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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/worm/fasta/RankLinear2.0_40/peb-1.fasta
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
chrX:2210323-2210403 1.0000 80 chrX:2214601-2214681 1.0000 80
chrX:2212300-2212380 1.0000 80 chrX:2208761-2208841 1.0000 80
chrX:2215925-2216005 1.0000 80 chrV:12736362-12736442 1.0000 80
chrX:2219133-2219213 1.0000 80 chrX:2216802-2216882 1.0000 80
chrII:15203867-15203947 1.0000 80 chrI:527513-527593 1.0000 80
chrX:10194585-10194665 1.0000 80 chrII:7405444-7405524 1.0000 80
chrII:7406582-7406662 1.0000 80 chrIII:13779775-13779855 1.0000 80
chrV:6354438-6354518 1.0000 80 chrII:11200484-11200564 1.0000 80
chrV:13413481-13413561 1.0000 80 chrX:2215235-2215315 1.0000 80
chrX:11474332-11474412 1.0000 80 chrII:12965779-12965859 1.0000 80
chrII:9285084-9285164 1.0000 80 chrIV:10817210-10817290 1.0000 80
chrII:1238046-1238126 1.0000 80 chrIV:1371471-1371551 1.0000 80
chrII:2455041-2455121 1.0000 80 chrV:13414810-13414890 1.0000 80
chrI:6958827-6958907 1.0000 80 chrV:9287693-9287773 1.0000 80
chrII:66469-66549 1.0000 80 chrIV:1221184-1221264 1.0000 80
chrX:4905586-4905666 1.0000 80 chrX:12655422-12655502 1.0000 80
chrV:8653804-8653884 1.0000 80 chrV:6970173-6970253 1.0000 80
chrX:16157046-16157126 1.0000 80 chrX:9637415-9637495 1.0000 80
chrI:1000967-1001047 1.0000 80 chrX:11798189-11798269 1.0000 80
chrIV:10175318-10175398 1.0000 80 chrX:11465346-11465426 1.0000 80
chrIV:3636550-3636630 1.0000 80 chrII:7623667-7623747 1.0000 80
chrV:14366748-14366828 1.0000 80 chrIII:8132560-8132640 1.0000 80
chrIII:4552113-4552193 1.0000 80 chrX:10395746-10395826 1.0000 80
chrIV:8302085-8302165 1.0000 80 chrX:5480336-5480416 1.0000 80
chrI:9087335-9087415 1.0000 80 chrI:10409442-10409522 1.0000 80
chrII:5901815-5901895 1.0000 80 chrIV:4454890-4454970 1.0000 80
chrX:4971618-4971698 1.0000 80 chrI:10769948-10770028 1.0000 80
chrX:11299761-11299841 1.0000 80 chrI:1251648-1251728 1.0000 80
chrX:14297288-14297368 1.0000 80 chrI:6173111-6173191 1.0000 80
chrX:12656714-12656794 1.0000 80 chrV:10036456-10036536 1.0000 80
chrX:10372617-10372697 1.0000 80 chrIII:623893-623973 1.0000 80
chrV:4651801-4651881 1.0000 80 chrIV:8782370-8782450 1.0000 80
chrX:5812096-5812176 1.0000 80 chrV:10717231-10717311 1.0000 80
chrV:7978971-7979051 1.0000 80 chrX:5475291-5475371 1.0000 80
chrX:5686308-5686388 1.0000 80 chrI:13065859-13065939 1.0000 80
chrV:15661084-15661164 1.0000 80 chrIII:12178287-12178367 1.0000 80
chrX:9999850-9999930 1.0000 80 chrV:12529016-12529096 1.0000 80
chrII:11620092-11620172 1.0000 80 chrIV:14824887-14824967 1.0000 80
chrI:14320501-14320581 1.0000 80 chrII:10502922-10503002 1.0000 80
chrIV:11027800-11027880 1.0000 80 chrII:8751161-8751241 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/worm/inference_raw/MEME/RankLinear2.0_40_peb-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/peb-1.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= 80 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= 6400 N= 80
sample: seed= 0 hsfrac= 0
searchsize= 6400 norand= no csites= 1000
Letter frequencies in dataset:
A 0.243 C 0.247 G 0.267 T 0.242
Background letter frequencies (from file dataset with add-one prior applied):
A 0.243 C 0.247 G 0.267 T 0.243
Background model order: 0
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MOTIF GAAARAGA MEME-1 width = 8 sites = 40 llr = 279 E-value = 2.5e-006
********************************************************************************
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Motif GAAARAGA MEME-1 Description
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Simplified A 395a47:a
pos.-specific C ::3:1:::
probability G 722:5:9:
matrix T 1::::31:
bits 2.0 * *
1.8 * *
1.6 * *
1.4 * * **
Relative 1.2 * * ***
