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MEME - Motif discovery tool
********************************************************************************
MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800)
For further information on how to interpret these results please access https://meme-suite.org/meme.
To get a copy of the MEME Suite software please access https://meme-suite.org.
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REFERENCE
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If you use this program in your research, please cite:
Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
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TRAINING SET
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PRIMARY SEQUENCES= ../result/final_prediction/K562/fasta/RankLinear0.6_40/COPS2.fasta
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
chr17:36301785-36301865 1.0000 80 chr2:145440315-145440395 1.0000 80
chr7:117845791-117845871 1.0000 80 chr21:11111241-11111321 1.0000 80
chr10:74144248-74144328 1.0000 80 chr6:33037149-33037229 1.0000 80
chr7:131053866-131053946 1.0000 80 chr4:190655937-190656017 1.0000 80
chr7:117807305-117807385 1.0000 80 chr6:138257368-138257448 1.0000 80
chr13:92276568-92276648 1.0000 80 chr6:38691447-38691527 1.0000 80
chr2:91766349-91766429 1.0000 80 chr21:11073622-11073702 1.0000 80
chr2:91790989-91791069 1.0000 80 chr21:11146225-11146305 1.0000 80
chr13:91557567-91557647 1.0000 80 chr2:152252300-152252380 1.0000 80
chr6:150128989-150129069 1.0000 80 chr7:110962323-110962403 1.0000 80
chr20:29649593-29649673 1.0000 80 chr9:66484483-66484563 1.0000 80
chr21:11093201-11093281 1.0000 80 chr6:158281868-158281948 1.0000 80
chr6:6657829-6657909 1.0000 80 chr6:57535512-57535592 1.0000 80
chr21:11057701-11057781 1.0000 80 chr7:133230691-133230771 1.0000 80
chr2:69787251-69787331 1.0000 80 chr20:43485664-43485744 1.0000 80
chr9:66461460-66461540 1.0000 80 chr5:43313793-43313873 1.0000 80
chr1:228045134-228045214 1.0000 80 chr21:11042077-11042157 1.0000 80
chr21:11171847-11171927 1.0000 80 chr4:166248651-166248731 1.0000 80
chr22:42228918-42228998 1.0000 80 chr6:158739474-158739554 1.0000 80
chr7:98684344-98684424 1.0000 80 chr5:74632811-74632891 1.0000 80
chr2:91783936-91784016 1.0000 80 chr2:177319680-177319760 1.0000 80
chr12:108511298-10851137 1.0000 80 chr10:102133170-10213325 1.0000 80
chr16:70946472-70946552 1.0000 80 chr2:91786025-91786105 1.0000 80
chr10:61705906-61705986 1.0000 80 chr20:49149119-49149199 1.0000 80
chr17:36981584-36981664 1.0000 80 chr21:11057088-11057168 1.0000 80
chr17:36305093-36305173 1.0000 80 chr21:11118676-11118756 1.0000 80
chr4:120375774-120375854 1.0000 80 chr1:145104329-145104409 1.0000 80
chr21:11112650-11112730 1.0000 80 chr6:57394362-57394442 1.0000 80
chr21:11048847-11048927 1.0000 80 chr1:234290832-234290912 1.0000 80
chr5:40829488-40829568 1.0000 80 chr6:32177057-32177137 1.0000 80
chr2:203829848-203829928 1.0000 80
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme -oc ../result/final_prediction/K562/inference_raw/MEME/RankLinear0.6_40_COPS2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/COPS2.fasta
model: mod= zoops nmotifs= 5 evt= inf
objective function: em= E-value of product of p-values
starts= E-value of product of p-values
strands: +
width: minw= 8 maxw= 8
nsites: minsites= 2 maxsites= 61 wnsites= 0.8
theta: spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
trim: wg= 11 ws= 1 endgaps= yes
data: n= 4880 N= 61
sample: seed= 0 hsfrac= 0
searchsize= 4880 norand= no csites= 1000
Letter frequencies in dataset:
A 0.281 C 0.208 G 0.21 T 0.301
Background letter frequencies (from file dataset with add-one prior applied):
A 0.281 C 0.208 G 0.21 T 0.301
Background model order: 0
