# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/seqs-shuffled # positives: 482 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/seqs-centered (Sun Jan 19 01:16:01 PST 2020) # negatives: 482 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/seqs-shuffled (Sun Jan 19 01:16:01 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:25:14 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 0.214 G 0.212 T 0.284 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 109 8 1.1e-026 3.0e-022 # GGTTCGA TCGAACC 92 5 5.7e-024 1.5e-019 # AGTTCGA TCGAACT 23 3 3.6e-005 9.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 109 E= 3.0e-022 0.174312 0.000000 0.825688 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 84 6 1.7e-020 4.6e-016 # AGTGGTT AACCACT 63 3 9.0e-017 2.4e-012 # AGTGGTA TACCACT 33 3 7.1e-008 1.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 4.6e-016 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 0.336735 0.000000 0.000000 0.663265 MOTIF CCCATDC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 86 10 5.9e-018 1.6e-013 # CCCATAC GTATGGG 49 3 1.7e-012 4.5e-008 # CCCATGC GCATGGG 26 3 5.8e-006 1.5e-001 # CCCATTC GAATGGG 16 4 5.5e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 1.6e-013 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 0.000000 0.000000 0.000000 1.000000 0.567010 0.000000 0.268041 0.164948 0.000000 1.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 47 0 2.2e-015 5.8e-011 # CAACTTGG CCAAGTTG 37 0 3.5e-012 9.4e-008 # CAACTGGG CCCAGTTG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 5.8e-011 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.212766 0.787234 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATCCRTAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATCCRTAC GTAYGGAT 40 0 3.9e-013 1.0e-008 # ATCCGTAC GTACGGAT 28 0 2.5e-009 6.6e-005 # ATCCATAC GTATGGAT 12 0 2.3e-004 6.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.0e-008 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 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 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 MOTIF BTAAGGCG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 44 2 6.0e-012 1.6e-007 # TTAAGGCG CGCCTTAA 19 1 1.7e-005 4.5e-001 # CTAAGGCG CGCCTTAG 14 0 5.5e-005 1.5e+000 # GTAAGGCG CGCCTTAC 11 1 3.0e-003 7.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.6e-007 0.000000 0.318182 0.250000 0.431818 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 GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 38 1 3.5e-011 9.2e-007 # GCGCTACC GGTAGCGC 26 1 1.5e-007 4.0e-003 # GCTCTACC GGTAGAGC 12 0 2.3e-004 6.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 9.2e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.684211 0.315789 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-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 32 0 1.4e-010 3.6e-006 # GTGATAGC GCTATCAC 18 0 3.2e-006 8.5e-002 # GTGATAGT ACTATCAC 15 0 2.7e-005 7.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.6e-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 0.545455 0.000000 0.454545 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 2 1.5e-009 3.8e-005 # ATGGCAAC GTTGCCAT 24 1 5.9e-007 1.5e-002 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 3.8e-005 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 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 44 5 1.7e-009 4.4e-005 # CACGGTG CACCGTG 31 3 2.5e-007 6.6e-003 # CACGGCG CGCCGTG 13 2 3.5e-003 9.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 4.4e-005 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 0.295455 0.000000 0.704545 0.000000 0.000000 1.000000 0.000000 MOTIF ATCTTYTG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 34 2 5.7e-009 1.5e-004 # ATCTTCTG CAGAAGAT 17 0 6.6e-006 1.7e-001 # ATCTTTTG CAAAAGAT 17 2 3.3e-004 8.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.5e-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 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACGCSAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACGCSAC GTSGCGT 29 1 1.9e-008 5.0e-004 # ACGCCAC GTGGCGT 17 1 6.4e-005 1.6e+000 # ACGCGAC GTCGCGT 12 0 2.3e-004 5.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 5.0e-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 0.586207 0.413793 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RAAAAAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST RAAAAAA TTTTTTY 117 52 2.2e-008 5.6e-004 # GAAAAAA TTTTTTC 65 23 1.6e-006 4.0e-002 # AAAAAAA TTTTTTT 88 42 9.4e-006 2.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 145 E= 5.6e-004 0.648276 0.000000 0.351724 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAASAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCAASAGA TCTSTTGG 28 1 3.8e-008 9.8e-004 # CCAAGAGA TCTCTTGG 16 1 1.2e-004 3.1e+000 # CCAACAGA TCTGTTGG 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 9.8e-004 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 0.413793 0.586207 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 AACACSCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AACACSCA TGSGTGTT 26 1 1.5e-007 3.9e-003 # AACACCCA TGGGTGTT 14 0 5.5e-005 1.4e+000 # AACACGCA TGCGTGTT 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.9e-003 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.538462 0.461538 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 26 1 1.5e-007 3.9e-003 # ATCGTGAG CTCACGAT 17 1 6.4e-005 1.6e+000 # ATCTTGAG CTCAAGAT 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.9e-003 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 0.653846 0.346154 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 MOTIF ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 22 0 1.9e-007 4.7e-003 # ACTGAGCT AGCTCAGT 22 0 1.9e-007 4.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.7e-003 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 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 MOTIF AAGCGWGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 25 1 3.0e-007 7.6e-003 # AAGCGTGA TCACGCTT 15 0 2.7e-005 6.9e-001 # AAGCGAGA TCTCGCTT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.6e-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 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGCSCAA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GGCSCAA TTGSGCC 34 5 7.8e-007 2.0e-002 # GGCCCAA TTGGGCC 22 4 2.3e-004 5.7e+000 # GGCGCAA TTGCGCC 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.0e-002 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 0.647059 0.352941 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 MOTIF ACACTATA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 23 1 1.2e-006 3.0e-002 # ACACTATA TATAGTGT 23 1 1.2e-006 3.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.0e-002 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCWC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST AGACCWC GWGGTCT 33 5 1.4e-006 3.6e-002 # AGACCAC GTGGTCT 24 4 7.3e-005 1.9e+000 # AGACCTC GAGGTCT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 3.6e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.705882 0.000000 0.000000 0.294118 0.000000 1.000000 0.000000 0.000000 MOTIF GGRGATCA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GGRGATCA TGATCYCC 19 0 1.6e-006 4.0e-002 # GGGGATCA TGATCCCC 10 0 9.3e-004 2.4e+001 # GGAGATCA TGATCTCC 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.0e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.473684 0.000000 0.526316 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 71.20 seconds