Entropy 1.0 * * ***
(10.1 bits) 0.8 ** * ***
0.6 ********
0.4 ********
0.2 ********
0.0 --------
Multilevel GAAAGAGA
consensus A C AT
sequence G
--------------------------------------------------------------------------------
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Motif GAAARAGA MEME-1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chrV:7978971-7979051 33 1.61e-05 GAGATAGAGA GAAAGAGA ACGAAGGACG
chrV:10717231-10717311 41 1.61e-05 ACGGCAGATG GAAAGAGA AGAAGATTTC
chrIII:8132560-8132640 30 1.61e-05 AGTGAACGCG GAAAGAGA GTAATTAGAA
chrI:6958827-6958907 27 1.61e-05 TCAATCCGGA GAAAGAGA GGGCGCAAAA
chrV:13414810-13414890 27 1.61e-05 GAGGTGAAGA GAAAGAGA GAAACACTTT
chrX:10372617-10372697 69 3.08e-05 GGTGAGATTA GAAAAAGA GATT
chrII:8751161-8751241 3 6.33e-05 ag gaaagtga aaACAATTAG
chrII:7405444-7405524 40 6.33e-05 ATTGAAACCG GAAAGTGA AATCGTTGCC
chrIV:11027800-11027880 51 1.11e-04 GAGCAATGTA GACAAAGA TACGCAGAGA
chrI:14320501-14320581 66 1.11e-04 gagagggaga gagagaga gagaTGC
chrIII:623893-623973 52 1.11e-04 CGAAGTACGA GAGAGAGA CGCAGAGAGT
chrIV:3636550-3636630 72 1.11e-04 gaggcgcaga gacaaaga c
chrII:1238046-1238126 64 1.11e-04 TGGGACGGGA GAGAGAGA GGGGGGCGA
chrX:10194585-10194665 22 1.11e-04 AGGTGGCAAG GACAAAGA GTGCGCGACG
chrII:10502922-10503002 21 1.55e-04 AAAAATGGAA GAGAAAGA GCGCTCGTTT
chrX:4971618-4971698 65 1.55e-04 CTGGTAAAGA GAGAAAGA CTGCGGCG
chrX:12656714-12656794 58 2.01e-04 TCAGAGGCTG AACAGAGA AGGGAGCGAG
chrI:10769948-10770028 56 2.48e-04 CTCTCGAACA AAAAGTGA ACGTGGTGTT
chrII:11620092-11620172 55 2.96e-04 CACAGACAGT AAGAGAGA TAGAAATGAA
chrX:5686308-5686388 27 2.96e-04 CACTATGGGC AAGAGAGA AGATAAAATG
chrV:12736362-12736442 72 3.25e-04 TACAAGATGG AAAAATGA A
chrIV:1221184-1221264 39 3.56e-04 TGGTGAATAG GGAAAAGA TGAAGGGCAT
chrIII:12178287-12178367 58 3.71e-04 CCCCCAAGTG GACACAGA AAGAGCGATG
chrII:7406582-7406662 70 4.01e-04 AGGGAGAAGC TAAAGAGA CAT
chrI:527513-527593 14 4.01e-04 TGCCGAGGCA GAAACTGA GGACCGATCT
chrIV:14824887-14824967 68 4.31e-04 AGACGGGGGA GAGACAGA ATCTG
chrX:4905586-4905666 63 4.31e-04 CCGAGGGATT GAGACAGA GGCCAAGAGC
chrI:6173111-6173191 68 4.59e-04 TGGCGATATT TAAAAAGA AGAAG
chrX:9637415-9637495 41 4.59e-04 ATGCGGAAAA AACAGTGA GACACTTGAG
chrII:9285084-9285164 67 4.59e-04 TGTTTATATA AACAGTGA GAGCTA
chrV:13413481-13413561 51 4.92e-04 CAATCATTTC GAAAGATA TGAAGAGAAA
chrII:15203867-15203947 55 4.92e-04 ACCAAAAGGT GGCAGAGA CGTGTGCTCC
chrX:14297288-14297368 68 6.05e-04 GGGGAGAGCT GGCAAAGA GGCGA
chrX:11299761-11299841 56 6.05e-04 GCCGGCGCTg agaagaga gcataggaaa
chrI:9087335-9087415 33 6.05e-04 TTTCCGCGCG GAAAAATA GTGGAATACG
chrX:2219133-2219213 49 6.98e-04 TCTGGCGCAA GACACTGA CAGTCGCCGC
chrX:9999850-9999930 32 8.46e-04 CCACAATCAA TAAAATGA CAGCGGGCAT
chrIII:13779775-13779855 23 1.02e-03 gagacctctc gaaaatta gtatggcact
chrX:10395746-10395826 60 1.14e-03 TGATTGTCGC AGAAATGA GGCAAACGAG
chrII:12965779-12965859 70 1.14e-03 TGGCGGCGGC AGAAATGA TGC
--------------------------------------------------------------------------------
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Motif GAAARAGA MEME-1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrV:7978971-7979051 1.6e-05 32_[+1]_40
chrV:10717231-10717311 1.6e-05 40_[+1]_32
chrIII:8132560-8132640 1.6e-05 29_[+1]_43
chrI:6958827-6958907 1.6e-05 26_[+1]_46
chrV:13414810-13414890 1.6e-05 26_[+1]_46
chrX:10372617-10372697 3.1e-05 68_[+1]_4
chrII:8751161-8751241 6.3e-05 2_[+1]_70
chrII:7405444-7405524 6.3e-05 39_[+1]_33
chrIV:11027800-11027880 0.00011 50_[+1]_22
chrI:14320501-14320581 0.00011 65_[+1]_7
chrIII:623893-623973 0.00011 51_[+1]_21
chrIV:3636550-3636630 0.00011 71_[+1]_1
chrII:1238046-1238126 0.00011 63_[+1]_9
chrX:10194585-10194665 0.00011 21_[+1]_51
chrII:10502922-10503002 0.00015 20_[+1]_52
chrX:4971618-4971698 0.00015 64_[+1]_8
chrX:12656714-12656794 0.0002 57_[+1]_15
chrI:10769948-10770028 0.00025 55_[+1]_17
