# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--IES2/seqs-shuffled
#   positives: 602 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--IES2/seqs-centered (Sat Jan 18 20:51:32 PST 2020)
#   negatives: 602 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--IES2/seqs-shuffled (Sat Jan 18 20:51:32 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 21:08:00 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 0.307 C 0.191 G 0.198 T 0.303


MOTIF SRGTTCGA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    SRGTTCGA   TCGAACYS         60          4   9.5e-015   3.0e-010
#         GGGTTCGA   TCGAACCC         24          3   2.1e-005   6.5e-001
#         CGGTTCGA   TCGAACCG         17          1   6.5e-005   2.1e+000
#         GAGTTCGA   TCGAACTC         12          0   2.3e-004   7.3e+000
#         CAGTTCGA   TCGAACTG          7          0   7.7e-003   2.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 3.0e-010
0.000000 0.400000 0.600000 0.000000
0.316667 0.000000 0.683333 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 ACTARACC DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ACTARACC   GGTYTAGT         25          0   2.3e-008   7.3e-004
#         ACTAGACC   GGTCTAGT         15          0   2.8e-005   8.8e-001
#         ACTAAACC   GGTTTAGT         10          0   9.4e-004   3.0e+001

letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.3e-004
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
0.400000 0.000000 0.600000 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 CCTTAVC DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CCTTAVC    GBTAAGG         56         14   1.0e-007   3.1e-003
#          CCTTAGC    GCTAAGG         17          3   1.2e-003   3.7e+001
#          CCTTACC    GGTAAGG         18          4   2.0e-003   6.3e+001
#          CCTTAAC    GTTAAGG         22          7   3.7e-003   1.2e+002

letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 3.1e-003
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
0.385965 0.315789 0.298246 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF GGYTATCA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    GGYTATCA   TGATARCC         20          0   8.1e-007   2.5e-002
#         GGCTATCA   TGATAGCC         11          0   4.7e-004   1.5e+001
#         GGTTATCA   TGATAACC          9          0   1.9e-003   5.9e+001

letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-002
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.550000 0.000000 0.450000
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 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 20.46 seconds