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comparison test-data/streme_output_test2.txt @ 20:faa378fa0c81 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
author iuc
date Mon, 14 Jul 2025 21:33:26 +0000
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19:7ce0fe11b411 20:faa378fa0c81
1 ********************************************************************************
2 STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation
3 ********************************************************************************
4 MEME version 5.5.8 (Release date: Thu May 15 15:01:46 2025 -0700)
5
6 For further information on how to interpret these results please access https://meme-suite.org/meme.
7 To get a copy of the MEME Suite software please access https://meme-suite.org.
8
9 ********************************************************************************
10
11
12 ********************************************************************************
13 REFERENCE
14 ********************************************************************************
15 If you use this program in your research, please cite:
16
17 Timothy L. Bailey,
18 "STREME: accurate and versatile sequence motif discovery",
19 Bioinformatics, Mar. 24, 2021.
20 ********************************************************************************
21
22
23 ********************************************************************************
24 ALPHABET "DNA with covalent modifications" DNA-LIKE
25 ********************************************************************************
26 A "Adenine" 8510A8 ~ T "Thymine" A89610
27 C "Cytosine" A50026 ~ G "Guanine" 313695
28 a "N6-methyladenine" 8510A8 ~ t "Thymine_lowercase" 756BB1
29 c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8
30 f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9
31 g "modified_g" 00897B ~ 5 "cytosine_lowercase" 53698A
32 h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1
33 m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4
34 ? = ACGTacfghmt12345
35 ********************************************************************************
36
37 strands: + -
38
39 Background letter frequencies
40 A 0.218 C 0.24 G 0.24 T 0.218 a 0.0266 c 0.0125 f 1.96e-05 g 0.00315 h 1.96e-05 m 1.96e-05 t 0.0266 1 1.96e-05 2 1.96e-05 3 1.96e-05 4 0.0125 5 0.00315
41
42 MOTIF 1-GTATAAAAGC STREME-1
43 letter-probability matrix: alength= 16 w= 10 nsites= 28 S= 7.0e-014
44 0.344606 0.001172 0.618858 0.034950 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
45 0.001065 0.001172 0.001172 0.996177 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
46 0.996177 0.001172 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
47 0.001065 0.001172 0.001172 0.996177 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
48 0.996177 0.001172 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
49 0.928407 0.001172 0.035057 0.034950 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
50 0.860638 0.136711 0.001172 0.001065 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
51 0.548672 0.001172 0.313139 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
52 0.068834 0.068941 0.725207 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
53 0.068834 0.485705 0.308443 0.136603 0.000130 0.000061 0.000000 0.000015 0.000000 0.000000 0.000130 0.000000 0.000000 0.000000 0.000061 0.000015
54
55 MOTIF 2-CCCACCAGA STREME-2
56 letter-probability matrix: alength= 16 w= 9 nsites= 20 S= 2.2e-007
57 0.001482 0.947685 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
58 0.143970 0.805197 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
59 0.095771 0.711962 0.143064 0.048626 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
60 0.947536 0.001631 0.048775 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
61 0.095771 0.710908 0.191263 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
62 0.001482 0.900540 0.001631 0.095771 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
63 0.663614 0.095920 0.096974 0.142915 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
64 0.095771 0.332697 0.569474 0.001482 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
65 0.473982 0.239462 0.143064 0.142915 0.000181 0.000085 0.000000 0.000021 0.000000 0.000000 0.000181 0.000000 0.000000 0.000000 0.000085 0.000021
66
67 MOTIF 3-4a4t4a4a4T STREME-3
68 letter-probability matrix: alength= 16 w= 10 nsites= 7 S= 5.5e-003
69 0.004400 0.004842 0.004842 0.004400 0.140510 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.840087 0.000064
70 0.004400 0.004842 0.004842 0.004400 0.700399 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.000253 0.000064
71 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.980059 0.000064
72 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.840371 0.000000 0.000000 0.000000 0.140226 0.000064
73 0.004400 0.004842 0.004842 0.004400 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.700115 0.000064
74 0.004400 0.004842 0.004842 0.004400 0.560427 0.000253 0.000000 0.000064 0.000000 0.000000 0.420454 0.000000 0.000000 0.000000 0.000253 0.000064
75 0.004400 0.004842 0.004842 0.144372 0.000537 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.560142 0.000064
76 0.004400 0.144814 0.144814 0.004400 0.420454 0.000253 0.000000 0.000064 0.000000 0.000000 0.280482 0.000000 0.000000 0.000000 0.000253 0.000064
77 0.004400 0.144814 0.144814 0.144372 0.140510 0.000253 0.000000 0.000064 0.000000 0.000000 0.140510 0.000000 0.000000 0.000000 0.280198 0.000064
78 0.004400 0.144814 0.004842 0.284344 0.280482 0.000253 0.000000 0.000064 0.000000 0.000000 0.000537 0.000000 0.000000 0.000000 0.280198 0.000064