chrII:11620092-11620172 0.0003 54_[+1]_18
chrX:5686308-5686388 0.0003 26_[+1]_46
chrV:12736362-12736442 0.00033 71_[+1]_1
chrIV:1221184-1221264 0.00036 38_[+1]_34
chrIII:12178287-12178367 0.00037 57_[+1]_15
chrII:7406582-7406662 0.0004 69_[+1]_3
chrI:527513-527593 0.0004 13_[+1]_59
chrIV:14824887-14824967 0.00043 67_[+1]_5
chrX:4905586-4905666 0.00043 62_[+1]_10
chrI:6173111-6173191 0.00046 67_[+1]_5
chrX:9637415-9637495 0.00046 40_[+1]_32
chrII:9285084-9285164 0.00046 66_[+1]_6
chrV:13413481-13413561 0.00049 50_[+1]_22
chrII:15203867-15203947 0.00049 54_[+1]_18
chrX:14297288-14297368 0.0006 67_[+1]_5
chrX:11299761-11299841 0.0006 55_[+1]_17
chrI:9087335-9087415 0.0006 32_[+1]_40
chrX:2219133-2219213 0.0007 48_[+1]_24
chrX:9999850-9999930 0.00085 31_[+1]_41
chrIII:13779775-13779855 0.001 22_[+1]_50
chrX:10395746-10395826 0.0011 59_[+1]_13
chrII:12965779-12965859 0.0011 69_[+1]_3
--------------------------------------------------------------------------------
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Motif GAAARAGA MEME-1 in BLOCKS format
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BL MOTIF GAAARAGA width=8 seqs=40
chrV:7978971-7979051 ( 33) GAAAGAGA 1
chrV:10717231-10717311 ( 41) GAAAGAGA 1
chrIII:8132560-8132640 ( 30) GAAAGAGA 1
chrI:6958827-6958907 ( 27) GAAAGAGA 1
chrV:13414810-13414890 ( 27) GAAAGAGA 1
chrX:10372617-10372697 ( 69) GAAAAAGA 1
chrII:8751161-8751241 ( 3) GAAAGTGA 1
chrII:7405444-7405524 ( 40) GAAAGTGA 1
chrIV:11027800-11027880 ( 51) GACAAAGA 1
chrI:14320501-14320581 ( 66) GAGAGAGA 1
chrIII:623893-623973 ( 52) GAGAGAGA 1
chrIV:3636550-3636630 ( 72) GACAAAGA 1
chrII:1238046-1238126 ( 64) GAGAGAGA 1
chrX:10194585-10194665 ( 22) GACAAAGA 1
chrII:10502922-10503002 ( 21) GAGAAAGA 1
chrX:4971618-4971698 ( 65) GAGAAAGA 1
chrX:12656714-12656794 ( 58) AACAGAGA 1
chrI:10769948-10770028 ( 56) AAAAGTGA 1
chrII:11620092-11620172 ( 55) AAGAGAGA 1
chrX:5686308-5686388 ( 27) AAGAGAGA 1
chrV:12736362-12736442 ( 72) AAAAATGA 1
chrIV:1221184-1221264 ( 39) GGAAAAGA 1
chrIII:12178287-12178367 ( 58) GACACAGA 1
chrII:7406582-7406662 ( 70) TAAAGAGA 1
chrI:527513-527593 ( 14) GAAACTGA 1
chrIV:14824887-14824967 ( 68) GAGACAGA 1
chrX:4905586-4905666 ( 63) GAGACAGA 1
chrI:6173111-6173191 ( 68) TAAAAAGA 1
chrX:9637415-9637495 ( 41) AACAGTGA 1
chrII:9285084-9285164 ( 67) AACAGTGA 1
chrV:13413481-13413561 ( 51) GAAAGATA 1
chrII:15203867-15203947 ( 55) GGCAGAGA 1
chrX:14297288-14297368 ( 68) GGCAAAGA 1
chrX:11299761-11299841 ( 56) AGAAGAGA 1
chrI:9087335-9087415 ( 33) GAAAAATA 1
chrX:2219133-2219213 ( 49) GACACTGA 1
chrX:9999850-9999930 ( 32) TAAAATGA 1
chrIII:13779775-13779855 ( 23) GAAAATTA 1
chrX:10395746-10395826 ( 60) AGAAATGA 1
chrII:12965779-12965859 ( 70) AGAAATGA 1
//
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Motif GAAARAGA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 8.12809 E= 2.5e-006
4 -1197 134 -169
180 -1197 -83 -1197
111 2 -25 -1197
204 -1197 -1197 -1197
62 -98 91 -1197
152 -1197 -1197 31
-1197 -1197 179 -169
204 -1197 -1197 -1197
--------------------------------------------------------------------------------
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Motif GAAARAGA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-006
0.250000 0.000000 0.675000 0.075000
0.850000 0.000000 0.150000 0.000000
0.525000 0.250000 0.225000 0.000000
1.000000 0.000000 0.000000 0.000000
0.375000 0.125000 0.500000 0.000000
0.700000 0.000000 0.000000 0.300000
0.000000 0.000000 0.925000 0.075000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
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Motif GAAARAGA MEME-1 regular expression
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[GA]A[ACG]A[GA][AT]GA
--------------------------------------------------------------------------------
Time 1.83 secs.
