# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG2/seqs-shuffled # positives: 632 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG2/seqs-centered (Sun Jan 19 08:13:54 PST 2020) # negatives: 632 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MIG2/seqs-shuffled (Sun Jan 19 08:13:54 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 08:30:12 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 0.293 C 0.209 G 0.208 T 0.290 MOTIF GTTCGABY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGABY RVTCGAAC 82 2 1.3e-023 4.1e-019 # GTTCGATC GATCGAAC 23 0 9.7e-008 3.2e-003 # GTTCGATT AATCGAAC 20 0 8.2e-007 2.7e-002 # GTTCGACT AGTCGAAC 11 0 4.7e-004 1.5e+001 # GTTCGAGT ACTCGAAC 9 0 1.9e-003 6.2e+001 # GTTCGAGC GCTCGAAC 12 2 6.2e-003 2.0e+002 # GTTCGACC GGTCGAAC 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 4.1e-019 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 0.219512 0.256098 0.524390 0.000000 0.512195 0.000000 0.487805 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 58 1 2.8e-017 9.0e-013 # CTCGGCCA TGGCCGAG 26 0 1.1e-008 3.7e-004 # CTTGGCCA TGGCCAAG 21 0 4.0e-007 1.3e-002 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 9.0e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.448276 0.189655 0.362069 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 CCHTAACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 57 5 5.1e-013 1.6e-008 # CCTTAACC GGTTAAGG 35 4 1.1e-007 3.7e-003 # CCATAACC GGTTATGG 13 0 1.1e-004 3.7e+000 # CCCTAACC GGTTAGGG 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 1.6e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.224138 0.172414 0.000000 0.603448 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 AGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 73 13 3.0e-012 9.7e-008 # AGTGGTA TACCACT 41 5 1.3e-008 4.2e-004 # AGTGGTT AACCACT 42 8 3.6e-007 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 85 E= 9.7e-008 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 0.494118 0.000000 0.000000 0.505882 MOTIF AAAAAWA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWA TWTTTTT 179 91 9.1e-010 2.9e-005 # AAAAAAA TTTTTTT 128 60 4.5e-008 1.5e-003 # AAAAATA TATTTTT 79 40 1.1e-004 3.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 211 E= 2.9e-005 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 0.625592 0.000000 0.000000 0.374408 1.000000 0.000000 0.000000 0.000000 MOTIF AGACCAY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGACCAY RTGGTCT 37 4 3.3e-008 1.1e-003 # AGACCAC GTGGTCT 22 1 2.4e-006 7.7e-002 # AGACCAT ATGGTCT 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.1e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.594595 0.000000 0.405405 MOTIF CACCGTS DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACCGTS SACGGTG 30 2 9.1e-008 2.9e-003 # CACCGTG CACGGTG 24 2 4.3e-006 1.4e-001 # CACCGTC GACGGTG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 2.9e-003 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 0.225806 0.774194 0.000000 MOTIF CCATCGTK DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCATCGTK MACGATGG 22 0 2.0e-007 6.3e-003 # CCATCGTT AACGATGG 12 0 2.3e-004 7.4e+000 # CCATCGTG CACGATGG 10 0 9.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.3e-003 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 0.000000 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 0.454545 0.545455 MOTIF CSTCCCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CSTCCCC GGGGASG 22 0 2.0e-007 6.3e-003 # CGTCCCC GGGGACG 13 0 1.1e-004 3.6e+000 # CCTCCCC GGGGAGG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 22 E= 6.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.409091 0.590909 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 1.000000 0.000000 0.000000 MOTIF SATGTAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST SATGTAA TTACATS 35 5 4.8e-007 1.5e-002 # GATGTAA TTACATC 19 3 3.9e-004 1.2e+001 # CATGTAA TTACATG 16 2 6.1e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 1.5e-002 0.000000 0.472222 0.527778 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AWTTGAAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AWTTGAAC GTTCAAWT 30 3 5.3e-007 1.7e-002 # AATTGAAC GTTCAATT 20 2 5.3e-005 1.7e+000 # ATTTGAAC GTTCAAAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.7e-002 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGKCGCC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAGKCGCC GGCGMCTT 24 1 6.3e-007 2.0e-002 # AAGGCGCC GGCGCCTT 14 0 5.7e-005 1.8e+000 # AAGTCGCC GGCGACTT 11 1 3.1e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 2.0e-002 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 0.560000 0.440000 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 GMTACCGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 24 1 6.3e-007 2.0e-002 # GCTACCGA TCGGTAGC 16 1 1.3e-004 4.0e+000 # GATACCGA TCGGTATC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGGRGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGCGGRGA TCYCCGCG 20 0 8.2e-007 2.6e-002 # CGCGGGGA TCCCCGCG 11 0 4.7e-004 1.5e+001 # CGCGGAGA TCTCCGCG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.450000 0.000000 0.550000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 61.75 seconds