# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--YAP1/seqs-shuffled
#   positives: 595 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--YAP1/seqs-centered (Sat Jan 18 09:27:53 PST 2020)
#   negatives: 595 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--YAP1/seqs-shuffled (Sat Jan 18 09:27:53 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 09:44:06 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 0.305 C 0.192 G 0.193 T 0.310


MOTIF GGWTCGA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGWTCGA    TCGAWCC         71         11   6.8e-013   2.2e-008
#          GGTTCGA    TCGAACC         58          9   1.2e-010   3.7e-006
#          GGATCGA    TCGATCC         15          2   1.1e-003   3.5e+001

letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 2.2e-008
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.197183 0.000000 0.000000 0.802817
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 GTGRTA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      GTGRTA     TAYCAC         91         30   2.2e-009   6.9e-005
#           GTGATA     TATCAC         50         16   1.0e-005   3.1e-001
#           GTGGTA     TACCAC         44         14   3.4e-005   1.1e+000

letter-probability matrix: alength= 4 w= 6 nsites= 98 E= 6.9e-005
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.520408 0.000000 0.479592 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000


MOTIF ARAAAAAT DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    ARAAAAAT   ATTTTTYT         85         31   7.0e-008   2.2e-003
#         AAAAAAAT   ATTTTTTT         64         26   2.0e-005   6.2e-001
#         AGAAAAAT   ATTTTTCT         24          6   6.2e-004   1.9e+001

letter-probability matrix: alength= 4 w= 8 nsites= 93 E= 2.2e-003
1.000000 0.000000 0.000000 0.000000
0.731183 0.000000 0.268817 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
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF CTTGGMA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CTTGGMA    TKCCAAG         38          7   1.0e-006   3.2e-002
#          CTTGGCA    TGCCAAG         14          1   4.6e-004   1.4e+001
#          CTTGGAA    TTCCAAG         24          6   6.2e-004   1.9e+001

letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 3.2e-002
0.000000 1.000000 0.000000 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 1.000000 0.000000
0.625000 0.375000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 19.30 seconds