Mercurial > repos > iuc > meme_meme
view test-data/meme_output_test2.txt @ 16:3c2ac7c3f0b8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 09:45:12 +0000 |
| parents | 3f0dd362b755 |
| children | 19237efe98d1 |
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******************************************************************************** MEME - Motif discovery tool MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700) REFERENCE TRAINING SET PRIMARY SEQUENCES= Galaxy_FASTA_Input CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 COMMAND LINE SUMMARY model: mod= zoops nmotifs= 1 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= 50 nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 trim: wg= 11 ws= 1 endgaps= yes data: n= 1500 N= 30 sample: seed= 0 hsfrac= 0 searchsize= 1500 norand= no csites= 1000 Dirichlet mixture priors file: Letter frequencies in dataset: A 0.294 C 0.231 G 0.257 T 0.217 Background letter frequencies (from file dataset with add-one prior applied): A 0.294 C 0.231 G 0.257 T 0.217 Background model order: 0 MOTIF GGSRTATAAAA MEME-1 width = 11 sites = 30 llr = 254 E-value = 5.1e-040 Motif GGSRTATAAAA MEME-1 Description Simplified A 3313:9:a798 pos.-specific C 1:3::1:::1: probability G 6756::::::2 matrix T 1:11a1a:3:: bits 2.2 * 2.0 * * 1.8 * * 1.5 * ** * Relative 1.3 * ** * Entropy 1.1 ****** (12.2 bits) 0.9 * ******* 0.7 * ******* 0.4 ** ******** 0.2 *********** 0.0 ----------- Multilevel GGGGTATAAAA consensus AACA T sequence Motif GGSRTATAAAA MEME-1 sites sorted by position p-value Sequence name Start P-value Site chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC Motif GGSRTATAAAA MEME-1 block diagrams SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_46046964_46047014_ 4.5e-07 12_[+1]_27 Motif GGSRTATAAAA MEME-1 in BLOCKS format BL MOTIF GGSRTATAAAA width=11 seqs=30 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 Motif GGSRTATAAAA MEME-1 position-specific scoring matrix log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 -14 -179 114 -112 3 -1155 137 -270 -114 20 86 -71 3 -279 122 -170 -1155 -1155 -295 215 156 -179 -1155 -170 -1155 -1155 -1155 220 172 -279 -1155 -1155 125 -1155 -1155 46 167 -179 -1155 -1155 144 -1155 -63 -270 Motif GGSRTATAAAA MEME-1 position-specific probability matrix letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 0.266667 0.066667 0.566667 0.100000 Motif GGSRTATAAAA MEME-1 regular expression [GA][GA][GC][GA]TATA[AT]AA SUMMARY OF MOTIFS Combined block diagrams: non-overlapping sites with p-value < 0.0001 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] Stopped because requested number of motifs (1) found.