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MOTIF GAKCMAAW MEME-1 width = 8 sites = 19 llr = 146 E-value = 4.9e+001
********************************************************************************
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Motif GAKCMAAW MEME-1 Description
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Simplified A 3a::5aa3
pos.-specific C :::95::2
probability G 7:41::::
matrix T ::6::::5
bits 2.3
2.0 *
1.8 * * **
1.6 * * **
Relative 1.4 * * **
Entropy 1.1 ** ****
(11.1 bits) 0.9 *******
0.7 *******
0.5 ********
0.2 ********
0.0 --------
Multilevel GATCAAAT
consensus A G C A
sequence C
--------------------------------------------------------------------------------
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Motif GAKCMAAW MEME-1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr1:228045134-228045214 44 1.83e-05 ctcattgcaa gatccaat cagatcatgc
chr20:43485664-43485744 22 1.83e-05 GTgaatgcag gatccaat cagactgtgc
chr6:6657829-6657909 33 1.83e-05 ctcattgcaa gatccaat cagatcatgc
chr6:150128989-150129069 8 1.83e-05 GCTAAGG GATCCAAT TGATCCCGTG
chr21:11118676-11118756 15 5.57e-05 AGTCTTTGCT GATCAAAT TCAGGGGAAG
chr10:102133170-10213325 51 5.57e-05 GACCACGCCG GAGCCAAT CAGCGGCCCC
chr4:166248651-166248731 28 5.57e-05 TCCATCCGCG GAGCCAAT GGCTGGGACC
chr20:29649593-29649673 26 5.57e-05 ggaattactg gatcaaat gatagatctg
chr21:11093201-11093281 13 1.03e-04 CCATAGAAAT GATCCAAA CTCACATACT
chr2:152252300-152252380 42 1.03e-04 tgggaggcat gatccaac tggatactgc
chr5:43313793-43313873 43 1.63e-04 GATACGGCGA GAGCCAAC GGGAGCGGAG
chr2:69787251-69787331 20 1.63e-04 TAAATCACGA GATCAAAA TCCACGCCTA
chr6:57394362-57394442 47 2.89e-04 CCCCATTCAC AAGCAAAT GTGAATTTGG
chr2:177319680-177319760 72 4.10e-04 GGGTTAGAGA AATCAAAA T
chr17:36301785-36301865 70 4.10e-04 atggaaatag aatcaaac aat
chr13:91557567-91557647 11 4.47e-04 aaaatacatg aagcaaaa actaataaaa
chr21:11146225-11146305 2 4.47e-04 A AAGCAAAC TATCATCATT
chr21:11073622-11073702 29 4.47e-04 ttaacaattg aagcaaaa attgttacat
chr21:11048847-11048927 33 5.04e-04 ATGACCAAGA GATGAAAT ACAATAGGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GAKCMAAW MEME-1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr1:228045134-228045214 1.8e-05 43_[+1]_29
chr20:43485664-43485744 1.8e-05 21_[+1]_51
chr6:6657829-6657909 1.8e-05 32_[+1]_40
chr6:150128989-150129069 1.8e-05 7_[+1]_65
chr21:11118676-11118756 5.6e-05 14_[+1]_58
chr10:102133170-10213325 5.6e-05 50_[+1]_22
chr4:166248651-166248731 5.6e-05 27_[+1]_45
chr20:29649593-29649673 5.6e-05 25_[+1]_47
chr21:11093201-11093281 0.0001 12_[+1]_60
chr2:152252300-152252380 0.0001 41_[+1]_31
chr5:43313793-43313873 0.00016 42_[+1]_30
chr2:69787251-69787331 0.00016 19_[+1]_53
chr6:57394362-57394442 0.00029 46_[+1]_26
chr2:177319680-177319760 0.00041 71_[+1]_1
chr17:36301785-36301865 0.00041 69_[+1]_3
chr13:91557567-91557647 0.00045 10_[+1]_62
chr21:11146225-11146305 0.00045 1_[+1]_71
chr21:11073622-11073702 0.00045 28_[+1]_44
chr21:11048847-11048927 0.0005 32_[+1]_40
--------------------------------------------------------------------------------
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Motif GAKCMAAW MEME-1 in BLOCKS format
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BL MOTIF GAKCMAAW width=8 seqs=19
chr1:228045134-228045214 ( 44) GATCCAAT 1
chr20:43485664-43485744 ( 22) GATCCAAT 1
chr6:6657829-6657909 ( 33) GATCCAAT 1
chr6:150128989-150129069 ( 8) GATCCAAT 1
chr21:11118676-11118756 ( 15) GATCAAAT 1
chr10:102133170-10213325 ( 51) GAGCCAAT 1
chr4:166248651-166248731 ( 28) GAGCCAAT 1
chr20:29649593-29649673 ( 26) GATCAAAT 1
chr21:11093201-11093281 ( 13) GATCCAAA 1
chr2:152252300-152252380 ( 42) GATCCAAC 1
chr5:43313793-43313873 ( 43) GAGCCAAC 1
chr2:69787251-69787331 ( 20) GATCAAAA 1
chr6:57394362-57394442 ( 47) AAGCAAAT 1
chr2:177319680-177319760 ( 72) AATCAAAA 1
