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comparison test-data/meme_output_test1.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 4
5 TRAINING SET
6 CONTROL SEQUENCES= --none--
7 ALPHABET= ACDEFGHIKLMNPQRSTVWY
8 Sequence name Weight Length Sequence name Weight Length
9 ------------- ------ ------ ------------- ------ ------
10 chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
11 COMMAND LINE SUMMARY
12 model: mod= zoops nmotifs= 1 evt= inf
13 objective function: em= E-value of product of p-values
14 starts= E-value of product of p-values
15 width: minw= 8 maxw= 50
16 nsites: minsites= 2 maxsites= 30 wnsites= 0.8
17 theta: spmap= pam spfuzz= 120
18 em: prior= megap b= 7500 maxiter= 50
19 distance= 1e-05
20 trim: wg= 11 ws= 1 endgaps= yes
21 data: n= 1500 N= 30
22 sample: seed= 0 hsfrac= 0
23 searchsize= 1500 norand= no csites= 1000
24 Dirichlet mixture priors file: prior30.plib
25 Letter frequencies in dataset:
26 A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0
27 L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0
28 W 0 Y 0
29 Background letter frequencies (from file dataset with add-one prior applied):
30 A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658
31 L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658
32 W 0.000658 Y 0.000658
33 Background model order: 0
34 MOTIF GGGGTATAAAA MEME-1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011
35 -------------------------------------------------------------------------------- 5 --------------------------------------------------------------------------------
36 Motif GGGGTATAAAA MEME-1 Description
37 Motif GGGGTATAAAA MEME-1 sites sorted by position p-value
38 Sequence name Start P-value Site
39 ------------- ----- --------- -----------
40 chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
41 Motif GGGGTATAAAA MEME-1 block diagrams
42 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
43 ------------- ---------------- -------------
44 chr21_46046964_46047014_ 1.1e-06 12_[1]_27
45 Motif GGGGTATAAAA MEME-1 in BLOCKS format
46 BL MOTIF GGGGTATAAAA width=11 seqs=25
47 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
48 Motif GGGGTATAAAA MEME-1 position-specific scoring matrix
49 log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011
50 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36
51 Motif GGGGTATAAAA MEME-1 position-specific probability matrix
52 letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011
53 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000
54 Motif GGGGTATAAAA MEME-1 regular expression
55 [GA][GA][GC][GA]TATA[AT]AA
56 SUMMARY OF MOTIFS
57 Combined block diagrams: non-overlapping sites with p-value < 0.0001 6 Combined block diagrams: non-overlapping sites with p-value < 0.0001
7 --------------------------------------------------------------------------------
58 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM 8 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
59 ------------- ---------------- ------------- 9 ------------- ---------------- -------------
60 chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] 10 chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]
61 Stopped because requested number of motifs (1) found. 11 chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12
12 chr21_28217753_28217803_ 7.29e-01 50
13 chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25
14 chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27
15 chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39
16 chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24
17 chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35
18 chr21_31962741_31962791_ 1.61e-02 50
19 chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26
20 chr21_31973364_31973414_ 1.99e-01 50
21 chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23
22 chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21
23 chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26
24 chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20
25 chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18
26 chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17
27 chr21_37838750_37838800_ 8.23e-02 50
28 chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2
29 chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30
30 chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35
31 chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32
32 chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37
33 chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24
34 chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27
35 chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3
36 chr21_46086869_46086919_ 4.30e-02 50
37 chr21_46102103_46102153_ 4.30e-02 50
38 chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7
39 chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9