# DREME 5.5.3
#     command: dreme -oc dreme_example_output_files -png -p Klf1.fna
#   positives: 904 from Klf1.fna (Mon Aug 16 16:20:49 PDT 2021)
#   negatives: 904 from shuffled positives
#        host: Timothys-iMac.local
#        when: Fri Jun 09 08:18:41 PDT 2023

MEME version 5.5.3

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 0.255 C 0.245 G 0.243 T 0.257


MOTIF CCMCRCCC DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCMCRCCC   GGGYGKGG        350         40   4.9e-078   2.1e-073
#         CCACACCC   GGGTGTGG        175         19   2.4e-036   1.0e-031
#         CCCCACCC   GGGTGGGG        128         16   8.3e-025   3.5e-020
#         CCCCGCCC   GGGCGGGG         53          3   2.0e-013   8.6e-009
#         CCACGCCC   GGGCGTGG         55          4   4.1e-013   1.7e-008

letter-probability matrix: alength= 4 w= 8 nsites= 454 E= 2.1e-073
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.550661 0.449339 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.733480 0.000000 0.266520 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


MOTIF TTATCW DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      TTATCW     WGATAA        496        243   2.9e-034   1.2e-029
#           TTATCT     AGATAA        352        138   1.8e-030   7.5e-026
#           TTATCA     TGATAA        250        124   1.3e-013   5.5e-009

letter-probability matrix: alength= 4 w= 6 nsites= 717 E= 1.2e-029
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 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.417015 0.000000 0.000000 0.582985


MOTIF ACRCCCW DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     ACRCCCW    WGGGYGT        263        108   5.5e-020   2.3e-015
#          ACGCCCT    AGGGCGT         54         11   1.8e-008   7.6e-004
#          ACGCCCA    TGGGCGT         46         12   3.0e-006   1.3e-001
#          ACACCCA    TGGGTGT        102         51   1.0e-005   4.3e-001
#          ACACCCT    AGGGTGT         95         47   1.7e-005   7.3e-001

letter-probability matrix: alength= 4 w= 7 nsites= 314 E= 2.3e-015
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.678344 0.000000 0.321656 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
0.503185 0.000000 0.000000 0.496815


MOTIF TTTMTW DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      TTTMTW     WAKAAA        607        443   3.3e-015   1.4e-010
#           TTTATT     AATAAA        239        132   2.7e-010   1.1e-005
#           TTTCTT     AAGAAA        335        234   2.0e-007   8.2e-003
#           TTTCTA     TAGAAA        243        159   1.3e-006   5.3e-002
#           TTTATA     TATAAA        151        110   3.7e-003   1.6e+002

letter-probability matrix: alength= 4 w= 6 nsites= 1166 E= 1.4e-010
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.388508 0.611492 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.391938 0.000000 0.000000 0.608062


MOTIF CWCCRCCC DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CWCCRCCC   GGGYGGWG        139         36   3.5e-017   1.4e-012
#         CTCCACCC   GGGTGGAG         77         16   1.6e-011   6.9e-007
#         CACCGCCC   GGGCGGTG         23          3   3.9e-005   1.6e+000
#         CTCCGCCC   GGGCGGAG         23          6   1.1e-003   4.5e+001
#         CACCACCC   GGGTGGTG         28         12   7.7e-003   3.2e+002

letter-probability matrix: alength= 4 w= 8 nsites= 158 E= 1.4e-012
0.000000 1.000000 0.000000 0.000000
0.335443 0.000000 0.000000 0.664557
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.702532 0.000000 0.297468 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


MOTIF RASAGAAA DREME-6

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    RASAGAAA   TTTCTSTY        153         52   2.0e-014   8.5e-010
#         AACAGAAA   TTTCTGTT         45         12   4.8e-006   2.0e-001
#         AAGAGAAA   TTTCTCTT         47         16   4.5e-005   1.9e+000
#         GACAGAAA   TTTCTGTC         32          8   7.8e-005   3.2e+000
#         GAGAGAAA   TTTCTCTC         39         17   2.0e-003   8.3e+001

letter-probability matrix: alength= 4 w= 8 nsites= 166 E= 8.5e-010
0.554217 0.000000 0.445783 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.475904 0.524096 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
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CMCGCCY DREME-7

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CMCGCCY    RGGCGKG        121         35   1.5e-013   6.1e-009
#          CCCGCCC    GGGCGGG         48         12   1.1e-006   4.6e-002
#          CACGCCT    AGGCGTG         34          6   3.4e-006   1.4e-001
#          CACGCCC    GGGCGTG         15          1   2.5e-004   1.0e+001
#          CCCGCCT    AGGCGGG         36         17   5.7e-003   2.4e+002

letter-probability matrix: alength= 4 w= 7 nsites= 139 E= 6.1e-009
0.000000 1.000000 0.000000 0.000000
0.352518 0.647482 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 0.474820 0.000000 0.525180