chr17:36301785-36301865 ( 70) AATCAAAC 1
chr13:91557567-91557647 ( 11) AAGCAAAA 1
chr21:11146225-11146305 ( 2) AAGCAAAC 1
chr21:11073622-11073702 ( 29) AAGCAAAA 1
chr21:11048847-11048927 ( 33) GATGAAAT 1
//
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Motif GAKCMAAW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 8.76676 E= 4.9e+001
17 -1089 170 -1089
183 -1089 -1089 -1089
-1089 -1089 81 107
-1089 219 -200 -1089
91 119 -1089 -1089
183 -1089 -1089 -1089
183 -1089 -1089 -1089
-9 2 -1089 81
--------------------------------------------------------------------------------
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Motif GAKCMAAW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.9e+001
0.315789 0.000000 0.684211 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.368421 0.631579
0.000000 0.947368 0.052632 0.000000
0.526316 0.473684 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.263158 0.210526 0.000000 0.526316
--------------------------------------------------------------------------------
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Motif GAKCMAAW MEME-1 regular expression
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[GA]A[TG]C[AC]AA[TAC]
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Time 2.28 secs.
********************************************************************************
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MOTIF TCACCCCA MEME-2 width = 8 sites = 9 llr = 84 E-value = 8.2e+001
********************************************************************************
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Motif TCACCCCA MEME-2 Description
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Simplified A 1:a:2::a
pos.-specific C :8:a79a:
probability G :2::::::
matrix T 9:::11::
bits 2.3 * *
2.0 * *
1.8 ** ***
1.6 *** ***
Relative 1.4 *** ***
Entropy 1.1 **** ***
(13.5 bits) 0.9 ********
0.7 ********
0.5 ********
0.2 ********
0.0 --------
Multilevel TCACCCCA
consensus G A
sequence
--------------------------------------------------------------------------------
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Motif TCACCCCA MEME-2 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr22:42228918-42228998 58 9.25e-06 TGACGCGCCA TCACCCCA CGCACCGCTT
chr20:43485664-43485744 47 9.25e-06 tgctctggca tcacccca tgacaggatc
chr7:110962323-110962403 53 1.86e-05 GAGGTCGAAT TGACCCCA TGACTGGTTA
chr2:152252300-152252380 67 1.86e-05 tgctatgggg tgacccca gggctc
chr4:190655937-190656017 52 3.11e-05 ctcttctctc tcacacca ttgcaccacc
chr6:33037149-33037229 58 3.11e-05 GAGAGGGGTA TCACACCA CTGACCAGCC
chr5:40829488-40829568 40 3.97e-05 TACCAACCCT ACACCCCA TCCTTCTAAC
chr4:166248651-166248731 14 5.31e-05 CTCACTATCC TCACTCCA TCCGCGGAGC
chr1:228045134-228045214 30 6.65e-05 cctctcaaca tcacctca ttgcaagatc
--------------------------------------------------------------------------------
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Motif TCACCCCA MEME-2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr22:42228918-42228998 9.3e-06 57_[+2]_15
chr20:43485664-43485744 9.3e-06 46_[+2]_26
chr7:110962323-110962403 1.9e-05 52_[+2]_20
chr2:152252300-152252380 1.9e-05 66_[+2]_6
chr4:190655937-190656017 3.1e-05 51_[+2]_21
chr6:33037149-33037229 3.1e-05 57_[+2]_15
chr5:40829488-40829568 4e-05 39_[+2]_33
chr4:166248651-166248731 5.3e-05 13_[+2]_59
chr1:228045134-228045214 6.7e-05 29_[+2]_43
--------------------------------------------------------------------------------
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Motif TCACCCCA MEME-2 in BLOCKS format
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BL MOTIF TCACCCCA width=8 seqs=9
chr22:42228918-42228998 ( 58) TCACCCCA 1
chr20:43485664-43485744 ( 47) TCACCCCA 1
chr7:110962323-110962403 ( 53) TGACCCCA 1
chr2:152252300-152252380 ( 67) TGACCCCA 1
