# DREME 4.9.1
# command:   dreme -oc dreme_example_output_files -png -p sample-dna-Klf1.fa
# host:      tlb-takumi-lt.imb.uq.edu.au
# when:      Fri Aug 23 17:03:55 EST 2013
# positives: 904
#      from: sample-dna-Klf1.fa (Thu Jun 06 11:58:08 EST 2013)
# negatives: 904
#      from: shuffled positives


MEME version 4.9.1

ALPHABET= ACGT

strands: + -

Background letter frequencies (from dataset):
A 0.255 C 0.244 G 0.243 T 0.258

MOTIF CCMCRCCC

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CCMCRCCC   GGGYGKGG        369         51   8.6e-077   3.7e-072
#         CCACACCC   GGGTGTGG        188         20   1.5e-039   6.5e-035
#         CCCCACCC   GGGTGGGG        139         24   6.3e-023   2.7e-018
#         CCACGCCC   GGGCGTGG         59          2   3.3e-016   1.4e-011
#         CCCCGCCC   GGGCGGGG         65          7   1.3e-013   5.7e-009

letter-probability matrix: alength= 4 w= 8 nsites= 510 E= 3.7e-072
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.549020 0.450980 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.725490 0.000000 0.274510 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

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      TTATCW     WGATAA        497        244   3.0e-034   1.3e-029
#           TTATCT     AGATAA        356        138   2.0e-031   8.5e-027
#           TTATCA     TGATAA        250        128   9.1e-013   3.9e-008

letter-probability matrix: alength= 4 w= 6 nsites= 722 E= 1.3e-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
0.414127 0.000000 0.000000 0.585873


MOTIF CACRCMC

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     CACRCMC    GKGYGTG        270         95   1.8e-025   7.7e-021
#          CACACCC    GGGTGTG        129         32   1.5e-016   6.5e-012
#          CACACAC    GTGTGTG        123         54   2.6e-008   1.1e-003
#          CACGCCC    GGGCGTG         46          9   1.5e-007   6.3e-003
#          CACGCAC    GTGCGTG         25          9   4.2e-003   1.8e+002

letter-probability matrix: alength= 4 w= 7 nsites= 350 E= 7.7e-021
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.785714 0.000000 0.214286 0.000000
0.000000 1.000000 0.000000 0.000000
0.457143 0.542857 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF RARGAAA

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     RARGAAA    TTTCYTY        412        240   2.0e-017   8.5e-013
#          AAAGAAA    TTTCTTT        161         82   3.0e-008   1.3e-003
#          GAGGAAA    TTTCCTC        113         50   1.3e-007   5.6e-003
#          GAAGAAA    TTTCTTC        125         68   8.9e-006   3.8e-001
#          AAGGAAA    TTTCCTT        138         80   1.8e-005   7.5e-001

letter-probability matrix: alength= 4 w= 7 nsites= 568 E= 8.5e-013
0.556338 0.000000 0.443662 0.000000
1.000000 0.000000 0.000000 0.000000
0.538732 0.000000 0.461268 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 TTTTAWW

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     TTTTAWW    WWTAAAA        292        154   2.7e-014   1.1e-009
#          TTTTAAA    TTTAAAA        124         54   1.8e-008   7.6e-004
#          TTTTATT    AATAAAA        103         54   2.7e-005   1.1e+000
#          TTTTAAT    ATTAAAA         75         37   1.4e-004   5.8e+000
#          TTTTATA    TATAAAA         66         36   1.5e-003   6.2e+001

letter-probability matrix: alength= 4 w= 7 nsites= 396 E= 1.1e-009
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
1.000000 0.000000 0.000000 0.000000
0.537879 0.000000 0.000000 0.462121
0.517677 0.000000 0.000000 0.482323


MOTIF CTCCDCCC

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CTCCDCCC   GGGHGGAG        164         61   7.7e-014   3.2e-009
#         CTCCACCC   GGGTGGAG         80         24   6.4e-009   2.7e-004
#         CTCCTCCC   GGGAGGAG         75         33   1.9e-005   8.2e-001
#         CTCCGCCC   GGGCGGAG         24          8   3.3e-003   1.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 191 E= 3.2e-009
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
0.455497 0.000000 0.125654 0.418848
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 ACACRK