********************************************************************************
********************************************************************************
MOTIF CTYTTTCT MEME-2 width = 8 sites = 23 llr = 187 E-value = 5.6e-004
********************************************************************************
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Motif CTYTTTCT MEME-2 Description
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Simplified A :::::1::
pos.-specific C 934:2:a1
probability G ::::::::
matrix T 176a89:9
bits 2.0 *
1.8 * *
1.6 * **
1.4 * * ***
Relative 1.2 ** *****
Entropy 1.0 ********
(11.7 bits) 0.8 ********
0.6 ********
0.4 ********
0.2 ********
0.0 --------
Multilevel CTTTTTCT
consensus CC C
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------
chrV:12529016-12529096 26 1.26e-05 GGCATACTCT CTTTTTCT GTTTTTCTAT
chrI:6173111-6173191 2 1.26e-05 T CTTTTTCT ACTCATTCCT
chrX:11798189-11798269 6 1.26e-05 CACGT CTTTTTCT ACTTCGTGTC
chrX:2208761-2208841 27 1.26e-05 ATTTGATCGT CTTTTTCT TTGCATTGAA
chrI:13065859-13065939 61 2.53e-05 CTCTTTCTCT CTCTTTCT GTTGCGCCAC
chrIII:4552113-4552193 1 2.53e-05 . CTCTTTCT GTGTCTGTCT
chrII:66469-66549 43 2.53e-05 TCGGTCTACA CTCTTTCT ACGTTATATT
chrV:9287693-9287773 18 2.53e-05 TTCAACTCTC CTCTTTCT GGAGAGGGCT
chrI:10409442-10409522 2 5.11e-05 C CCCTTTCT GTCGGCGTTT
chrII:1238046-1238126 19 5.11e-05 ACTGCCGGTG CCCTTTCT CCCGCTGTCG
chrX:2214601-2214681 30 5.11e-05 TTTGGAGACC CCCTTTCT GGTGCCTATT
chrX:9999850-9999930 4 8.92e-05 ttc ttttttct tttttttcCG
chrII:11200484-11200564 16 8.92e-05 ATCGTTCTCC CTCTCTCT TCAATTTGCC
chrX:12656714-12656794 34 1.02e-04 CTCCCCTTCA CCTTCTCT CTATCATCAG
chrV:14366748-14366828 46 1.02e-04 GGCGCGCGCG CCTTCTCT CCGTGCCGCC
chrIII:13779775-13779855 73 1.27e-04 aatagtcttg cttttact
chrX:10395746-10395826 17 1.66e-04 TTCTTCTCCC TCTTTTCT CTCATTCAAA
chrII:9285084-9285164 36 1.92e-04 TCGCCGACGT CTCTTTCC GCCGCAGACA
chrIV:4454890-4454970 48 2.04e-04 TTCTCTGCAT CTTTTCCT TGCCTGTCTG
chrIV:1371471-1371551 12 2.43e-04 CTCTCCCATG CTTCTTCT TCTAGATGAC
chrX:5812096-5812176 14 2.68e-04 GACCACCCTG TTTTCTCT GCCGCACGGC
chrV:13414810-13414890 73 2.68e-04 TATCAATTGT CCTTTTCC
chrX:2219133-2219213 73 3.46e-04 CCGCCATCCA CTTTCACT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrV:12529016-12529096 1.3e-05 25_[+2]_47
chrI:6173111-6173191 1.3e-05 1_[+2]_71
chrX:11798189-11798269 1.3e-05 5_[+2]_67
chrX:2208761-2208841 1.3e-05 26_[+2]_46
chrI:13065859-13065939 2.5e-05 60_[+2]_12
chrIII:4552113-4552193 2.5e-05 [+2]_72
chrII:66469-66549 2.5e-05 42_[+2]_30
chrV:9287693-9287773 2.5e-05 17_[+2]_55
chrI:10409442-10409522 5.1e-05 1_[+2]_71
chrII:1238046-1238126 5.1e-05 18_[+2]_54
chrX:2214601-2214681 5.1e-05 29_[+2]_43
chrX:9999850-9999930 8.9e-05 3_[+2]_69
chrII:11200484-11200564 8.9e-05 15_[+2]_57
chrX:12656714-12656794 0.0001 33_[+2]_39
chrV:14366748-14366828 0.0001 45_[+2]_27
chrIII:13779775-13779855 0.00013 72_[+2]
chrX:10395746-10395826 0.00017 16_[+2]_56
chrII:9285084-9285164 0.00019 35_[+2]_37
chrIV:4454890-4454970 0.0002 47_[+2]_25
chrIV:1371471-1371551 0.00024 11_[+2]_61
chrX:5812096-5812176 0.00027 13_[+2]_59
chrV:13414810-13414890 0.00027 72_[+2]