chr4:190655937-190656017 ( 52) TCACACCA 1
chr6:33037149-33037229 ( 58) TCACACCA 1
chr5:40829488-40829568 ( 40) ACACCCCA 1
chr4:166248651-166248731 ( 14) TCACTCCA 1
chr1:228045134-228045214 ( 30) TCACCTCA 1
//
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Motif TCACCCCA MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 9.79701 E= 8.2e+001
-133 -982 -982 156
-982 190 8 -982
183 -982 -982 -982
-982 226 -982 -982
-34 168 -982 -143
-982 209 -982 -143
-982 226 -982 -982
183 -982 -982 -982
--------------------------------------------------------------------------------
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Motif TCACCCCA MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 8.2e+001
0.111111 0.000000 0.000000 0.888889
0.000000 0.777778 0.222222 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.222222 0.666667 0.000000 0.111111
0.000000 0.888889 0.000000 0.111111
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
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Motif TCACCCCA MEME-2 regular expression
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T[CG]AC[CA]CCA
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Time 4.01 secs.
********************************************************************************
********************************************************************************
MOTIF CCACGCCT MEME-3 width = 8 sites = 2 llr = 24 E-value = 3.1e+003
********************************************************************************
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Motif CCACGCCT MEME-3 Description
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Simplified A ::a:::::
pos.-specific C aa:a:aa:
probability G ::::a:::
matrix T :::::::a
bits 2.3 ** ****
2.0 ** ****
1.8 ********
1.6 ********
Relative 1.4 ********
Entropy 1.1 ********
(17.1 bits) 0.9 ********
0.7 ********
0.5 ********
0.2 ********
0.0 --------
Multilevel CCACGCCT
consensus
sequence
--------------------------------------------------------------------------------
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Motif CCACGCCT MEME-3 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr4:120375774-120375854 2 6.92e-06 C CCACGCCT CTGACGTCGC
chr2:69787251-69787331 29 6.92e-06 AGATCAAAAT CCACGCCT AACAGGACTT
--------------------------------------------------------------------------------
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Motif CCACGCCT MEME-3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr4:120375774-120375854 6.9e-06 1_[+3]_71
chr2:69787251-69787331 6.9e-06 28_[+3]_44
--------------------------------------------------------------------------------
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Motif CCACGCCT MEME-3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF CCACGCCT width=8 seqs=2
chr4:120375774-120375854 ( 2) CCACGCCT 1
chr2:69787251-69787331 ( 29) CCACGCCT 1
//
--------------------------------------------------------------------------------
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Motif CCACGCCT MEME-3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 11.1199 E= 3.1e+003
-765 226 -765 -765
-765 226 -765 -765
183 -765 -765 -765
-765 226 -765 -765
-765 -765 224 -765
-765 226 -765 -765
-765 226 -765 -765
-765 -765 -765 173
--------------------------------------------------------------------------------
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Motif CCACGCCT MEME-3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.1e+003
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 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CCACGCCT MEME-3 regular expression
--------------------------------------------------------------------------------
CCACGCCT
--------------------------------------------------------------------------------
Time 4.70 secs.
