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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/fly/fasta/RankLinear8.0_60/prd.fasta
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
chr2L:3709854-3709974 1.0000 120 chr2R:8277560-8277680 1.0000 120
chr3R:2448960-2449080 1.0000 120 chrX:22433571-22433691 1.0000 120
chr2L:11105329-11105449 1.0000 120 chr2R:20280006-20280126 1.0000 120
chr3R:19890407-19890527 1.0000 120 chrX:12901425-12901545 1.0000 120
chr3L:888888-889008 1.0000 120 chrM:13670-13790 1.0000 120
chr2L:3189099-3189219 1.0000 120 chrM:6507-6627 1.0000 120
chr3R:28811565-28811685 1.0000 120 chr3R:30105125-30105245 1.0000 120
chr3R:15094343-15094463 1.0000 120 chrM:1004-1124 1.0000 120
chrM:9574-9694 1.0000 120 chrM:4738-4858 1.0000 120
chrM:3018-3138 1.0000 120 chrM:12477-12597 1.0000 120
chrX:22433114-22433234 1.0000 120 chr2L:8100612-8100732 1.0000 120
chrM:6073-6193 1.0000 120
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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/fly/inference_raw/MEME/RankLinear8.0_60_prd/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/prd.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= 23 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= 2760 N= 23
sample: seed= 0 hsfrac= 0
searchsize= 2760 norand= no csites= 1000
Letter frequencies in dataset:
A 0.32 C 0.181 G 0.176 T 0.323
Background letter frequencies (from file dataset with add-one prior applied):
A 0.32 C 0.181 G 0.176 T 0.323
Background model order: 0
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MOTIF AASGCCGC MEME-1 width = 8 sites = 7 llr = 68 E-value = 2.5e+000
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Motif AASGCCGC MEME-1 Description
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Simplified A 79::::::
pos.-specific C 114:991a
probability G 1:6a119:
matrix T ::::::::
bits 2.5 * *
2.3 * *
2.0 * **
1.8 *****
Relative 1.5 ******
Entropy 1.3 *******
(14.0 bits) 1.0 *******
0.8 ********
0.5 ********
0.3 ********
0.0 --------
Multilevel AAGGCCGC
consensus C
sequence
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Motif AASGCCGC MEME-1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr2L:11105329-11105449 99 3.31e-06 TCCTGCGCCC AAGGCCGC TCAGCCACGC
chr3R:2448960-2449080 66 6.71e-06 TCAAATACAT AACGCCGC TTTATGTTGA
chr2R:20280006-20280126 113 1.04e-05 TGATGCCGCC CAGGCCGC
chr2R:8277560-8277680 63 1.42e-05 ATTTATGCCA GACGCCGC GGCGAGCGTT
chr2L:3709854-3709974 24 2.44e-05 ACCTGCCTTA AAGGGCGC AGGGCGGGAT
chrM:9574-9694 44 2.78e-05 TGATAAACCT AAGGCCCC TTCACATACT
chr2L:3189099-3189219 69 7.38e-05 TATTCTTGCG ACCGCGGC TGTAGGGAGC
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Motif AASGCCGC MEME-1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr2L:11105329-11105449 3.3e-06 98_[+1]_14
chr3R:2448960-2449080 6.7e-06 65_[+1]_47
chr2R:20280006-20280126 1e-05 112_[+1]
chr2R:8277560-8277680 1.4e-05 62_[+1]_50
chr2L:3709854-3709974 2.4e-05 23_[+1]_89
chrM:9574-9694 2.8e-05 43_[+1]_69
chr2L:3189099-3189219 7.4e-05 68_[+1]_44
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Motif AASGCCGC MEME-1 in BLOCKS format
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BL MOTIF AASGCCGC width=8 seqs=7
chr2L:11105329-11105449 ( 99) AAGGCCGC 1
chr3R:2448960-2449080 ( 66) AACGCCGC 1
chr2R:20280006-20280126 ( 113) CAGGCCGC 1
chr2R:8277560-8277680 ( 63) GACGCCGC 1
chr2L:3709854-3709974 ( 24) AAGGGCGC 1
chrM:9574-9694 ( 44) AAGGCCCC 1
chr2L:3189099-3189219 ( 69) ACCGCGGC 1
//
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Motif AASGCCGC MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 2599 bayes= 9.13955 E= 2.5e+000
116 -34 -30 -945
142 -34 -945 -945
-945 124 170 -945
-945 -945 251 -945
-945 224 -30 -945
-945 224 -30 -945
-945 -34 228 -945
-945 246 -945 -945
--------------------------------------------------------------------------------
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Motif AASGCCGC MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.5e+000
0.714286 0.142857 0.142857 0.000000
0.857143 0.142857 0.000000 0.000000
0.000000 0.428571 0.571429 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.857143 0.142857 0.000000
0.000000 0.857143 0.142857 0.000000
0.000000 0.142857 0.857143 0.000000
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
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Motif AASGCCGC MEME-1 regular expression
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AA[GC]GCCGC
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Time 4.71 secs.