chrX:2219133-2219213 0.00035 72_[+2]
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF CTYTTTCT width=8 seqs=23
chrV:12529016-12529096 ( 26) CTTTTTCT 1
chrI:6173111-6173191 ( 2) CTTTTTCT 1
chrX:11798189-11798269 ( 6) CTTTTTCT 1
chrX:2208761-2208841 ( 27) CTTTTTCT 1
chrI:13065859-13065939 ( 61) CTCTTTCT 1
chrIII:4552113-4552193 ( 1) CTCTTTCT 1
chrII:66469-66549 ( 43) CTCTTTCT 1
chrV:9287693-9287773 ( 18) CTCTTTCT 1
chrI:10409442-10409522 ( 2) CCCTTTCT 1
chrII:1238046-1238126 ( 19) CCCTTTCT 1
chrX:2214601-2214681 ( 30) CCCTTTCT 1
chrX:9999850-9999930 ( 4) TTTTTTCT 1
chrII:11200484-11200564 ( 16) CTCTCTCT 1
chrX:12656714-12656794 ( 34) CCTTCTCT 1
chrV:14366748-14366828 ( 46) CCTTCTCT 1
chrIII:13779775-13779855 ( 73) CTTTTACT 1
chrX:10395746-10395826 ( 17) TCTTTTCT 1
chrII:9285084-9285164 ( 36) CTCTTTCC 1
chrIV:4454890-4454970 ( 48) CTTTTCCT 1
chrIV:1371471-1371551 ( 12) CTTCTTCT 1
chrX:5812096-5812176 ( 14) TTTTCTCT 1
chrV:13414810-13414890 ( 73) CCTTTTCC 1
chrX:2219133-2219213 ( 73) CTTTCACT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 9.87795 E= 5.6e-004
-1117 181 -1117 -89
-1117 30 -1117 152
-1117 66 -1117 133
-1117 -251 -1117 198
-1117 -19 -1117 169
-148 -251 -1117 184
-1117 201 -1117 -1117
-1117 -151 -1117 191
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 5.6e-004
0.000000 0.869565 0.000000 0.130435
0.000000 0.304348 0.000000 0.695652
0.000000 0.391304 0.000000 0.608696
0.000000 0.043478 0.000000 0.956522
0.000000 0.217391 0.000000 0.782609
0.086957 0.043478 0.000000 0.869565
0.000000 1.000000 0.000000 0.000000
0.000000 0.086957 0.000000 0.913043
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CTYTTTCT MEME-2 regular expression
--------------------------------------------------------------------------------
C[TC][TC]T[TC]TCT
--------------------------------------------------------------------------------
Time 2.63 secs.
********************************************************************************
********************************************************************************
MOTIF GGCGGCRG MEME-3 width = 8 sites = 19 llr = 151 E-value = 3.2e+002
********************************************************************************
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 Description
--------------------------------------------------------------------------------
Simplified A :1:1::4:
pos.-specific C 3:9::a2:
probability G 7919a:3a
matrix T ::::::1:
bits 2.0 *
1.8 ** *
1.6 ** *
1.4 ***** *
Relative 1.2 ***** *
Entropy 1.0 ****** *
(11.4 bits) 0.8 ****** *
0.6 ****** *
0.4 ****** *
0.2 ********
0.0 --------
Multilevel GGCGGCAG
consensus C G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------
chrX:4971618-4971698 39 2.01e-05 GGAGGGCGGA GGCGGCAG ACAATGGCCT
chrV:8653804-8653884 23 2.01e-05 CTACAGCGGT GGCGGCAG CGGATCAAAA
chrIII:623893-623973 9 4.22e-05 CCGATGCC GGCGGCGG GCGTGTGACA
chrI:1251648-1251728 73 4.22e-05 TTTCCAACCC GGCGGCGG
chrII:2455041-2455121 3 4.22e-05 CC GGCGGCGG GCCGACACAG
chrII:12965779-12965859 61 4.22e-05 AGCGCTCTGT GGCGGCGG CAGAAATGAT
chrIV:3636550-3636630 4 6.08e-05 CCG CGCGGCAG AGAGGCACGA
chrX:2216802-2216882 61 6.08e-05 ATGGCAGGCA CGCGGCAG CGCGCGCGGG
