Mercurial > repos > iuc > meme_fimo

annotate test-data/dreme2.txt @ 12:02f6ad791bbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:12:47 -0400
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12
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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1 # DREME 4.12.0
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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2 # command: dreme -oc dreme_out_adv -rna -norc -p dreme_test_sites.fa -e 0.00001 -mink 4 -maxk 10
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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3 # positives: 1000 from dreme_test_sites.fa (Thu Apr 19 19:09:45 CEST 2018)
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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4 # negatives: 1000 from shuffled positives
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5 # host: ThinkPad-T450s
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6 # when: Tue Apr 24 18:44:36 CEST 2018
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7
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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8 MEME version 4.12.0
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9
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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10 ALPHABET "RNA" RNA-LIKE
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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11 A "Adenine" CC0000
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12 C "Cytosine" 0000CC
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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13 G "Guanine" FFB300
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14 U "Uracil" 008000
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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15 N "Any base" = ACGU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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16 X = ACGU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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17 . = ACGU
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18 V "Not U" = ACG
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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19 H "Not G" = ACU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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20 D "Not C" = AGU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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21 B "Not A" = CGU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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22 M "Amino" = AC
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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23 R "Purine" = AG
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24 W "Weak" = AU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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25 S "Strong" = CG
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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26 Y "Pyrimidine" = CU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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27 K "Keto" = GU
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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28 T = U
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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29 END ALPHABET
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30
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31 Background letter frequencies (from dataset):
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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32 A 0.221 C 0.245 G 0.221 U 0.312
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33
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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34
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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35 MOTIF UUYUCY DREME-1
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36
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37 # Word Pos Neg P-value E-value
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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38 # BEST UUYUCY 387 210 2.6e-018 3.3e-013
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39 # UUUUCC 147 75 1.8e-007 2.2e-002
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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40 # UUUUCU 155 94 2.2e-005 2.8e+000
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41 # UUCUCU 94 51 1.3e-004 1.7e+001
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42 # UUCUCC 75 42 1.1e-003 1.4e+002
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43
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44 letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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45 0.000000 0.000000 0.000000 1.000000
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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46 0.000000 0.000000 0.000000 1.000000
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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47 0.000000 0.294118 0.000000 0.705882
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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48 0.000000 0.000000 0.000000 1.000000
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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49 0.000000 1.000000 0.000000 0.000000
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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50 0.000000 0.474946 0.000000 0.525054
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51
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52
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53 MOTIF YAGG DREME-2
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54
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55 # Word Pos Neg P-value E-value
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56 # BEST YAGG 600 416 1.1e-016 1.4e-011
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57 # CAGG 441 304 1.5e-010 1.8e-005
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58 # UAGG 232 165 1.1e-004 1.3e+001
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59
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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60 letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011
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61 0.000000 0.692308 0.000000 0.307692
02f6ad791bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
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62 1.000000 0.000000 0.000000 0.000000
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63 0.000000 0.000000 1.000000 0.000000
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64 0.000000 0.000000 1.000000 0.000000
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65
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67 # Stopping reason: E-value threshold exceeded
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68 # Running time: 18.17 seconds