# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--IES2/seqs-shuffled # positives: 774 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--IES2/seqs-centered (Sat Jan 18 23:21:26 PST 2020) # negatives: 774 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--IES2/seqs-shuffled (Sat Jan 18 23:21:26 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:35:12 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 0.287 C 0.209 G 0.211 T 0.293 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 115 7 2.3e-028 7.7e-024 # GGTTCGA TCGAACC 94 6 7.1e-023 2.4e-018 # GGATCGA TCGATCC 26 2 1.3e-006 4.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 7.7e-024 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.224138 0.000000 0.000000 0.775862 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 AGTGGTYW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTYW WRACCACT 71 3 7.6e-019 2.5e-014 # AGTGGTTA TAACCACT 34 1 7.4e-010 2.5e-005 # AGTGGTTT AAACCACT 23 2 8.5e-006 2.8e-001 # AGTGGTCT AGACCACT 8 0 3.8e-003 1.3e+002 # AGTGGTCA TGACCACT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 2.5e-014 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 0.000000 0.208333 0.000000 0.791667 0.569444 0.000000 0.000000 0.430556 MOTIF SAAGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 436 289 4.4e-014 1.4e-009 # GAAGA TCTTC 258 149 1.9e-010 6.2e-006 # CAAGA TCTTG 241 176 1.2e-004 4.0e+000 letter-probability matrix: alength= 4 w= 5 nsites= 622 E= 1.4e-009 0.000000 0.464630 0.535370 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 42 2 3.4e-011 1.1e-006 # ATGTATGG CCATACAT 28 1 4.4e-008 1.4e-003 # ATGTACGG CCGTACAT 16 1 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.1e-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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.361702 0.000000 0.638298 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GTGATAGY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 34 0 4.0e-011 1.3e-006 # GTGATAGC GCTATCAC 17 0 7.0e-006 2.2e-001 # GTGATAGT ACTATCAC 17 0 7.0e-006 2.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.3e-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 0.500000 0.000000 0.500000 MOTIF CGGHCAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGGHCAA TTGDCCG 55 9 8.8e-010 2.8e-005 # CGGTCAA TTGACCG 14 0 5.8e-005 1.8e+000 # CGGCCAA TTGGCCG 30 7 8.1e-005 2.6e+000 # CGGACAA TTGTCCG 16 3 2.1e-003 6.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 2.8e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.266667 0.500000 0.000000 0.233333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCMA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCMA TKGCCAT 61 13 3.2e-009 1.0e-004 # ATGGCAA TTGCCAT 42 9 1.2e-006 3.8e-002 # ATGGCCA TGGCCAT 19 4 1.2e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 1.0e-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 1.000000 0.000000 0.000000 0.688525 0.311475 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGYTAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGYTAC GTARCG 80 24 5.5e-009 1.7e-004 # CGTTAC GTAACG 44 14 3.7e-005 1.2e+000 # CGCTAC GTAGCG 37 10 3.9e-005 1.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 82 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.451220 0.000000 0.548780 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGTGM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 25 0 2.4e-008 7.7e-004 # CACGGTGA TCACCGTG 17 0 7.0e-006 2.2e-001 # CACGGTGC GCACCGTG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.7e-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 0.680000 0.320000 0.000000 0.000000 MOTIF AGAYCGG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGG CCGRTCT 39 5 4.8e-008 1.5e-003 # AGATCGG CCGATCT 22 2 1.6e-005 5.0e-001 # AGACCGG CCGGTCT 17 3 1.2e-003 3.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.5e-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 0.435897 0.000000 0.564103 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 AGTTGGTW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGTTGGTW WACCAACT 39 5 4.8e-008 1.5e-003 # AGTTGGTT AACCAACT 27 4 1.4e-005 4.5e-001 # AGTTGGTA TACCAACT 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 1.5e-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 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 0.307692 0.000000 0.000000 0.692308 MOTIF AGMATGGG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGMATGGG CCCATKCT 24 0 5.0e-008 1.6e-003 # AGAATGGG CCCATTCT 17 0 7.0e-006 2.2e-001 # AGCATGGG CCCATGCT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.708333 0.291667 0.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CRCACGCC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CRCACGCC GGCGTGYG 23 0 1.0e-007 3.2e-003 # CACACGCC GGCGTGTG 15 0 2.8e-005 9.0e-001 # CGCACGCC GGCGTGCG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-003 0.000000 1.000000 0.000000 0.000000 0.652174 0.000000 0.347826 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGRTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTGRTA TAYCACT 45 9 2.4e-007 7.5e-003 # AGTGGTA TACCACT 34 8 2.8e-005 8.7e-001 # AGTGATA TATCACT 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 7.5e-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 0.000000 1.000000 0.000000 0.260870 0.000000 0.739130 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGTGRC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CAGTGRC GYCACTG 33 4 4.1e-007 1.3e-002 # CAGTGAC GTCACTG 23 4 1.4e-004 4.3e+000 # CAGTGGC GCCACTG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.696970 0.000000 0.303030 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 76.51 seconds