# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--RPD3/seqs-shuffled
#   positives: 922 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--RPD3/seqs-centered (Sat Jan 18 06:51:15 PST 2020)
#   negatives: 922 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--RPD3/seqs-shuffled (Sat Jan 18 06:51:15 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 07:08:12 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 0.300 C 0.194 G 0.198 T 0.308


MOTIF GGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC         82         16   1.1e-012   3.9e-008
#          GGTTCGA    TCGAACC         49          7   2.3e-009   8.4e-005
#          GGTTCAA    TTGAACC         34         10   1.7e-004   6.1e+000

letter-probability matrix: alength= 4 w= 7 nsites= 83 E= 3.9e-008
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 1.000000
0.000000 1.000000 0.000000 0.000000
0.409639 0.000000 0.590361 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF TCTTGR DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      TCTTGR     YCAAGA        199         96   3.2e-011   1.2e-006
#           TCTTGA     TCAAGA        114         49   5.4e-008   2.0e-003
#           TCTTGG     CCAAGA         99         50   1.8e-005   6.5e-001

letter-probability matrix: alength= 4 w= 6 nsites= 224 E= 1.2e-006
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.535714 0.000000 0.464286 0.000000


MOTIF CCWTAACC DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCWTAACC   GGTTAWGG         30          1   1.2e-008   4.3e-004
#         CCTTAACC   GGTTAAGG         21          1   4.9e-006   1.8e-001
#         CCATAACC   GGTTATGG          9          0   1.9e-003   6.9e+001

letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 4.3e-004
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.300000 0.000000 0.000000 0.700000
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 GTGGTA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      GTGGTA     TACCAC         67         21   2.5e-007   9.1e-003
#           GTGGTA     TACCAC         67         21   2.5e-007   9.1e-003

letter-probability matrix: alength= 4 w= 6 nsites= 69 E= 9.1e-003
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
1.000000 0.000000 0.000000 0.000000


MOTIF CTTGTM DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      CTTGTM     KACAAG        128         64   6.4e-007   2.3e-002
#           CTTGTC     GACAAG         64         28   7.7e-005   2.8e+000
#           CTTGTA     TACAAG         65         37   2.9e-003   1.0e+002

letter-probability matrix: alength= 4 w= 6 nsites= 132 E= 2.3e-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 0.000000 1.000000
0.507576 0.492424 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 35.43 seconds