# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/seqs-shuffled # positives: 490 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/seqs-centered (Sat Jan 18 01:18:28 PST 2020) # negatives: 490 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/seqs-shuffled (Sat Jan 18 01:18:28 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 01:27:56 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 0.293 C 0.207 G 0.206 T 0.293 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 107 7 6.9e-027 1.8e-022 # GGTTCGA TCGAACC 89 6 5.0e-022 1.3e-017 # AGTTCGA TCGAACT 24 1 5.9e-007 1.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 107 E= 1.8e-022 0.186916 0.000000 0.813084 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 81 3 1.8e-022 4.7e-018 # TGTACGGA TCCGTACA 31 0 2.9e-010 7.6e-006 # TGTATGGG CCCATACA 38 2 3.8e-010 1.0e-005 # TGTATGGA TCCATACA 14 1 4.5e-004 1.2e+001 # TGTACGGG CCCGTACA 9 0 1.9e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 4.7e-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 0.431579 0.000000 0.568421 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.494737 0.000000 0.505263 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 59 2 1.4e-016 3.8e-012 # CTCGGCCA TGGCCGAG 29 0 1.2e-009 3.2e-005 # CTTGGCCA TGGCCAAG 19 1 1.7e-005 4.5e-001 # CTGGGCCA TGGCCCAG 11 1 3.0e-003 8.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 3.8e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.491525 0.186441 0.322034 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-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 69 8 2.1e-014 5.4e-010 # CGCCTTA TAAGGCG 55 5 1.4e-012 3.6e-008 # CGCGTTA TAACGCG 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 5.4e-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 0.797101 0.202899 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 43 0 4.3e-014 1.1e-009 # GCGCTACC GGTAGCGC 27 0 5.2e-009 1.3e-004 # GCTCTACC GGTAGAGC 16 0 1.3e-005 3.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.1e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.627907 0.372093 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 AARAAAWA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 113 38 1.3e-011 3.4e-007 # AAGAAAAA TTTTTCTT 38 9 8.0e-006 2.1e-001 # AAAAAAAA TTTTTTTT 52 20 5.9e-005 1.5e+000 # AAAAAATA TATTTTTT 29 12 4.9e-003 1.3e+002 # AAGAAATA TATTTCTT 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 124 E= 3.4e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.612903 0.000000 0.387097 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 0.693548 0.000000 0.000000 0.306452 1.000000 0.000000 0.000000 0.000000 MOTIF CTARACCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 34 0 3.2e-011 8.3e-007 # CTAGACCA TGGTCTAG 20 0 7.8e-007 2.0e-002 # CTAAACCA TGGTTTAG 14 0 5.6e-005 1.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 8.3e-007 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 CAASGATG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 37 1 7.3e-011 1.9e-006 # CAACGATG CATCGTTG 25 1 3.0e-007 7.8e-003 # CAAGGATG CATCCTTG 12 0 2.3e-004 5.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.9e-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 0.675676 0.324324 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 AMATCCG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AMATCCG CGGATKT 46 5 4.8e-010 1.2e-005 # ACATCCG CGGATGT 17 0 6.6e-006 1.7e-001 # AAATCCG CGGATTT 29 5 1.4e-005 3.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 1.2e-005 1.000000 0.000000 0.000000 0.000000 0.625000 0.375000 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATAGTKTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 43 4 6.3e-010 1.6e-005 # ATAGTGTA TACACTAT 26 0 1.1e-008 2.7e-004 # ATAGTTTA TAAACTAT 17 4 3.3e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.6e-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 0.604651 0.395349 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 28 0 2.5e-009 6.4e-005 # CACCGTGG CCACGGTG 16 0 1.3e-005 3.4e-001 # CACCGTGC GCACGGTG 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 6.4e-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 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 0.428571 0.571429 0.000000 MOTIF GTGATARC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGATARC GYTATCAC 28 1 3.9e-008 9.9e-004 # GTGATAGC GCTATCAC 18 1 3.3e-005 8.5e-001 # GTGATAAC GTTATCAC 10 0 9.3e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.9e-004 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 0.357143 0.000000 0.642857 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTAASAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 24 0 4.5e-008 1.1e-003 # ATTAAGAG CTCTTAAT 13 0 1.1e-004 2.9e+000 # ATTAACAG CTGTTAAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-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 0.458333 0.541667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTGAGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGC GCTCAGT 23 0 9.2e-008 2.3e-003 # ACTGAGC GCTCAGT 23 0 9.2e-008 2.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 2.3e-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 MOTIF GCCATWAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCCATWAC GTWATGGC 23 0 9.2e-008 2.3e-003 # GCCATTAC GTAATGGC 12 0 2.3e-004 5.8e+000 # GCCATAAC GTTATGGC 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.3e-003 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 0.000000 0.000000 1.000000 0.478261 0.000000 0.000000 0.521739 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACACSCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACACSCA TGSGTGT 47 12 1.3e-006 3.4e-002 # ACACCCA TGGGTGT 35 10 8.9e-005 2.3e+000 # ACACGCA TGCGTGT 12 2 6.2e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 3.4e-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 0.750000 0.250000 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: 53.60 seconds