MOTIF TTTAAAWW DREME-8

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    TTTAAAWW   WWTTTAAA        110         32   2.6e-012   1.1e-007
#         TTTAAAAA   TTTTTAAA         65         15   3.4e-009   1.4e-004
#         TTTAAAAT   ATTTTAAA         33         10   2.6e-004   1.1e+001
#         TTTAAATA   TATTTAAA         18          5   5.1e-003   2.1e+002
#         TTTAAATT   AATTTAAA         26         11   9.4e-003   3.9e+002

letter-probability matrix: alength= 4 w= 8 nsites= 120 E= 1.1e-007
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.716667 0.000000 0.000000 0.283333
0.616667 0.000000 0.000000 0.383333


MOTIF RCAGASA DREME-9

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     RCAGASA    TSTCTGY        355        231   2.9e-010   1.2e-005
#          ACAGACA    TGTCTGT        109         55   6.1e-006   2.5e-001
#          GCAGAGA    TCTCTGC        119         72   2.0e-004   8.5e+000
#          GCAGACA    TGTCTGC         82         51   3.3e-003   1.4e+002
#          ACAGAGA    TCTCTGT        121         87   7.4e-003   3.1e+002

letter-probability matrix: alength= 4 w= 7 nsites= 451 E= 1.2e-005
0.523282 0.000000 0.476718 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.434590 0.565410 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF CATTTCH DREME-10

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CATTTCH    DGAAATG        187         94   8.8e-010   3.7e-005
#          CATTTCC    GGAAATG         94         45   9.5e-006   3.9e-001
#          CATTTCA    TGAAATG         68         34   3.5e-004   1.4e+001
#          CATTTCT    AGAAATG         43         20   2.2e-003   9.1e+001

letter-probability matrix: alength= 4 w= 7 nsites= 216 E= 3.7e-005
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000
0.314815 0.476852 0.000000 0.208333


MOTIF ACASAG DREME-11

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      ACASAG     CTSTGT        450        325   1.8e-009   7.4e-005
#           ACACAG     CTGTGT        299        204   3.8e-007   1.6e-002
#           ACAGAG     CTCTGT        242        172   5.5e-005   2.3e+000

letter-probability matrix: alength= 4 w= 6 nsites= 616 E= 7.4e-005
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.545455 0.454545 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF AGGAAV DREME-12

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      AGGAAV     BTTCCT        625        505   3.5e-009   1.4e-004
#           AGGAAG     CTTCCT        360        269   4.3e-006   1.8e-001
#           AGGAAA     TTTCCT        316        243   1.2e-004   5.0e+000
#           AGGAAC     GTTCCT        212        170   9.1e-003   3.7e+002

letter-probability matrix: alength= 4 w= 6 nsites= 1116 E= 1.4e-004
1.000000 0.000000 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 0.000000
1.000000 0.000000 0.000000 0.000000
0.364695 0.211470 0.423835 0.000000


MOTIF CSTCCCAG DREME-13

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CSTCCCAG   CTGGGASG         71         19   7.2e-009   2.9e-004
#         CCTCCCAG   CTGGGAGG         61         17   1.6e-007   6.6e-003
#         CGTCCCAG   CTGGGACG         12          2   6.3e-003   2.6e+002

letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 2.9e-004
0.000000 1.000000 0.000000 0.000000
0.000000 0.837838 0.162162 0.000000
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 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF AHATACA DREME-14

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     AHATACA    TGTATDT        138         66   5.0e-008   2.1e-003
#          ATATACA    TGTATAT         45         15   5.2e-005   2.1e+000
#          ACATACA    TGTATGT         50         26   3.3e-003   1.4e+002
#          AAATACA    TGTATTT         51         27   3.7e-003   1.5e+002

letter-probability matrix: alength= 4 w= 7 nsites= 153 E= 2.1e-003
1.000000 0.000000 0.000000 0.000000
0.346405 0.352941 0.000000 0.300654
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AGAGRCAG DREME-15

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AGAGRCAG   CTGYCTCT         85         30   5.9e-008   2.4e-003
#         AGAGGCAG   CTGCCTCT         51         15   3.5e-006   1.4e-001
#         AGAGACAG   CTGTCTCT         36         16   3.5e-003   1.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 2.4e-003
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.411111 0.000000 0.588889 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000


MOTIF ACACGB DREME-16

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      ACACGB     VCGTGT        147         79   8.1e-007   3.3e-002
#           ACACGG     CCGTGT         61         31   8.9e-004   3.6e+001
#           ACACGT     ACGTGT         51         26   2.4e-003   1.0e+002
#           ACACGC     GCGTGT         47         26   8.2e-003   3.3e+002

letter-probability matrix: alength= 4 w= 6 nsites= 167 E= 3.3e-002
1.000000 0.000000 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 1.000000 0.000000
0.000000 0.299401 0.371257 0.329341


# Stopping reason: E-value threshold exceeded
#    Running time: 433.08 seconds
