11_115384558_115384668|Sumo2
LENGTH = 111 COMBINED P-VALUE = 4.18e-02 E-VALUE = 2.3
DIAGRAM: 111
5_40005230_40005342|Hs3st1
LENGTH = 113 COMBINED P-VALUE = 4.26e-02 E-VALUE = 2.3
DIAGRAM: 113
2_91460599_91460720|Ckap5
LENGTH = 122 COMBINED P-VALUE = 4.61e-02 E-VALUE = 2.5
DIAGRAM: 122
Example DREME:
# DREME 4.11.3
# command: dreme -dna -p neurite.fasta -n soma.fasta -oc ./DREME_neurite -e 1 -mink 3 -maxk 10 -norc
# positives: 54 from neurite.fasta (Fri Jul 28 11:16:55 CEST 2017)
# negatives: 76 from soma.fasta (Fri Jul 28 11:16:55 CEST 2017)
# host: sl-cheku-p-cs1
# when: Mon Jul 31 21:17:40 CEST 2017
MEME version 4.11.3
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 0.227 C 0.273 G 0.259 T 0.242
MOTIF TTTTRD DREME
# Word RC Word Pos Neg P-value E-value
# BEST TTTTRD HYAAAA 45 2 2.4e-023 1.5e-018
# TTTTGA TCAAAA 17 0 5.8e-008 3.6e-003
# TTTTGT ACAAAA 17 0 5.8e-008 3.6e-003
# TTTTAA TTAAAA 19 1 8.5e-008 5.3e-003
# TTTTAT ATAAAA 16 0 1.7e-007 1.1e-002
# TTTTAG CTAAAA 9 0 2.4e-004 1.5e+001
# TTTTGG CCAAAA 7 1 8.9e-003 5.6e+002
letter-probability matrix: alength= 4 w= 6 nsites= 130 E= 1.5e-018
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
0.584615 0.000000 0.415385 0.000000
0.446154 0.000000 0.146154 0.407692
I also used the web version of MAST, but again the alignments in the HTML file are not shown.
http://meme-suite.org/info/status?service=MAST&id=appMAST_4.12.01501533185562-749754134
Thank you.