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comparison test-data/meme_output_test2.txt @ 18:19237efe98d1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
author iuc
date Sat, 09 Apr 2022 08:34:02 +0000
parents 3f0dd362b755
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17:e7242484929c 18:19237efe98d1
1 ******************************************************************************** 1 ********************************************************************************
2 MEME - Motif discovery tool 2 SUMMARY OF MOTIFS
3 MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700) 3 ********************************************************************************
4 REFERENCE
5 TRAINING SET
6 PRIMARY SEQUENCES= Galaxy_FASTA_Input
7 CONTROL SEQUENCES= --none--
8 ALPHABET= ACGT
9 Sequence name Weight Length Sequence name Weight Length
10 ------------- ------ ------ ------------- ------ ------
11 chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
12 COMMAND LINE SUMMARY
13 model: mod= zoops nmotifs= 1 evt= inf
14 objective function: em= E-value of product of p-values
15 starts= E-value of product of p-values
16 strands: +
17 width: minw= 8 maxw= 50
18 nsites: minsites= 2 maxsites= 30 wnsites= 0.8
19 theta: spmap= uni spfuzz= 0.5
20 em: prior= dirichlet b= 0.01 maxiter= 50
21 distance= 0.001
22 trim: wg= 11 ws= 1 endgaps= yes
23 data: n= 1500 N= 30
24 sample: seed= 0 hsfrac= 0
25 searchsize= 1500 norand= no csites= 1000
26 Dirichlet mixture priors file:
27 Letter frequencies in dataset:
28 A 0.294 C 0.231 G 0.257 T 0.217
29 Background letter frequencies (from file dataset with add-one prior applied):
30 A 0.294 C 0.231 G 0.257 T 0.217
31 Background model order: 0
32 MOTIF GGSRTATAAAA MEME-1 width = 11 sites = 30 llr = 254 E-value = 5.1e-040
33 Motif GGSRTATAAAA MEME-1 Description
34 Simplified A 3313:9:a798
35 pos.-specific C 1:3::1:::1:
36 probability G 6756::::::2
37 matrix T 1:11a1a:3::
38 4
39 bits 2.2 * 5 --------------------------------------------------------------------------------
40 2.0 * * 6 Combined block diagrams: non-overlapping sites with p-value < 0.0001
41 1.8 * * 7 --------------------------------------------------------------------------------
42 1.5 * ** * 8 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
43 Relative 1.3 * ** *
44 Entropy 1.1 ******
45 (12.2 bits) 0.9 * *******
46 0.7 * *******
47 0.4 ** ********
48 0.2 ***********
49 0.0 -----------
50
51 Multilevel GGGGTATAAAA
52 consensus AACA T
53 sequence
54 Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
55 Sequence name Start P-value Site
56 chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
57 Motif GGSRTATAAAA MEME-1 block diagrams
58 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
59 ------------- ---------------- ------------- 9 ------------- ---------------- -------------
60 chr21_46046964_46047014_ 4.5e-07 12_[+1]_27
61 Motif GGSRTATAAAA MEME-1 in BLOCKS format
62 BL MOTIF GGSRTATAAAA width=11 seqs=30
63 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
64 Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
65 log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040
66 -14 -179 114 -112
67 3 -1155 137 -270
68 -114 20 86 -71
69 3 -279 122 -170
70 -1155 -1155 -295 215
71 156 -179 -1155 -170
72 -1155 -1155 -1155 220
73 172 -279 -1155 -1155
74 125 -1155 -1155 46
75 167 -179 -1155 -1155
76 144 -1155 -63 -270
77 Motif GGSRTATAAAA MEME-1 position-specific probability matrix
78 letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040
79 0.266667 0.066667 0.566667 0.100000
80 Motif GGSRTATAAAA MEME-1 regular expression
81 [GA][GA][GC][GA]TATA[AT]AA
82 SUMMARY OF MOTIFS
83 Combined block diagrams: non-overlapping sites with p-value < 0.0001
84 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
85 chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] 10 chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)]
86 Stopped because requested number of motifs (1) found. 11 chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12
12 chr21_28217753_28217803_ 1.00e-01 50
13 chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25
14 chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27
15 chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39
16 chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24
17 chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35
18 chr21_31962741_31962791_ 3.37e-02 50
19 chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26
20 chr21_31973364_31973414_ 5.73e-02 50
21 chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23
22 chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21
23 chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26
24 chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22
25 chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18
26 chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17
27 chr21_37838750_37838800_ 1.90e-02 50
28 chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2
29 chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30
30 chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35
31 chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32
32 chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37
33 chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24
34 chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27
35 chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3
36 chr21_46086869_46086919_ 5.54e-03 50
37 chr21_46102103_46102153_ 5.54e-03 50
38 chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7
39 chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9
40 --------------------------------------------------------------------------------