# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/seqs-shuffled # positives: 850 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/seqs-centered (Sat Jan 18 03:28:56 PST 2020) # negatives: 850 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MOT3/seqs-shuffled (Sat Jan 18 03:28:56 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:42:38 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 0.300 C 0.203 G 0.201 T 0.296 MOTIF GRVTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRVTCGAA TTCGABYC 121 4 3.2e-033 1.1e-028 # GAATCGAA TTCGATTC 32 0 1.7e-010 5.8e-006 # GGATCGAA TTCGATCC 30 0 7.2e-010 2.4e-005 # GAGTCGAA TTCGACTC 23 1 1.3e-006 4.3e-002 # GGCTCGAA TTCGAGCC 15 1 2.5e-004 8.2e+000 # GGGTCGAA TTCGACCC 11 1 3.1e-003 1.0e+002 # GACTCGAA TTCGAGTC 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 122 E= 1.1e-028 0.000000 0.000000 1.000000 0.000000 0.532787 0.000000 0.467213 0.000000 0.516393 0.204918 0.278689 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 1.000000 0.000000 0.000000 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 82 7 2.2e-018 7.2e-014 # TGTATGGG CCCATACA 33 1 1.5e-009 5.0e-005 # TGTACGGA TCCGTACA 32 1 3.0e-009 9.9e-005 # TGTATGGA TCCATACA 17 4 3.4e-003 1.1e+002 # TGTACGGG CCCGTACA 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 96 E= 7.2e-014 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 0.458333 0.000000 0.541667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.541667 0.000000 0.458333 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 62 1 2.3e-018 7.5e-014 # CTCGGCCA TGGCCGAG 29 0 1.5e-009 4.8e-005 # CTTGGCCA TGGCCAAG 19 0 1.7e-006 5.7e-002 # CTGGGCCA TGGCCCAG 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 7.5e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.467742 0.225806 0.306452 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 71 8 1.4e-014 4.8e-010 # CGCCTTA TAAGGCG 55 4 3.9e-013 1.3e-008 # CGCGTTA TAACGCG 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 4.8e-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 0.763889 0.236111 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 AGARA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGARA TYTCT 495 339 2.3e-014 7.7e-010 # AGAAA TTTCT 410 266 5.9e-013 2.0e-008 # AGAGA TCTCT 168 128 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 5 nsites= 725 E= 7.7e-010 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.740690 0.000000 0.259310 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 45 1 3.8e-013 1.2e-008 # TAGTGGTA TACCACTA 26 0 1.2e-008 3.9e-004 # TAGTGGTT AACCACTA 19 1 1.8e-005 5.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.2e-008 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.577778 0.000000 0.000000 0.422222 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 1.2e-011 3.9e-007 # GCGCTACC GGTAGCGC 28 1 4.5e-008 1.4e-003 # GCTCTACC GGTAGAGC 12 0 2.3e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.9e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.300000 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 ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 41 3 5.3e-010 1.7e-005 # ATGGCAAC GTTGCCAT 29 2 1.9e-007 5.9e-003 # ATGGCATC GATGCCAT 12 1 1.7e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.7e-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 0.707317 0.000000 0.000000 0.292683 0.000000 1.000000 0.000000 0.000000 MOTIF RCACCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 74 19 1.5e-009 4.8e-005 # ACACCCA TGGGTGT 58 13 1.7e-008 5.4e-004 # GCACCCA TGGGTGC 19 6 7.0e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 115 E= 4.8e-005 0.791304 0.000000 0.208696 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCGMTGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGMTGA TCAKCGG 37 3 6.9e-009 2.2e-004 # CCGATGA TCATCGG 22 0 2.1e-007 6.5e-003 # CCGCTGA TCAGCGG 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.2e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.594595 0.405405 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 MOTIF CACGGYG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 46 7 1.3e-008 4.0e-004 # CACGGTG CACCGTG 32 5 3.0e-006 9.4e-002 # CACGGCG CGCCGTG 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 4.0e-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 0.304348 0.000000 0.695652 0.000000 0.000000 1.000000 0.000000 MOTIF ACCGGKG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCGGKG CMCCGGT 40 6 1.1e-007 3.5e-003 # ACCGGGG CCCCGGT 23 3 3.9e-005 1.2e+000 # ACCGGTG CACCGGT 17 3 1.2e-003 3.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 3.5e-003 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 1.000000 0.000000 0.000000 0.000000 0.575000 0.425000 0.000000 0.000000 1.000000 0.000000 MOTIF ACWAGACC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACWAGACC GGTCTWGT 30 3 5.7e-007 1.8e-002 # ACTAGACC GGTCTAGT 15 0 2.9e-005 9.0e-001 # ACAAGACC GGTCTTGT 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.8e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 MOTIF GTGATAGY DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 27 2 6.8e-007 2.1e-002 # GTGATAGT ACTATCAC 11 0 4.7e-004 1.5e+001 # GTGATAGC GCTATCAC 16 2 6.2e-004 1.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-002 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 0.592593 0.000000 0.407407 MOTIF ACCGAAAK DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACCGAAAK MTTTCGGT 26 2 1.3e-006 4.0e-002 # ACCGAAAT ATTTCGGT 12 0 2.3e-004 7.3e+000 # ACCGAAAG CTTTCGGT 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-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 0.000000 0.000000 1.000000 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 0.000000 0.000000 0.538462 0.461538 # Stopping reason: E-value threshold exceeded # Running time: 80.50 seconds