chrV:4651801-4651881 59 8.13e-05 TCGCGGCAAC GGCGGCCG AGCGAGTTTT
chrI:14320501-14320581 47 1.02e-04 TGCTAAACGG CGCGGCGg agagagggag
chrV:14366748-14366828 25 1.22e-04 TGGCACAGGA GGCGGCTG AGGGGCGCGC
chrIV:8302085-8302165 65 1.41e-04 CTTCGCGCCC CGCGGCCG AAAACCAG
chrV:10717231-10717311 30 1.77e-04 CACTTCTGCA GACGGCAG ATGGAAAGAG
chrX:11299761-11299841 16 1.77e-04 CTCCCTCCCT GGCAGCAG GTCGGGTCTC
chrII:1238046-1238126 41 1.96e-04 CTGTCGCTGC CGCGGCTG GCACTTGGGA
chrV:10036456-10036536 64 2.18e-04 CAAAACCCGT GGGGGCAG CCCCGCAAA
chrV:12736362-12736442 21 2.18e-04 TCAGTACCTG GGGGGCAG TAACTAGGTA
chrX:2215235-2215315 40 3.73e-04 TGTCTTAGTT GGCAGCCG GTTGGTGCCT
chrX:5812096-5812176 26 4.10e-04 TTCTCTGCCG CACGGCGG AGCTAGCCGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrX:4971618-4971698 2e-05 38_[+3]_34
chrV:8653804-8653884 2e-05 22_[+3]_50
chrIII:623893-623973 4.2e-05 8_[+3]_64
chrI:1251648-1251728 4.2e-05 72_[+3]
chrII:2455041-2455121 4.2e-05 2_[+3]_70
chrII:12965779-12965859 4.2e-05 60_[+3]_12
chrIV:3636550-3636630 6.1e-05 3_[+3]_69
chrX:2216802-2216882 6.1e-05 60_[+3]_12
chrV:4651801-4651881 8.1e-05 58_[+3]_14
chrI:14320501-14320581 0.0001 46_[+3]_26
chrV:14366748-14366828 0.00012 24_[+3]_48
chrIV:8302085-8302165 0.00014 64_[+3]_8
chrV:10717231-10717311 0.00018 29_[+3]_43
chrX:11299761-11299841 0.00018 15_[+3]_57
chrII:1238046-1238126 0.0002 40_[+3]_32
chrV:10036456-10036536 0.00022 63_[+3]_9
chrV:12736362-12736442 0.00022 20_[+3]_52
chrX:2215235-2215315 0.00037 39_[+3]_33
chrX:5812096-5812176 0.00041 25_[+3]_47
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF GGCGGCRG width=8 seqs=19
chrX:4971618-4971698 ( 39) GGCGGCAG 1
chrV:8653804-8653884 ( 23) GGCGGCAG 1
chrIII:623893-623973 ( 9) GGCGGCGG 1
chrI:1251648-1251728 ( 73) GGCGGCGG 1
chrII:2455041-2455121 ( 3) GGCGGCGG 1
chrII:12965779-12965859 ( 61) GGCGGCGG 1
chrIV:3636550-3636630 ( 4) CGCGGCAG 1
chrX:2216802-2216882 ( 61) CGCGGCAG 1
chrV:4651801-4651881 ( 59) GGCGGCCG 1
chrI:14320501-14320581 ( 47) CGCGGCGG 1
chrV:14366748-14366828 ( 25) GGCGGCTG 1
chrIV:8302085-8302165 ( 65) CGCGGCCG 1
chrV:10717231-10717311 ( 30) GACGGCAG 1
chrX:11299761-11299841 ( 16) GGCAGCAG 1
chrII:1238046-1238126 ( 41) CGCGGCTG 1
chrV:10036456-10036536 ( 64) GGGGGCAG 1
chrV:12736362-12736442 ( 21) GGGGGCAG 1
chrX:2215235-2215315 ( 40) GGCAGCCG 1
chrX:5812096-5812176 ( 26) CACGGCGG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 8.45453 E= 3.2e+002
-1089 35 136 -1089
-121 -1089 175 -1089
-1089 185 -134 -1089
-121 -1089 175 -1089
-1089 -1089 191 -1089
-1089 201 -1089 -1089
79 -65 24 -120
-1089 -1089 191 -1089
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.2e+002
0.000000 0.315789 0.684211 0.000000
0.105263 0.000000 0.894737 0.000000
0.000000 0.894737 0.105263 0.000000
0.105263 0.000000 0.894737 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.421053 0.157895 0.315789 0.105263
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GGCGGCRG MEME-3 regular expression
--------------------------------------------------------------------------------
[GC]GCGGC[AG]G
--------------------------------------------------------------------------------
Time 3.40 secs.