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      ACACRK     MYGTGT        476        335   1.6e-011   6.9e-007
#           ACACAG     CTGTGT        309        200   7.4e-009   3.1e-004
#           ACACGG     CCGTGT         69         31   6.0e-005   2.5e+000
#           ACACAT     ATGTGT        182        125   2.2e-004   9.2e+000
#           ACACGT     ACGTGT         56         32   5.8e-003   2.4e+002

letter-probability matrix: alength= 4 w= 6 nsites= 716 E= 6.9e-007
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
0.818436 0.000000 0.181564 0.000000
0.000000 0.000000 0.613128 0.386872


MOTIF MCGCCCW

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     MCGCCCW    WGGGCGK        137         48   1.8e-012   7.4e-008
#          ACGCCCT    AGGGCGT         30          7   8.3e-005   3.4e+000
#          ACGCCCA    TGGGCGT         37         11   9.2e-005   3.8e+000
#          CCGCCCA    TGGGCGG         35         14   1.7e-003   7.0e+001
#          CCGCCCT    AGGGCGG         40         19   3.8e-003   1.6e+002

letter-probability matrix: alength= 4 w= 7 nsites= 147 E= 7.4e-008
0.455782 0.544218 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 1.000000 0.000000 0.000000
0.489796 0.000000 0.000000 0.510204


MOTIF TTCTCTB

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST     TTCTCTB    VAGAGAA        305        188   3.9e-010   1.6e-005
#          TTCTCTT    AAGAGAA        121         65   9.1e-006   3.8e-001
#          TTCTCTG    CAGAGAA        122         75   2.5e-004   1.0e+001
#          TTCTCTC    GAGAGAA        114         74   1.3e-003   5.3e+001

letter-probability matrix: alength= 4 w= 7 nsites= 383 E= 1.6e-005
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 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.310705 0.344648 0.344648


MOTIF AAATRT

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      AAATRT     AYATTT        319        202   7.6e-010   3.1e-005
#           AAATGT     ACATTT        207        129   1.5e-006   6.2e-002
#           AAATAT     ATATTT        163         98   8.5e-006   3.5e-001

letter-probability matrix: alength= 4 w= 6 nsites= 447 E= 3.1e-005
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 0.000000 1.000000
0.445190 0.000000 0.554810 0.000000
0.000000 0.000000 0.000000 1.000000


MOTIF AKATA

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST       AKATA      TATMT        484        370   4.9e-008   2.0e-003
#            AGATA      TATCT        370        282   1.0e-005   4.1e-001
#            ATATA      TATAT        212        158   9.9e-004   4.1e+001

letter-probability matrix: alength= 4 w= 5 nsites= 734 E= 2.0e-003
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.652589 0.347411
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000


MOTIF AAAAHAAA

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    AAAAHAAA   TTTDTTTT        126         58   7.0e-008   2.9e-003
#         AAAAAAAA   TTTTTTTT         58         24   7.9e-005   3.2e+000
#         AAAATAAA   TTTATTTT         26          7   6.0e-004   2.4e+001
#         AAAACAAA   TTTGTTTT         52         29   6.0e-003   2.4e+002

letter-probability matrix: alength= 4 w= 8 nsites= 148 E= 2.9e-003
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
0.445946 0.371622 0.000000 0.182432
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 CTGGGRAC

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST    CTGGGRAC   GTYCCCAG         59         17   4.2e-007   1.7e-002
#         CTGGGAAC   GTTCCCAG         29          5   1.6e-005   6.7e-001
#         CTGGGGAC   GTCCCCAG         32         13   3.0e-003   1.2e+002

letter-probability matrix: alength= 4 w= 8 nsites= 61 E= 1.7e-002
0.000000 1.000000 0.000000 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 1.000000 0.000000
0.475410 0.000000 0.524590 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000


MOTIF SACAGA

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      SACAGA     TCTGTS        425        322   5.4e-007   2.2e-002
#           GACAGA     TCTGTC        263        188   2.8e-005   1.1e+000
#           CACAGA     TCTGTG        232        175   8.0e-004   3.2e+001

letter-probability matrix: alength= 4 w= 6 nsites= 590 E= 2.2e-002
0.000000 0.461017 0.538983 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
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000



Time 525.54 secs.
