# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP3/seqs-shuffled
#   positives: 680 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP3/seqs-centered (Sat Jan 18 20:04:40 PST 2020)
#   negatives: 680 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YAP3/seqs-shuffled (Sat Jan 18 20:04:40 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 20:21:24 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 0.306 C 0.190 G 0.193 T 0.311


MOTIF BACCA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST       BACCA      TGGTV        342        226   1.1e-010   3.8e-006
#            TACCA      TGGTA        172        101   9.7e-007   3.2e-002
#            CACCA      TGGTG        130         81   1.5e-004   5.1e+000
#            GACCA      TGGTC        123         85   2.6e-003   8.6e+001

letter-probability matrix: alength= 4 w= 5 nsites= 479 E= 3.8e-006
0.000000 0.302714 0.286013 0.411273
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


MOTIF SAAGA DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST       SAAGA      TCTTS        387        274   5.6e-010   1.8e-005
#            GAAGA      TCTTC        232        157   4.3e-006   1.4e-001
#            CAAGA      TCTTG        229        158   1.2e-005   3.9e-001

letter-probability matrix: alength= 4 w= 5 nsites= 563 E= 1.8e-005
0.000000 0.477798 0.522202 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


MOTIF GGTTCRA DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     GGTTCRA    TYGAACC         64         16   1.2e-008   3.6e-004
#          GGTTCGA    TCGAACC         38          8   3.3e-006   1.0e-001
#          GGTTCAA    TTGAACC         26          8   1.3e-003   3.9e+001

letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 3.6e-004
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
0.406250 0.000000 0.593750 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CTTASC DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      CTTASC     GSTAAG         84         31   1.3e-007   3.9e-003
#           CTTACC     GGTAAG         35          7   5.6e-006   1.7e-001
#           CTTAGC     GCTAAG         50         24   1.3e-003   3.9e+001

letter-probability matrix: alength= 4 w= 6 nsites= 86 E= 3.9e-003
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
0.000000 0.406977 0.593023 0.000000
0.000000 1.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 20.74 seconds