********************************************************************************
********************************************************************************
MOTIF TCATTTTT MEME-4 width = 8 sites = 2 llr = 23 E-value = 7.9e+003
********************************************************************************
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 Description
--------------------------------------------------------------------------------
Simplified A ::a:::::
pos.-specific C :a::::::
probability G ::::::::
matrix T a::aaaaa
bits 2.0 ********
1.8 ********
1.6 ********
1.4 ********
Relative 1.2 ********
Entropy 1.0 ********
(16.3 bits) 0.8 ********
0.6 ********
0.4 ********
0.2 ********
0.0 --------
Multilevel TCATTTTT
consensus
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------
chrX:4905586-4905666 6 1.24e-05 TTGTG TCATTTTT TGAGCGCGCT
chrX:2214601-2214681 61 1.24e-05 AAAACTTGCT TCATTTTT GGTCACTTTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrX:4905586-4905666 1.2e-05 5_[+4]_67
chrX:2214601-2214681 1.2e-05 60_[+4]_12
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF TCATTTTT width=8 seqs=2
chrX:4905586-4905666 ( 6) TCATTTTT 1
chrX:2214601-2214681 ( 61) TCATTTTT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 11.5113 E= 7.9e+003
-765 -765 -765 204
-765 201 -765 -765
203 -765 -765 -765
-765 -765 -765 204
-765 -765 -765 204
-765 -765 -765 204
-765 -765 -765 204
-765 -765 -765 204
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.9e+003
0.000000 0.000000 0.000000 1.000000
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 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TCATTTTT MEME-4 regular expression
--------------------------------------------------------------------------------
TCATTTTT
--------------------------------------------------------------------------------
Time 4.26 secs.
********************************************************************************
********************************************************************************
MOTIF CGCAGAGA MEME-5 width = 8 sites = 7 llr = 70 E-value = 2.1e+004
********************************************************************************
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 Description
--------------------------------------------------------------------------------
Simplified A :::a:a:a
pos.-specific C a:7:::1:
probability G :a::a:9:
matrix T ::3:::::
bits 2.0 * * * *
1.8 ** *** *
1.6 ** *** *
1.4 ** *****
Relative 1.2 ********
Entropy 1.0 ********
(14.4 bits) 0.8 ********
0.6 ********
0.4 ********
0.2 ********
0.0 --------
Multilevel CGCAGAGA
consensus T
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------
chrIV:11027800-11027880 61 1.67e-05 GACAAAGATA CGCAGAGA ATGCCGTTGA
chrIII:623893-623973 60 1.67e-05 GAGAGAGAGA CGCAGAGA GTTCGAGCAA
chrX:9637415-9637495 62 1.67e-05 ACTTGAGAGG CGCAGAGA AAACAAAACT
chrII:2455041-2455121 58 1.67e-05 ACGTGAGAGA CGCAGAGA ACTCTTTGGC
chrX:5686308-5686388 53 3.31e-05 TGAAGAGATG CGTAGAGA AAATTGGACT
chrV:7978971-7979051 51 3.31e-05 ACGAAGGACG CGTAGAGA TAAAGGTATG
chrII:9285084-9285164 46 4.85e-05 CTCTTTCCGC CGCAGACA ATTTGTTTAT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrIV:11027800-11027880 1.7e-05 60_[+5]_12
chrIII:623893-623973 1.7e-05 59_[+5]_13
chrX:9637415-9637495 1.7e-05 61_[+5]_11
chrII:2455041-2455121 1.7e-05 57_[+5]_15
chrX:5686308-5686388 3.3e-05 52_[+5]_20
chrV:7978971-7979051 3.3e-05 50_[+5]_22
chrII:9285084-9285164 4.8e-05 45_[+5]_27
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF CGCAGAGA width=8 seqs=7
chrIV:11027800-11027880 ( 61) CGCAGAGA 1
chrIII:623893-623973 ( 60) CGCAGAGA 1
chrX:9637415-9637495 ( 62) CGCAGAGA 1
chrII:2455041-2455121 ( 58) CGCAGAGA 1
chrX:5686308-5686388 ( 53) CGTAGAGA 1
chrV:7978971-7979051 ( 51) CGTAGAGA 1
chrII:9285084-9285164 ( 46) CGCAGACA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 9.54635 E= 2.1e+004
-945 201 -945 -945
-945 -945 191 -945
-945 153 -945 24
204 -945 -945 -945
-945 -945 191 -945
204 -945 -945 -945
-945 -79 168 -945
204 -945 -945 -945
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.1e+004
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.714286 0.000000 0.285714
