# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--NRG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--NRG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--NRG1/seqs-shuffled
#   positives: 716 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--NRG1/seqs-centered (Sun Jan 19 09:31:27 PST 2020)
#   negatives: 716 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--NRG1/seqs-shuffled (Sun Jan 19 09:31:27 PST 2020)
#        host: kali.stanford.edu
#        when: Sun Jan 19 09:48:22 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 0.302 C 0.199 G 0.201 T 0.298


MOTIF GGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC        107         15   5.4e-020   1.9e-015
#          GGTTCGA    TCGAACC         79          8   6.6e-017   2.3e-012
#          GGTTCAA    TTGAACC         32          7   2.8e-005   9.8e-001

letter-probability matrix: alength= 4 w= 7 nsites= 111 E= 1.9e-015
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
0.288288 0.000000 0.711712 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF SAARAAA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     SAARAAA    TTTYTTS        222        120   1.5e-010   5.3e-006
#          CAAGAAA    TTTCTTG         38         12   1.2e-004   4.1e+000
#          CAAAAAA    TTTTTTG         81         48   1.5e-003   5.2e+001
#          GAAAAAA    TTTTTTC         82         51   3.1e-003   1.1e+002
#          GAAGAAA    TTTCTTC         47         24   3.5e-003   1.2e+002

letter-probability matrix: alength= 4 w= 7 nsites= 254 E= 5.3e-006
0.000000 0.476378 0.523622 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.677165 0.000000 0.322835 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


MOTIF AGTGGTW DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AGTGGTW    WACCACT         63         14   2.9e-009   1.0e-004
#          AGTGGTA    TACCACT         35          7   5.7e-006   2.0e-001
#          AGTGGTT    AACCACT         33          7   1.7e-005   5.7e-001

letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 1.0e-004
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 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.514286 0.000000 0.000000 0.485714


MOTIF CTTGGCY DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CTTGGCY    RGCCAAG         34          5   9.1e-007   3.1e-002
#          CTTGGCC    GGCCAAG         19          1   1.8e-005   6.1e-001
#          CTTGGCT    AGCCAAG         15          4   9.2e-003   3.1e+002

letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 3.1e-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
0.000000 1.000000 0.000000 0.000000
0.000000 0.542857 0.000000 0.457143


# Stopping reason: E-value threshold exceeded
#    Running time: 23.76 seconds