# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PDR1/seqs-shuffled
#   positives: 589 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PDR1/seqs-centered (Sun Jan 19 08:31:23 PST 2020)
#   negatives: 589 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PDR1/seqs-shuffled (Sun Jan 19 08:31:23 PST 2020)
#        host: kali.stanford.edu
#        when: Sun Jan 19 08:47:22 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 0.309 C 0.197 G 0.189 T 0.306


MOTIF SRGTTCGA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    SRGTTCGA   TCGAACYS         69          2   1.5e-019   4.6e-015
#         GGGTTCGA   TCGAACCC         26          0   1.1e-008   3.5e-004
#         CGGTTCGA   TCGAACCG         25          2   2.3e-006   7.1e-002
#         GAGTTCGA   TCGAACTC         11          0   4.7e-004   1.5e+001
#         CAGTTCGA   TCGAACTG          7          0   7.7e-003   2.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 69 E= 4.6e-015
0.000000 0.463768 0.536232 0.000000
0.260870 0.000000 0.739130 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 AARAAAW DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AARAAAW    WTTTYTT        233        127   1.2e-011   3.8e-007
#          AAGAAAA    TTTTCTT         78         33   4.5e-006   1.4e-001
#          AAAAAAT    ATTTTTT        105         53   5.6e-006   1.7e-001
#          AAAAAAA    TTTTTTT        119         68   3.1e-005   9.6e-001
#          AAGAAAT    ATTTCTT         38         18   4.4e-003   1.4e+002

letter-probability matrix: alength= 4 w= 7 nsites= 297 E= 3.8e-007
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.612795 0.000000 0.387205 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
0.565657 0.000000 0.000000 0.434343


MOTIF ACCWCT DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      ACCWCT     AGWGGT        109         39   3.5e-010   1.1e-005
#           ACCACT     AGTGGT         74         23   3.1e-008   9.5e-004
#           ACCTCT     AGAGGT         37         17   3.8e-003   1.2e+002

letter-probability matrix: alength= 4 w= 6 nsites= 122 E= 1.1e-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
0.680328 0.000000 0.000000 0.319672
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF AGTTGRT DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AGTTGRT    AYCAACT         51          8   2.0e-009   6.2e-005
#          AGTTGGT    ACCAACT         36          6   9.6e-007   2.9e-002
#          AGTTGAT    ATCAACT         15          2   1.1e-003   3.4e+001

letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 6.2e-005
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 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.294118 0.000000 0.705882 0.000000
0.000000 0.000000 0.000000 1.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 19.22 seconds