# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-shuffled
#   positives: 533 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered (Sat Jan 18 01:23:31 PST 2020)
#   negatives: 533 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-shuffled (Sat Jan 18 01:23:31 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 01:36:23 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 0.308 C 0.195 G 0.196 T 0.300


MOTIF GGTTCRA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC         92         18   1.1e-014   3.4e-010
#          GGTTCGA    TCGAACC         64          9   2.6e-012   8.1e-008
#          GGTTCAA    TTGAACC         29          9   6.8e-004   2.1e+001

letter-probability matrix: alength= 4 w= 7 nsites= 93 E= 3.4e-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
0.311828 0.000000 0.688172 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AARAARA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AARAARA    TYTTYTT        196        103   1.4e-010   4.2e-006
#          AAAAAAA    TTTTTTT        110         52   4.6e-007   1.4e-002
#          AAGAAGA    TCTTCTT         35          8   1.5e-005   4.5e-001
#          AAGAAAA    TTTTCTT         59         30   9.0e-004   2.7e+001
#          AAAAAGA    TCTTTTT         60         35   4.8e-003   1.5e+002

letter-probability matrix: alength= 4 w= 7 nsites= 249 E= 4.2e-006
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.646586 0.000000 0.353414 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.654618 0.000000 0.345382 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF ACCACT DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      ACCACT     AGTGGT         58         12   3.9e-009   1.2e-004
#           ACCACT     AGTGGT         58         12   3.9e-009   1.2e-004

letter-probability matrix: alength= 4 w= 6 nsites= 62 E= 1.2e-004
1.000000 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 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF GATGWC DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      GATGWC     GWCATC         60         19   9.0e-007   2.7e-002
#           GATGTC     GACATC         32         10   3.7e-004   1.1e+001
#           GATGAC     GTCATC         28         10   2.2e-003   6.6e+001

letter-probability matrix: alength= 4 w= 6 nsites= 61 E= 2.7e-002
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.475410 0.000000 0.000000 0.524590
0.000000 1.000000 0.000000 0.000000


MOTIF RCGGGGA DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     RCGGGGA    TCCCCGY         29          3   9.3e-007   2.8e-002
#          GCGGGGA    TCCCCGC         14          1   4.5e-004   1.3e+001
#          ACGGGGA    TCCCCGT         15          2   1.1e-003   3.2e+001

letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 2.8e-002
0.517241 0.000000 0.482759 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 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CGCCTTA DREME-6

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CGCCTTA    TAAGGCG         23          1   1.2e-006   3.5e-002
#          CGCCTTA    TAAGGCG         23          1   1.2e-006   3.5e-002

letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.5e-002
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: 24.09 seconds