********************************************************************************
********************************************************************************
MOTIF TCAWRGAA MEME-4 width = 8 sites = 11 llr = 95 E-value = 3.7e+003
********************************************************************************
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Motif TCAWRGAA MEME-4 Description
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Simplified A ::755:aa
pos.-specific C :a32::::
probability G ::::5a::
matrix T a::4::::
bits 2.3 * *
2.0 * *
1.8 ** ***
1.6 ** ***
Relative 1.4 ** ***
Entropy 1.1 *** ****
(12.5 bits) 0.9 *** ****
0.7 *** ****
0.5 ********
0.2 ********
0.0 --------
Multilevel TCAAGGAA
consensus CTA
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr13:91557567-91557647 30 1.72e-05 ctaataaaac tcaaggaa aactgaaata
chr6:32177057-32177137 28 3.57e-05 aaagttagtc tcatggaa gtagggtaga
chr17:36301785-36301865 58 3.57e-05 tctagacact tcatggaa atagaatcaa
chr13:92276568-92276648 30 5.87e-05 tacctacttt tcaaagaa aatatagtat
chr7:117845791-117845871 35 5.87e-05 GTAATAATTA TCaaagaa aaagaagaga
chr4:120375774-120375854 66 7.14e-05 CATTGTGACG TCACGGAA GGCGCGC
chr10:61705906-61705986 44 8.42e-05 gaatgtgaat tccaggaa acaagtgcaa
chr16:70946472-70946552 72 1.09e-04 gatgctggct tcatagaa t
chr21:11111241-11111321 17 1.22e-04 CCCACCTGTG TCCTGGAA GTGCTCAGAG
chr21:11048847-11048927 3 1.40e-04 AA TCACAGAA AAGACTGGAG
chr21:11057701-11057781 5 1.57e-04 AATT TCCAAGAA TTTCAGAAGT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr13:91557567-91557647 1.7e-05 29_[+4]_43
chr6:32177057-32177137 3.6e-05 27_[+4]_45
chr17:36301785-36301865 3.6e-05 57_[+4]_15
chr13:92276568-92276648 5.9e-05 29_[+4]_43
chr7:117845791-117845871 5.9e-05 34_[+4]_38
chr4:120375774-120375854 7.1e-05 65_[+4]_7
chr10:61705906-61705986 8.4e-05 43_[+4]_29
chr16:70946472-70946552 0.00011 71_[+4]_1
chr21:11111241-11111321 0.00012 16_[+4]_56
chr21:11048847-11048927 0.00014 2_[+4]_70
chr21:11057701-11057781 0.00016 4_[+4]_68
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF TCAWRGAA width=8 seqs=11
chr13:91557567-91557647 ( 30) TCAAGGAA 1
chr6:32177057-32177137 ( 28) TCATGGAA 1
chr17:36301785-36301865 ( 58) TCATGGAA 1
chr13:92276568-92276648 ( 30) TCAAAGAA 1
chr7:117845791-117845871 ( 35) TCAAAGAA 1
chr4:120375774-120375854 ( 66) TCACGGAA 1
chr10:61705906-61705986 ( 44) TCCAGGAA 1
chr16:70946472-70946552 ( 72) TCATAGAA 1
chr21:11111241-11111321 ( 17) TCCTGGAA 1
chr21:11048847-11048927 ( 3) TCACAGAA 1
chr21:11057701-11057781 ( 5) TCCAAGAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 8.2088 E= 3.7e+003
-1010 -1010 -1010 173
-1010 226 -1010 -1010
137 39 -1010 -1010
69 -19 -1010 27
69 -1010 137 -1010
-1010 -1010 225 -1010
183 -1010 -1010 -1010
183 -1010 -1010 -1010
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 3.7e+003
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.727273 0.272727 0.000000 0.000000
0.454545 0.181818 0.000000 0.363636
0.454545 0.000000 0.545455 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCAWRGAA MEME-4 regular expression
--------------------------------------------------------------------------------
TC[AC][AT][GA]GAA
--------------------------------------------------------------------------------
Time 5.30 secs.
