# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--INO80/seqs-shuffled
#   positives: 577 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--INO80/seqs-centered (Sat Jan 18 09:44:29 PST 2020)
#   negatives: 577 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--INO80/seqs-shuffled (Sat Jan 18 09:44:29 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 09:59:49 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 0.304 C 0.194 G 0.197 T 0.306


MOTIF GGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC         75         12   2.2e-013   6.8e-009
#          GGTTCGA    TCGAACC         51          5   2.3e-011   7.2e-007
#          GGTTCAA    TTGAACC         26          7   5.6e-004   1.8e+001

letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 6.8e-009
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
0.337662 0.000000 0.662338 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AGTGGTWA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AGTGGTWA   TWACCACT         30          1   1.0e-008   3.3e-004
#         AGTGGTTA   TAACCACT         20          1   9.0e-006   2.8e-001
#         AGTGGTAA   TTACCACT         10          0   9.4e-004   2.9e+001

letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.3e-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
0.333333 0.000000 0.000000 0.666667
1.000000 0.000000 0.000000 0.000000


MOTIF AARAARA DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AARAARA    TYTTYTT        184        102   1.4e-008   4.4e-004
#          AAAAAAA    TTTTTTT         98         54   8.4e-005   2.6e+000
#          AAGAAAA    TTTTCTT         55         25   3.4e-004   1.1e+001
#          AAAAAGA    TCTTTTT         59         32   2.1e-003   6.7e+001
#          AAGAAGA    TCTTCTT         28         12   7.4e-003   2.3e+002

letter-probability matrix: alength= 4 w= 7 nsites= 231 E= 4.4e-004
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.666667 0.000000 0.333333 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.675325 0.000000 0.324675 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF GCTRCTA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GCTRCTA    TAGYAGC         24          1   6.2e-007   1.9e-002
#          GCTGCTA    TAGCAGC         15          1   2.4e-004   7.4e+000
#          GCTACTA    TAGTAGC          9          0   1.9e-003   5.9e+001

letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 1.9e-002
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.360000 0.000000 0.640000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 18.67 seconds