# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--ARR1/seqs-shuffled
#   positives: 472 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--ARR1/seqs-centered (Sun Jan 19 06:04:28 PST 2020)
#   negatives: 472 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--ARR1/seqs-shuffled (Sun Jan 19 06:04:28 PST 2020)
#        host: kali.stanford.edu
#        when: Sun Jan 19 06:14:20 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 0.193 G 0.190 T 0.313


MOTIF GGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC         66          7   2.7e-014   7.8e-010
#          GGTTCGA    TCGAACC         43          3   9.7e-011   2.8e-006
#          GGTTCAA    TTGAACC         23          4   1.3e-004   3.7e+000

letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 7.8e-010
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
0.348485 0.000000 0.651515 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CGCCTTA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CGCCTTA    TAAGGCG         30          1   9.5e-009   2.8e-004
#          CGCCTTA    TAAGGCG         30          1   9.5e-009   2.8e-004

letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.8e-004
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


MOTIF AAAAAKAA DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AAAAAKAA   TTMTTTTT         70         20   1.3e-008   3.8e-004
#         AAAAAGAA   TTCTTTTT         36          5   2.3e-007   6.7e-003
#         AAAAATAA   TTATTTTT         38         15   8.1e-004   2.3e+001

letter-probability matrix: alength= 4 w= 8 nsites= 78 E= 3.8e-004
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 0.487179 0.512821
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF RGAAGA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      RGAAGA     TCTTCY         83         35   1.4e-006   4.1e-002
#           GGAAGA     TCTTCC         44         16   1.3e-004   3.6e+000
#           AGAAGA     TCTTCT         48         19   1.6e-004   4.6e+000

letter-probability matrix: alength= 4 w= 6 nsites= 92 E= 4.1e-002
0.521739 0.000000 0.478261 0.000000
0.000000 0.000000 1.000000 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
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 16.21 seconds