********************************************************************************
********************************************************************************
MOTIF GCWGCTCT MEME-5 width = 8 sites = 4 llr = 43 E-value = 5.6e+003
********************************************************************************
--------------------------------------------------------------------------------
Motif GCWGCTCT MEME-5 Description
--------------------------------------------------------------------------------
Simplified A ::5:::::
pos.-specific C :a::a:a:
probability G a::a::::
matrix T ::5::a:a
bits 2.3 ** ** *
2.0 ** ** *
1.8 ** *****
1.6 ** *****
Relative 1.4 ** *****
Entropy 1.1 ** *****
(15.5 bits) 0.9 ** *****
0.7 ********
0.5 ********
0.2 ********
0.0 --------
Multilevel GCAGCTCT
consensus T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GCWGCTCT MEME-5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------
chr20:43485664-43485744 1 1.01e-05 . GCAGCTCT GAGGTgaatg
chr6:33037149-33037229 32 1.01e-05 AGATTTTATG GCAGCTCT GAATCACAGA
chr5:40829488-40829568 5 2.09e-05 GATC GCTGCTCT TCCCTGAATT
chr21:11042077-11042157 16 2.09e-05 gaataaatgt gctgctct acaacccaga
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GCWGCTCT MEME-5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr20:43485664-43485744 1e-05 [+5]_72
chr6:33037149-33037229 1e-05 31_[+5]_41
chr5:40829488-40829568 2.1e-05 4_[+5]_68
chr21:11042077-11042157 2.1e-05 15_[+5]_57
--------------------------------------------------------------------------------
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Motif GCWGCTCT MEME-5 in BLOCKS format
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BL MOTIF GCWGCTCT width=8 seqs=4
chr20:43485664-43485744 ( 1) GCAGCTCT 1
chr6:33037149-33037229 ( 32) GCAGCTCT 1
chr5:40829488-40829568 ( 5) GCTGCTCT 1
chr21:11042077-11042157 ( 16) GCTGCTCT 1
//
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Motif GCWGCTCT MEME-5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 10.1193 E= 5.6e+003
-865 -865 225 -865
-865 226 -865 -865
83 -865 -865 73
-865 -865 225 -865
-865 226 -865 -865
-865 -865 -865 173
-865 226 -865 -865
-865 -865 -865 173
--------------------------------------------------------------------------------
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Motif GCWGCTCT MEME-5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 5.6e+003
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.000000 0.500000
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 0.000000 1.000000
--------------------------------------------------------------------------------
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Motif GCWGCTCT MEME-5 regular expression
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GC[AT]GCTCT
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Time 5.90 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr17:36301785-36301865 2.69e-03 57_[+4(3.57e-05)]_15
chr2:145440315-145440395 7.06e-01 80
