# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/seqs-shuffled # positives: 483 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/seqs-centered (Sun Jan 19 10:38:04 PST 2020) # negatives: 483 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/seqs-shuffled (Sun Jan 19 10:38:04 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:47:36 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 0.292 C 0.210 G 0.207 T 0.291 MOTIF SGGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 87 2 1.1e-025 3.0e-021 # CGGTTCGA TCGAACCG 31 0 2.8e-010 7.7e-006 # GGGTTCGA TCGAACCC 35 2 2.9e-009 7.8e-005 # GGGTTCAA TTGAACCC 12 0 2.3e-004 6.2e+000 # CGGTTCAA TTGAACCG 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 3.0e-021 0.000000 0.459770 0.540230 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.241379 0.000000 0.758621 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 81 3 1.7e-022 4.5e-018 # TGTATGGG CCCATACA 37 2 7.5e-010 2.0e-005 # TGTACGGA TCCGTACA 31 1 4.8e-009 1.3e-004 # TGTATGGA TCCATACA 12 0 2.3e-004 6.1e+000 # TGTACGGG CCCGTACA 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 4.5e-018 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 0.457447 0.000000 0.542553 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.478723 0.000000 0.521277 0.000000 MOTIF ACTBGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 59 0 2.6e-019 7.0e-015 # ACTTGGCC GGCCAAGT 29 0 1.2e-009 3.2e-005 # ACTCGGCC GGCCGAGT 26 0 1.1e-008 2.8e-004 # ACTGGGCC GGCCCAGT 12 0 2.3e-004 6.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 7.0e-015 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 0.372881 0.203390 0.423729 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 78 11 5.4e-015 1.4e-010 # CGCCTTA TAAGGCG 62 7 3.9e-013 1.0e-008 # CGCGTTA TAACGCG 16 4 5.5e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 1.4e-010 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 0.794872 0.205128 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 AGTGRTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGTGRTA TAYCACT 55 3 2.6e-014 6.9e-010 # AGTGGTA TACCACT 37 1 7.2e-011 1.9e-006 # AGTGATA TATCACT 19 2 9.6e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 6.9e-010 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 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 176 75 6.1e-014 1.6e-009 # AAAAAAT ATTTTTT 87 37 9.3e-007 2.5e-002 # AAAAAAA TTTTTTT 89 40 2.3e-006 5.9e-002 # AAGAAAA TTTTCTT 52 16 3.4e-006 9.0e-002 # AAGAAAT ATTTCTT 30 13 5.9e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 228 E= 1.6e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.653509 0.000000 0.346491 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 0.548246 0.000000 0.000000 0.451754 MOTIF TAGTGTR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGTGTR YACACTA 47 3 6.6e-012 1.7e-007 # TAGTGTA TACACTA 34 2 5.7e-009 1.5e-004 # TAGTGTG CACACTA 13 1 8.5e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 1.7e-007 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 0.000000 1.000000 0.734694 0.000000 0.265306 0.000000 MOTIF CAASGATG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 36 1 1.5e-010 3.8e-006 # CAACGATG CATCGTTG 22 0 1.9e-007 4.8e-003 # CAAGGATG CATCCTTG 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 3.8e-006 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 0.611111 0.388889 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 AGCGCV DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGCGCV BGCGCT 85 24 2.0e-010 5.2e-006 # AGCGCA TGCGCT 26 4 2.3e-005 6.0e-001 # AGCGCG CGCGCT 37 12 1.7e-004 4.3e+000 # AGCGCC GGCGCT 28 8 4.8e-004 1.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 92 E= 5.2e-006 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 0.282609 0.304348 0.413043 0.000000 MOTIF ACCCAVAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 38 2 3.8e-010 9.6e-006 # ACCCAAAC GTTTGGGT 12 0 2.3e-004 5.8e+000 # ACCCACAC GTGTGGGT 15 1 2.4e-004 6.0e+000 # ACCCAGAC GTCTGGGT 15 1 2.4e-004 6.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 9.6e-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 0.279070 0.372093 0.348837 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GATTRGAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GATTRGAA TTCYAATC 28 0 2.5e-009 6.3e-005 # GATTAGAA TTCTAATC 20 0 7.8e-007 2.0e-002 # GATTGGAA TTCCAATC 8 0 3.8e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 6.3e-005 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 0.000000 1.000000 0.714286 0.000000 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGTGM DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 28 1 3.8e-008 9.7e-004 # CACGGTGA TCACCGTG 15 0 2.7e-005 6.9e-001 # CACGGTGC GCACCGTG 13 1 8.5e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.7e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.535714 0.464286 0.000000 0.000000 MOTIF KTAGCTCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST KTAGCTCA TGAGCTAM 24 0 4.4e-008 1.1e-003 # TTAGCTCA TGAGCTAA 17 0 6.6e-006 1.7e-001 # GTAGCTCA TGAGCTAC 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 0.000000 0.000000 0.291667 0.708333 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 1.000000 0.000000 0.000000 0.000000 MOTIF CATYACGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 27 1 7.6e-008 1.9e-003 # CATTACGC GCGTAATG 13 0 1.1e-004 2.8e+000 # CATCACGC GCGTGATG 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.9e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.518519 0.000000 0.481481 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 MOTIF AGACCACR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGACCACR YGTGGTCT 21 0 3.8e-007 9.6e-003 # AGACCACA TGTGGTCT 11 0 4.6e-004 1.2e+001 # AGACCACG CGTGGTCT 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.6e-003 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 0.000000 1.000000 0.000000 0.000000 0.523810 0.000000 0.476190 0.000000 MOTIF ACCATTRA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACCATTRA TYAATGGT 20 0 7.8e-007 2.0e-002 # ACCATTAA TTAATGGT 13 0 1.1e-004 2.8e+000 # ACCATTGA TCAATGGT 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 2.0e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATTGSGCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATTGSGCC GGCSCAAT 19 0 1.6e-006 4.0e-002 # ATTGCGCC GGCGCAAT 12 0 2.3e-004 5.7e+000 # ATTGGGCC GGCCCAAT 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.0e-002 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 0.000000 0.631579 0.368421 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 GAGACC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GAGACC GGTCTC 37 7 1.6e-006 4.1e-002 # GAGACC GGTCTC 37 7 1.6e-006 4.1e-002 letter-probability matrix: alength= 4 w= 6 nsites= 39 E= 4.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 58.35 seconds