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MOTIF GCASTYGG MEME-2 width = 8 sites = 7 llr = 68 E-value = 2.7e+001
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Motif GCASTYGG MEME-2 Description
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Simplified A ::9:::::
pos.-specific C :a1413::
probability G a::611aa
matrix T ::::76::
bits 2.5 ** **
2.3 ** **
2.0 ** **
1.8 ** **
Relative 1.5 ** * **
Entropy 1.3 **** **
(14.0 bits) 1.0 **** **
0.8 ***** **
0.5 ********
0.3 ********
0.0 --------
Multilevel GCAGTTGG
consensus C C
sequence
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Motif GCASTYGG MEME-2 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr3L:888888-889008 10 9.05e-06 AAAGTCGAC GCAGTCGG TGTCGGTCAC
chr3R:15094343-15094463 56 1.50e-05 TAAGGTTAGC GCACTTGG GTAGGTCTTT
chr2L:3189099-3189219 88 1.50e-05 GTAGGGAGCA GCACTTGG ATGGACGTGC
chr3R:2448960-2449080 12 2.15e-05 ctccgaggta gcagtggg atgagacgta
chr2R:20280006-20280126 43 3.29e-05 GGGTCCACCT GCAGGCGG CACTTGACCA
chr2L:11105329-11105449 45 3.29e-05 TCCGTGCCTA GCAGCTGG CGATGCTCGT
chr2L:3709854-3709974 103 5.35e-05 CTGCCTTGGC GCCCTTGG CTTTAACTTT
--------------------------------------------------------------------------------
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Motif GCASTYGG MEME-2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr3L:888888-889008 9e-06 9_[+2]_103
chr3R:15094343-15094463 1.5e-05 55_[+2]_57
chr2L:3189099-3189219 1.5e-05 87_[+2]_25
chr3R:2448960-2449080 2.2e-05 11_[+2]_101
chr2R:20280006-20280126 3.3e-05 42_[+2]_70
chr2L:11105329-11105449 3.3e-05 44_[+2]_68
chr2L:3709854-3709974 5.4e-05 102_[+2]_10
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Motif GCASTYGG MEME-2 in BLOCKS format
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BL MOTIF GCASTYGG width=8 seqs=7
chr3L:888888-889008 ( 10) GCAGTCGG 1
chr3R:15094343-15094463 ( 56) GCACTTGG 1
chr2L:3189099-3189219 ( 88) GCACTTGG 1
chr3R:2448960-2449080 ( 12) GCAGTGGG 1
chr2R:20280006-20280126 ( 43) GCAGGCGG 1
chr2L:11105329-11105449 ( 45) GCAGCTGG 1
chr2L:3709854-3709974 ( 103) GCCCTTGG 1
//
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Motif GCASTYGG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 2599 bayes= 9.13955 E= 2.7e+001
-945 -945 251 -945
-945 246 -945 -945
142 -34 -945 -945
-945 124 170 -945
-945 -34 -30 115
-945 66 -30 82
-945 -945 251 -945
-945 -945 251 -945
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Motif GCASTYGG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.7e+001
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.857143 0.142857 0.000000 0.000000
0.000000 0.428571 0.571429 0.000000
0.000000 0.142857 0.142857 0.714286
0.000000 0.285714 0.142857 0.571429
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
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Motif GCASTYGG MEME-2 regular expression
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GCA[GC]T[TC]GG
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Time 5.62 secs.