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 0.142857 0.857143 0.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCAGAGA MEME-5 regular expression
--------------------------------------------------------------------------------
CG[CT]AGAGA
--------------------------------------------------------------------------------
Time 5.04 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrX:2210323-2210403 7.91e-01 80
chrX:2214601-2214681 3.13e-03 29_[+2(5.11e-05)]_23_[+4(1.24e-05)]_\
12
chrX:2212300-2212380 1.47e-01 80
chrX:2208761-2208841 3.89e-03 26_[+2(1.26e-05)]_46
chrX:2215925-2216005 2.67e-01 80
chrV:12736362-12736442 3.25e-02 80
chrX:2219133-2219213 4.35e-02 80
chrX:2216802-2216882 4.36e-02 60_[+3(6.08e-05)]_12
chrII:15203867-15203947 4.10e-02 80
chrI:527513-527593 1.39e-01 80
chrX:10194585-10194665 8.90e-02 80
chrII:7405444-7405524 2.98e-02 39_[+1(6.33e-05)]_33
chrII:7406582-7406662 5.03e-01 80
chrIII:13779775-13779855 5.79e-02 80
chrV:6354438-6354518 4.78e-01 80
chrII:11200484-11200564 1.08e-01 15_[+2(8.92e-05)]_57
chrV:13413481-13413561 1.70e-01 80
chrX:2215235-2215315 5.58e-01 80
chrX:11474332-11474412 7.04e-01 80
chrII:12965779-12965859 1.45e-02 63_[+3(2.01e-05)]_9
chrII:9285084-9285164 5.73e-04 45_[+5(4.85e-05)]_27
chrIV:10817210-10817290 8.31e-01 80
chrII:1238046-1238126 2.21e-04 18_[+2(5.11e-05)]_54
chrIV:1371471-1371551 1.82e-01 80
chrII:2455041-2455121 1.93e-03 2_[+3(4.22e-05)]_47_[+5(1.67e-05)]_\
15
chrV:13414810-13414890 1.46e-03 26_[+1(1.61e-05)]_46
chrI:6958827-6958907 1.05e-03 26_[+1(1.61e-05)]_46
chrV:9287693-9287773 4.44e-02 17_[+2(2.53e-05)]_55
chrII:66469-66549 4.89e-02 42_[+2(2.53e-05)]_30
chrIV:1221184-1221264 4.07e-01 80
chrX:4905586-4905666 9.75e-03 5_[+4(1.24e-05)]_67
chrX:12655422-12655502 5.54e-01 80
chrV:8653804-8653884 1.12e-01 22_[+3(2.01e-05)]_50
chrV:6970173-6970253 3.55e-01 80
chrX:16157046-16157126 3.93e-01 80
chrX:9637415-9637495 2.10e-02 61_[+5(1.67e-05)]_11
chrI:1000967-1001047 9.86e-01 80
chrX:11798189-11798269 1.78e-02 5_[+2(1.26e-05)]_67
chrIV:10175318-10175398 8.90e-01 80
chrX:11465346-11465426 3.87e-01 80
chrIV:3636550-3636630 1.91e-04 3_[+3(6.08e-05)]_54_[+5(1.67e-05)]_\
7
chrII:7623667-7623747 6.81e-01 80
chrV:14366748-14366828 2.72e-02 80
chrIII:8132560-8132640 2.91e-02 29_[+1(1.61e-05)]_43
chrIII:4552113-4552193 7.45e-03 [+2(2.53e-05)]_72
chrX:10395746-10395826 3.46e-03 80
chrIV:8302085-8302165 2.79e-01 80
chrX:5480336-5480416 4.36e-01 80
chrI:9087335-9087415 3.92e-02 80
chrI:10409442-10409522 1.45e-01 1_[+2(5.11e-05)]_71
chrII:5901815-5901895 9.69e-01 80
chrIV:4454890-4454970 9.94e-02 80
chrX:4971618-4971698 2.40e-03 38_[+3(2.01e-05)]_34
chrI:10769948-10770028 2.91e-02 80
chrX:11299761-11299841 1.88e-03 80
chrI:1251648-1251728 6.82e-02 72_[+3(4.22e-05)]
chrX:14297288-14297368 1.16e-01 80
chrI:6173111-6173191 6.26e-03 1_[+2(1.26e-05)]_71
chrX:12656714-12656794 8.63e-03 80
chrV:10036456-10036536 4.21e-01 80
chrX:10372617-10372697 1.15e-02 68_[+1(3.08e-05)]_4
chrIII:623893-623973 1.25e-04 8_[+3(4.22e-05)]_43_[+5(1.67e-05)]_\
13
chrV:4651801-4651881 5.92e-02 58_[+3(8.13e-05)]_14
chrIV:8782370-8782450 3.20e-01 80
chrX:5812096-5812176 4.31e-02 80
chrV:10717231-10717311 1.30e-03 40_[+1(1.61e-05)]_32
chrV:7978971-7979051 4.33e-03 32_[+1(1.61e-05)]_10_[+5(3.31e-05)]_\
22
chrX:5475291-5475371 1.00e+00 80
chrX:5686308-5686388 1.01e-02 52_[+5(3.31e-05)]_20
chrI:13065859-13065939 2.71e-02 50_[+2(2.53e-05)]_2_[+2(2.53e-05)]_\
12
chrV:15661084-15661164 2.84e-01 80
chrIII:12178287-12178367 3.30e-01 80
chrX:9999850-9999930 1.07e-03 3_[+2(8.92e-05)]_69
chrV:12529016-12529096 6.64e-02 25_[+2(1.26e-05)]_27_[+2(6.38e-05)]_\
12
chrII:11620092-11620172 4.51e-02 80
chrIV:14824887-14824967 5.89e-02 80
chrI:14320501-14320581 8.90e-04 51_[+5(9.80e-05)]_21
chrII:10502922-10503002 6.23e-03 80
chrIV:11027800-11027880 1.08e-03 60_[+5(1.67e-05)]_12
chrII:8751161-8751241 1.76e-01 2_[+1(6.33e-05)]_70
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because requested number of motifs (5) found.
********************************************************************************
CPU: c27n12.farnam.hpc.yale.internal
********************************************************************************