# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-shuffled
#   positives: 527 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered (Sat Jan 18 17:58:03 PST 2020)
#   negatives: 527 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-shuffled (Sat Jan 18 17:58:03 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 18:10:41 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 0.314 C 0.192 G 0.188 T 0.306


MOTIF RGTTCGA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     RGTTCGA    TCGAACY         65          6   1.2e-014   3.5e-010
#          GGTTCGA    TCGAACC         51          6   1.0e-010   3.1e-006
#          AGTTCGA    TCGAACT         20          1   8.9e-006   2.6e-001

letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 3.5e-010
0.287879 0.000000 0.712121 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 ACCRACT DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     ACCRACT    AGTYGGT         50          5   3.9e-011   1.2e-006
#          ACCAACT    AGTTGGT         35          3   2.0e-008   6.1e-004
#          ACCGACT    AGTCGGT         15          2   1.1e-003   3.2e+001

letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.2e-006
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.705882 0.000000 0.294118 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF AGTGST DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      AGTGST     ASCACT         95         28   4.6e-011   1.4e-006
#           AGTGGT     ACCACT         71         21   2.2e-008   6.6e-004
#           AGTGCT     AGCACT         24          7   1.4e-003   4.3e+001

letter-probability matrix: alength= 4 w= 6 nsites= 106 E= 1.4e-006
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 0.226415 0.773585 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF ATGTAYGG DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ATGTAYGG   CCRTACAT         27          1   7.9e-008   2.3e-003
#         ATGTATGG   CCATACAT         18          1   3.3e-005   9.8e-001
#         ATGTACGG   CCGTACAT         10          0   9.4e-004   2.7e+001

letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.3e-003
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
0.000000 0.387097 0.000000 0.612903
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 17.93 seconds