chr7:117845791-117845871 1.84e-01 34_[+4(5.87e-05)]_38
chr21:11111241-11111321 3.44e-03 80
chr10:74144248-74144328 4.99e-01 80
chr6:33037149-33037229 3.48e-04 31_[+5(1.01e-05)]_18_[+2(3.11e-05)]_\
15
chr7:131053866-131053946 8.50e-01 80
chr4:190655937-190656017 1.00e-02 51_[+2(3.11e-05)]_21
chr7:117807305-117807385 8.00e-01 80
chr6:138257368-138257448 7.57e-01 80
chr13:92276568-92276648 6.07e-02 29_[+4(5.87e-05)]_43
chr6:38691447-38691527 7.70e-01 80
chr2:91766349-91766429 9.72e-01 80
chr21:11073622-11073702 6.00e-01 80
chr2:91790989-91791069 9.78e-01 80
chr21:11146225-11146305 1.90e-01 80
chr13:91557567-91557647 2.44e-02 29_[+4(1.72e-05)]_43
chr2:152252300-152252380 7.65e-04 66_[+2(1.86e-05)]_6
chr6:150128989-150129069 1.13e-01 7_[+1(1.83e-05)]_65
chr7:110962323-110962403 2.41e-02 52_[+2(1.86e-05)]_20
chr20:29649593-29649673 1.13e-01 25_[+1(5.57e-05)]_47
chr9:66484483-66484563 1.76e-01 80
chr21:11093201-11093281 8.99e-02 80
chr6:158281868-158281948 7.95e-01 80
chr6:6657829-6657909 4.50e-04 18_[+2(6.65e-05)]_6_[+1(1.83e-05)]_\
19_[+2(6.65e-05)]_13
chr6:57535512-57535592 9.90e-01 80
chr21:11057701-11057781 1.95e-01 80
chr7:133230691-133230771 8.21e-01 80
chr2:69787251-69787331 3.64e-03 28_[+3(6.92e-06)]_44
chr20:43485664-43485744 2.46e-06 [+5(1.01e-05)]_13_[+1(1.83e-05)]_17_\
[+2(9.25e-06)]_26
chr9:66461460-66461540 6.29e-01 80
chr5:43313793-43313873 1.29e-01 80
chr1:228045134-228045214 6.34e-05 2_[+1(1.83e-05)]_19_[+2(6.65e-05)]_\
6_[+1(1.83e-05)]_29
chr21:11042077-11042157 1.34e-03 15_[+5(2.09e-05)]_57
chr21:11171847-11171927 8.63e-01 80
chr4:166248651-166248731 1.24e-03 13_[+2(5.31e-05)]_6_[+1(5.57e-05)]_\
45
chr22:42228918-42228998 2.17e-03 57_[+2(9.25e-06)]_15
chr6:158739474-158739554 2.45e-01 80
chr7:98684344-98684424 4.99e-01 80
chr5:74632811-74632891 7.89e-01 80
chr2:91783936-91784016 5.86e-01 80
chr2:177319680-177319760 1.51e-01 80
chr12:108511298-10851137 5.84e-01 80
chr10:102133170-10213325 5.53e-04 42_[+3(2.30e-05)]_[+1(5.57e-05)]_22
chr16:70946472-70946552 9.86e-02 80
chr2:91786025-91786105 4.07e-01 80
chr10:61705906-61705986 2.80e-01 43_[+4(8.42e-05)]_29
chr20:49149119-49149199 4.59e-01 80
chr17:36981584-36981664 1.44e-01 80
chr21:11057088-11057168 9.91e-01 80
chr17:36305093-36305173 6.80e-01 80
chr21:11118676-11118756 4.62e-02 14_[+1(5.57e-05)]_58
chr4:120375774-120375854 3.08e-04 1_[+3(6.92e-06)]_56_[+4(7.14e-05)]_\
7
chr1:145104329-145104409 1.84e-02 12_[+5(8.29e-05)]_60
chr21:11112650-11112730 5.34e-01 80
chr6:57394362-57394442 1.92e-01 80
chr21:11048847-11048927 5.54e-02 80
chr1:234290832-234290912 7.97e-01 80
chr5:40829488-40829568 3.70e-04 4_[+5(2.09e-05)]_27_[+2(3.97e-05)]_\
33
chr6:32177057-32177137 8.49e-02 27_[+4(3.57e-05)]_45
chr2:203829848-203829928 9.01e-01 80
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because requested number of motifs (5) found.
********************************************************************************
CPU: c17n09.farnam.hpc.yale.internal
********************************************************************************