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MOTIF GCTGCGGB MEME-3 width = 8 sites = 5 llr = 49 E-value = 3.8e+002
********************************************************************************
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Motif GCTGCGGB MEME-3 Description
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Simplified A ::::::::
pos.-specific C 28:28::4
probability G 82:8:aa2
matrix T ::a:2::4
bits 2.5 **
2.3 **
2.0 **
1.8 **** **
Relative 1.5 *******
Entropy 1.3 *******
(14.1 bits) 1.0 *******
0.8 *******
0.5 ********
0.3 ********
0.0 --------
Multilevel GCTGCGGC
consensus CG CT T
sequence G
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Motif GCTGCGGB MEME-3 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chr3L:888888-889008 68 6.90e-06 TGGAGTGGGT GCTGCGGG CAAAGCCAAC
chr2R:8277560-8277680 23 1.25e-05 ATATATCCTG GCTCCGGC TAAGTCAACT
chr3R:30105125-30105245 107 1.57e-05 GGTATATAAT GGTGCGGT GTATAT
chr3R:19890407-19890527 88 2.74e-05 AACCTTGAAC CCTGCGGT CCAGTATTGC
chr2L:11105329-11105449 10 2.74e-05 GTCGTCGCT GCTGTGGC GATCGGAAGA
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Motif GCTGCGGB MEME-3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr3L:888888-889008 6.9e-06 67_[+3]_45
chr2R:8277560-8277680 1.2e-05 22_[+3]_90
chr3R:30105125-30105245 1.6e-05 106_[+3]_6
chr3R:19890407-19890527 2.7e-05 87_[+3]_25
chr2L:11105329-11105449 2.7e-05 9_[+3]_103
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Motif GCTGCGGB MEME-3 in BLOCKS format
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BL MOTIF GCTGCGGB width=8 seqs=5
chr3L:888888-889008 ( 68) GCTGCGGG 1
chr2R:8277560-8277680 ( 23) GCTCCGGC 1
chr3R:30105125-30105245 ( 107) GGTGCGGT 1
chr3R:19890407-19890527 ( 88) CCTGCGGT 1
chr2L:11105329-11105449 ( 10) GCTGTGGC 1
//
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Motif GCTGCGGB MEME-3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 2599 bayes= 9.27102 E= 3.8e+002
-897 14 218 -897
-897 214 19 -897
-897 -897 -897 163
-897 14 218 -897
-897 214 -897 -69
-897 -897 251 -897
-897 -897 251 -897
-897 114 19 31
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Motif GCTGCGGB MEME-3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 3.8e+002
0.000000 0.200000 0.800000 0.000000
0.000000 0.800000 0.200000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.200000 0.800000 0.000000
0.000000 0.800000 0.000000 0.200000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.400000 0.200000 0.400000
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Motif GCTGCGGB MEME-3 regular expression
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[GC][CG]T[GC][CT]GG[CTG]
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Time 6.02 secs.
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MOTIF AGCCACGC MEME-4 width = 8 sites = 2 llr = 25 E-value = 1.0e+003
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Motif AGCCACGC MEME-4 Description
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Simplified A a:::a:::
pos.-specific C ::aa:a:a
probability G :a::::a:
matrix T ::::::::
bits 2.5 *** ***
2.3 *** ***
2.0 *** ***
1.8 ********
Relative 1.5 ********
Entropy 1.3 ********
(18.2 bits) 1.0 ********
0.8 ********
0.5 ********
0.3 ********
0.0 --------
Multilevel AGCCACGC
consensus
sequence
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Motif AGCCACGC MEME-4 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chrX:12901425-12901545 103 3.40e-06 ATTACACTAT AGCCACGC AAATGGAATC
chr2L:11105329-11105449 109 3.40e-06 AAGGCCGCTC AGCCACGC TGTT
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Motif AGCCACGC MEME-4 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrX:12901425-12901545 3.4e-06 102_[+4]_10
chr2L:11105329-11105449 3.4e-06 108_[+4]_4
--------------------------------------------------------------------------------
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Motif AGCCACGC MEME-4 in BLOCKS format
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BL MOTIF AGCCACGC width=8 seqs=2
chrX:12901425-12901545 ( 103) AGCCACGC 1
chr2L:11105329-11105449 ( 109) AGCCACGC 1
//
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Motif AGCCACGC MEME-4 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 2599 bayes= 10.3426 E= 1.0e+003
164 -765 -765 -765
-765 -765 250 -765
-765 246 -765 -765
-765 246 -765 -765
164 -765 -765 -765
-765 246 -765 -765
-765 -765 250 -765
-765 246 -765 -765
--------------------------------------------------------------------------------
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Motif AGCCACGC MEME-4 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.0e+003
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
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
--------------------------------------------------------------------------------
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Motif AGCCACGC MEME-4 regular expression
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AGCCACGC
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Time 6.40 secs.
