTCAA TTGAACC 31 7 4.2e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 2.6e-022 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 0.258333 0.000000 0.741667 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTRCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTRCA TGYAYGG 99 10 5.9e-022 1.5e-017 # CCGTACA TGTACGG 39 1 1.7e-011 4.4e-007 # CCATACA TGTATGG 47 4 4.3e-011 1.1e-006 # CCGTGCA TGCACGG 14 2 1.9e-003 5.1e+001 # CCATGCA TGCATGG 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 126 E= 1.5e-017 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.563492 0.000000 0.436508 0.000000 0.000000 0.000000 0.000000 1.000000 0.777778 0.000000 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 86 10 5.1e-018 1.3e-013 # AGTGGTT AACCACT 61 5 2.2e-014 5.6e-010 # AGTGGTA TACCACT 37 5 1.3e-007 3.2e-003 letter-probability matrix: alength= 4 w= 7 nsites= 101 E= 1.3e-013 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 0.366337 0.000000 0.000000 0.633663 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 43 0 4.1e-014 1.0e-009 # AACTTGGC GCCAAGTT 32 0 1.3e-010 3.4e-006 # AACTGGGC GCCCAGTT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.0e-009 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 0.000000 0.255814 0.744186 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RCGCCTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST RCGCCTTA TAAGGCGY 37 0 3.4e-012 8.8e-008 # GCGCCTTA TAAGGCGC 23 0 9.0e-008 2.3e-003 # ACGCCTTA TAAGGCGT 14 0 5.5e-005 1.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 8.8e-008 0.378378 0.000000 0.621622 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAASGATG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 34 0 3.1e-011 7.9e-007 # CAACGATG CATCGTTG 23 0 9.0e-008 2.3e-003 # CAAGGATG CATCCTTG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 7.9e-007 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 0.676471 0.323529 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 MOTIF CTCTMCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 30 0 5.7e-010 1.5e-005 # CTCTCCCA TGGGAGAG 18 0 3.2e-006 8.2e-002 # CTCTACCA TGGTAGAG 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.5e-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 0.400000 0.600000 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 TGGCGYA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 39 3 1.4e-009 3.5e-005 # TGGCGCA TGCGCCA 21 1 4.4e-006 1.1e-001 # TGGCGTA TACGCCA 18 2 1.8e-004 4.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 3.5e-005 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 0.538462 0.000000 0.461538 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 167 86 1.4e-009 3.6e-005 # AAGAAAA TTTTCTT 51 18 2.3e-005 5.9e-001 # AAAAAAA TTTTTTT 80 42 1.5e-004 3.7e+000 # AAAAAAT ATTTTTT 80 43 2.3e-004 5.7e+000 # AAGAAAT ATTTCTT 32 13 2.7e-003 6.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 212 E= 3.6e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.655660 0.000000 0.344340 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 0.518868 0.000000 0.000000 0.481132 MOTIF GTGATAGY DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 32 1 2.3e-009 5.8e-005 # GTGATAGT ACTATCAC 15 0 2.7e-005 6.8e-001 # GTGATAGC GCTATCAC 18 1 3.3e-005 8.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 5.8e-005 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 0.545455 0.000000 0.454545 MOTIF ATCTTWC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCTTWC GWAAGAT 26 0 1.0e-008 2.6e-004 # ATCTTTC GAAAGAT 16 0 1.3e-005 3.3e-001 # ATCTTAC GTAAGAT 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.6e-004 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 0.000000 1.000000 0.370370 0.000000 0.000000 0.629630 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 77 24 1.1e-008 2.7e-004 # CGCCCA TGGGCG 32 8 6.6e-005 1.6e+000 # CACCCA TGGGTG 45 17 1.6e-004 3.9e+000 letter-probability matrix: alength= 4 w= 6 nsites= 92 E= 2.7e-004 0.000000 1.000000 0.000000 0.000000 0.641304 0.000000 0.358696 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 AATCTTYT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AATCTTYT ARAAGATT 38 4 1.5e-008 3.6e-004 # AATCTTCT AGAAGATT 20 1 8.7e-006 2.1e-001 # AATCTTTT AAAAGATT 18 3 6.6e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 3.6e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.526316 0.000000 0.473684 0.000000 0.000000 0.000000 1.000000 MOTIF CGTMTGAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGTMTGAC GTCAKACG 24 0 4.4e-008 1.1e-003 # CGTATGAC GTCATACG 12 0 2.3e-004 5.5e+000 # CGTCTGAC GTCAGACG 12 0 2.3e-004 5.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-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 0.500000 0.500000 0.000000 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 1.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 27 1 7.5e-008 1.8e-003 # CACCGTGG CCACGGTG 16 1 1.2e-004 3.0e+000 # CACCGTGC GCACGGTG 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.8e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.407407 0.592593 0.000000 MOTIF CGGTRGC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGGTRGC GCYACCG 29 2 1.6e-007 3.8e-003 # CGGTAGC GCTACCG 21 2 2.7e-005 6.6e-001 # CGGTGGC GCCACCG 8 0 3.8e-003 9.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.8e-003 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 0.000000 1.000000 0.724138 0.000000 0.275862 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACACTAK DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACACTAK MTAGTGT 34 4 1.8e-007 4.5e-003 # ACACTAT ATAGTGT 26 4 2.3e-005 5.5e-001 # ACACTAG CTAGTGT 8 0 3.8e-003 9.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.5e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.228571 0.771429 MOTIF CTGAGCTA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 22 0 1.8e-007 4.5e-003 # CTGAGCTA TAGCTCAG 22 0 1.8e-007 4.5e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.5e-003 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGAYCGG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGG CCGRTCT 35 5 4.2e-007 1.0e-002 # AGATCGG CCGATCT 19 3 3.7e-004 9.0e+000 # AGACCGG CCGGTCT 16 2 5.9e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.0e-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 0.457143 0.000000 0.542857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF KAGACCA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST KAGACCA TGGTCTM 29 3 8.9e-007 2.1e-002 # TAGACCA TGGTCTA 19 2 9.5e-005 2.3e+000 # GAGACCA TGGTCTC 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.1e-002 0.000000 0.000000 0.366667 0.633333 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGGGSA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 23 1 1.2e-006 2.8e-002 # CGCGGGCA TGCCCGCG 12 0 2.3e-004 5.5e+000 # CGCGGGGA TCCCCGCG 11 1 3.0e-003 7.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.8e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.521739 0.478261 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 63.82 seconds