# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--STE12/seqs-shuffled # positives: 868 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--STE12/seqs-centered (Sat Jan 18 15:18:07 PST 2020) # negatives: 868 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--STE12/seqs-shuffled (Sat Jan 18 15:18:07 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 15:32:32 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 0.296 C 0.208 G 0.203 T 0.293 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 79 6 2.5e-018 8.6e-014 # TGTACGGA TCCGTACA 31 0 3.5e-010 1.2e-005 # TGTATGGG CCCATACA 36 4 6.9e-008 2.4e-003 # TGTACGGG CCCGTACA 10 0 9.5e-004 3.3e+001 # TGTATGGA TCCATACA 14 2 2.0e-003 7.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 8.6e-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 0.457447 0.000000 0.542553 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.510638 0.000000 0.489362 0.000000 MOTIF CCHTAACC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 68 5 5.3e-016 1.8e-011 # CCTTAACC GGTTAAGG 34 4 2.3e-007 8.1e-003 # CCATAACC GGTTATGG 21 1 4.9e-006 1.7e-001 # CCCTAACC GGTTAGGG 14 0 5.8e-005 2.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 1.8e-011 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.304348 0.202899 0.000000 0.492754 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 50 3 1.4e-012 5.0e-008 # CTCGGCCA TGGCCGAG 31 1 5.9e-009 2.1e-004 # CTTGGCCA TGGCCAAG 19 2 1.0e-004 3.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 5.0e-008 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.620000 0.000000 0.380000 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 GGTTCGAY DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGAY RTCGAACC 46 3 2.0e-011 7.1e-007 # GGTTCGAC GTCGAACC 22 1 2.5e-006 8.8e-002 # GGTTCGAT ATCGAACC 24 2 4.6e-006 1.6e-001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 7.1e-007 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.478261 0.000000 0.521739 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 39 1 2.5e-011 8.5e-007 # GCGCTACC GGTAGCGC 25 0 2.5e-008 8.6e-004 # GCTCTACC GGTAGAGC 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 8.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.641026 0.358974 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 GTATGACW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTATGACW WGTCATAC 32 0 1.7e-010 6.0e-006 # GTATGACA TGTCATAC 20 0 8.5e-007 2.9e-002 # GTATGACT AGTCATAC 12 0 2.3e-004 8.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.0e-006 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.000000 0.375000 MOTIF TGTTGWA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TGTTGWA TWCAACA 93 28 3.3e-010 1.1e-005 # TGTTGTA TACAACA 48 14 6.2e-006 2.1e-001 # TGTTGAA TTCAACA 46 14 1.6e-005 5.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 1.1e-005 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.494845 0.000000 0.000000 0.505155 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAYTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACCAYTA TARTGGT 70 16 6.7e-010 2.3e-005 # ACCACTA TAGTGGT 48 8 1.5e-008 5.0e-004 # ACCATTA TAATGGT 23 8 5.0e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 2.3e-005 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 0.676056 0.000000 0.323944 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AMCGATG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AMCGATG CATCGKT 54 9 1.7e-009 5.8e-005 # AACGATG CATCGTT 33 3 8.8e-008 3.0e-003 # ACCGATG CATCGGT 21 6 2.8e-003 9.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 5.8e-005 1.000000 0.000000 0.000000 0.000000 0.611111 0.388889 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGWGATA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATGWGATA TATCWCAT 41 4 3.1e-009 1.1e-004 # ATGAGATA TATCTCAT 23 3 3.9e-005 1.3e+000 # ATGTGATA TATCACAT 18 2 1.9e-004 6.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.1e-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 0.560976 0.000000 0.000000 0.439024 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 MOTIF KTAGCTCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST KTAGCTCA TGAGCTAM 27 0 6.1e-009 2.1e-004 # TTAGCTCA TGAGCTAA 19 0 1.7e-006 5.9e-002 # GTAGCTCA TGAGCTAC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-004 0.000000 0.000000 0.296296 0.703704 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 AWGAAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AWGAAA TTTCWT 300 193 7.7e-009 2.6e-004 # AAGAAA TTTCTT 206 117 2.5e-008 8.4e-004 # ATGAAA TTTCAT 122 84 3.0e-003 1.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 361 E= 2.6e-004 1.000000 0.000000 0.000000 0.000000 0.650970 0.000000 0.000000 0.349030 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 MOTIF AGGAWGAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGGAWGAC GTCWTCCT 23 0 1.0e-007 3.5e-003 # AGGATGAC GTCATCCT 12 0 2.3e-004 7.9e+000 # AGGAAGAC GTCTTCCT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 3.5e-003 1.000000 0.000000 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 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GMTCGAAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GMTCGAAC GTTCGAKC 23 0 1.0e-007 3.5e-003 # GCTCGAAC GTTCGAGC 14 0 5.8e-005 2.0e+000 # GATCGAAC GTTCGATC 9 0 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-003 0.000000 0.000000 1.000000 0.000000 0.391304 0.608696 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TCKCCCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TCKCCCAA TTGGGMGA 22 0 2.1e-007 7.0e-003 # TCGCCCAA TTGGGCGA 11 0 4.7e-004 1.6e+001 # TCTCCCAA TTGGGAGA 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.0e-003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACACSCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACACSCA TGSGTGT 69 22 2.1e-007 7.1e-003 # ACACCCA TGGGTGT 52 19 4.1e-005 1.4e+000 # ACACGCA TGCGTGT 17 4 3.4e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 7.1e-003 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 0.849558 0.150442 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGYGGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCGYGGA TCCRCGG 31 3 3.1e-007 1.0e-002 # CCGTGGA TCCACGG 23 3 3.9e-005 1.3e+000 # CCGCGGA TCCGCGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 1.0e-002 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 0.281250 0.000000 0.718750 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCCTTA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 30 3 5.7e-007 1.9e-002 # CGCCTTA TAAGGCG 30 3 5.7e-007 1.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.9e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACGAWACC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACGAWACC GGTWTCGT 29 3 1.1e-006 3.5e-002 # ACGAAACC GGTTTCGT 21 3 1.3e-004 4.2e+000 # ACGATACC GGTATCGT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.5e-002 1.000000 0.000000 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 0.724138 0.000000 0.000000 0.275862 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: 107.92 seconds