# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--HSF1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--HSF1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--HSF1/seqs-shuffled
#   positives: 568 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--HSF1/seqs-centered (Sat Jan 18 11:20:35 PST 2020)
#   negatives: 568 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--HSF1/seqs-shuffled (Sat Jan 18 11:20:35 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 11:35:34 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 0.297 C 0.200 G 0.200 T 0.302


MOTIF RGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     RGTTCRA    TYGAACY        123         24   1.1e-019   3.6e-015
#          GGTTCGA    TCGAACC         53          5   6.1e-012   1.9e-007
#          GGTTCAA    TTGAACC         34          8   2.5e-005   8.0e-001
#          AGTTCAA    TTGAACT         24          8   3.1e-003   9.8e+001
#          AGTTCGA    TCGAACT         16          4   5.6e-003   1.7e+002

letter-probability matrix: alength= 4 w= 7 nsites= 125 E= 3.6e-015
0.320000 0.000000 0.680000 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
0.472000 0.000000 0.528000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AAAAARWA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AAAAARWA   TWYTTTTT        133         38   7.0e-016   2.2e-011
#         AAAAAGAA   TTCTTTTT         44          9   3.5e-007   1.1e-002
#         AAAAAATA   TATTTTTT         51         13   4.8e-007   1.5e-002
#         AAAAAAAA   TTTTTTTT         52         17   8.3e-006   2.6e-001
#         AAAAAGTA   TACTTTTT         18          3   6.8e-004   2.1e+001

letter-probability matrix: alength= 4 w= 8 nsites= 151 E= 2.2e-011
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
0.602649 0.000000 0.397351 0.000000
0.596026 0.000000 0.000000 0.403974
1.000000 0.000000 0.000000 0.000000


MOTIF CGCCTTA DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CGCCTTA    TAAGGCG         30          0   6.3e-010   2.0e-005
#          CGCCTTA    TAAGGCG         30          0   6.3e-010   2.0e-005

letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.0e-005
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 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 15.27 seconds