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MOTIF TGGCTDGG MEME-5 width = 8 sites = 4 llr = 41 E-value = 2.2e+003
********************************************************************************
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Motif TGGCTDGG MEME-5 Description
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Simplified A :::::3::
pos.-specific C ::3a3:::
probability G :a8::3aa
matrix T a:::85::
bits 2.5 * * **
2.3 * * **
2.0 * * **
1.8 **** **
Relative 1.5 **** **
Entropy 1.3 **** **
(14.7 bits) 1.0 ***** **
0.8 ***** **
0.5 ***** **
0.3 ********
0.0 --------
Multilevel TGGCTTGG
consensus C CA
sequence G
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Motif TGGCTDGG MEME-5 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------
chrX:22433571-22433691 45 5.85e-06 gagataaatg tggcttgg aagtttttga
chr2R:20280006-20280126 28 1.41e-05 CTCTTGTACT TGGCCGGG TCCACCTGCA
chrX:22433114-22433234 109 1.99e-05 AAtgttagtg tggctagg tcca
chr2L:3709854-3709974 94 2.59e-05 CGTTGTGCTC TGCCTTGG CGCCCTTGGC
--------------------------------------------------------------------------------
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Motif TGGCTDGG MEME-5 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chrX:22433571-22433691 5.9e-06 44_[+5]_68
chr2R:20280006-20280126 1.4e-05 27_[+5]_85
chrX:22433114-22433234 2e-05 108_[+5]_4
chr2L:3709854-3709974 2.6e-05 93_[+5]_19
--------------------------------------------------------------------------------
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Motif TGGCTDGG MEME-5 in BLOCKS format
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BL MOTIF TGGCTDGG width=8 seqs=4
chrX:22433571-22433691 ( 45) TGGCTTGG 1
chr2R:20280006-20280126 ( 28) TGGCCGGG 1
chrX:22433114-22433234 ( 109) TGGCTAGG 1
chr2L:3709854-3709974 ( 94) TGCCTTGG 1
//
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Motif TGGCTDGG MEME-5 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 2599 bayes= 9.34152 E= 2.2e+003
-865 -865 -865 163
-865 -865 250 -865
-865 46 209 -865
-865 246 -865 -865
-865 46 -865 121
-36 -865 51 63
-865 -865 250 -865
-865 -865 250 -865
--------------------------------------------------------------------------------
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Motif TGGCTDGG MEME-5 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 2.2e+003
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.250000 0.750000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.250000 0.000000 0.750000
0.250000 0.000000 0.250000 0.500000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
--------------------------------------------------------------------------------
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Motif TGGCTDGG MEME-5 regular expression
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TG[GC]C[TC][TAG]GG
--------------------------------------------------------------------------------
Time 6.79 secs.
********************************************************************************
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SUMMARY OF MOTIFS
********************************************************************************
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
chr2L:3709854-3709974 3.17e-05 23_[+1(2.44e-05)]_62_[+5(2.59e-05)]_\
1_[+2(5.35e-05)]_10
chr2R:8277560-8277680 6.84e-05 22_[+3(1.25e-05)]_32_[+1(1.42e-05)]_\
50
chr3R:2448960-2449080 2.99e-04 11_[+2(2.15e-05)]_46_[+1(6.71e-06)]_\
47
chrX:22433571-22433691 2.12e-02 44_[+5(5.85e-06)]_68
chr2L:11105329-11105449 6.80e-09 9_[+3(2.74e-05)]_27_[+2(3.29e-05)]_\
46_[+1(3.31e-06)]_2_[+4(3.40e-06)]_4
chr2R:20280006-20280126 6.33e-07 27_[+5(1.41e-05)]_7_[+2(3.29e-05)]_\
62_[+1(1.04e-05)]
chr3R:19890407-19890527 4.05e-02 87_[+3(2.74e-05)]_25
chrX:12901425-12901545 3.08e-02 102_[+4(3.40e-06)]_10
chr3L:888888-889008 5.95e-05 9_[+2(9.05e-06)]_50_[+3(6.90e-06)]_\
45
chrM:13670-13790 1.00e+00 120
chr2L:3189099-3189219 4.09e-04 68_[+1(7.38e-05)]_11_[+2(1.50e-05)]_\
25
chrM:6507-6627 1.00e+00 120
chr3R:28811565-28811685 8.77e-01 120
chr3R:30105125-30105245 4.08e-02 106_[+3(1.57e-05)]_6
chr3R:15094343-15094463 2.27e-02 55_[+2(1.50e-05)]_57
chrM:1004-1124 9.86e-01 120
chrM:9574-9694 1.92e-01 43_[+1(2.78e-05)]_69
chrM:4738-4858 8.72e-01 120
chrM:3018-3138 9.97e-01 120
chrM:12477-12597 1.00e+00 120
chrX:22433114-22433234 4.92e-02 108_[+5(1.99e-05)]_4
chr2L:8100612-8100732 9.93e-01 120
chrM:6073-6193 9.41e-01 120
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because requested number of motifs (5) found.
********************************************************************************
CPU: c28n02.farnam.hpc.yale.internal
********************************************************************************