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comparison test-data/meme_output_test1.xml @ 1:cb8a2242bf03 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:27 -0400
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children 3e5c80594237
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0:b386032d758d 1:cb8a2242bf03
1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
2 <!-- Document definition -->
3 <!DOCTYPE MEME[
4 <!ELEMENT MEME (
5 training_set,
6 model,
7 motifs,
8 scanned_sites_summary?
9 )>
10 <!ATTLIST MEME
11 version CDATA #REQUIRED
12 release CDATA #REQUIRED
13 >
14 <!-- Training-set elements -->
15 <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
16 <!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>
17 <!ELEMENT alphabet (letter*)>
18 <!ATTLIST alphabet name CDATA #REQUIRED>
19 <!ELEMENT ambigs (letter*)>
20 <!ELEMENT letter EMPTY>
21 <!ATTLIST letter id ID #REQUIRED>
22 <!ATTLIST letter symbol CDATA #REQUIRED>
23 <!ATTLIST letter equals CDATA #IMPLIED>
24 <!ATTLIST letter aliases CDATA #IMPLIED>
25 <!ATTLIST letter complement CDATA #IMPLIED>
26 <!ATTLIST letter name CDATA #IMPLIED>
27 <!ATTLIST letter colour CDATA #IMPLIED>
28 <!ELEMENT sequence EMPTY>
29 <!ATTLIST sequence id ID #REQUIRED
30 name CDATA #REQUIRED
31 length CDATA #REQUIRED
32 weight CDATA #REQUIRED
33 >
34 <!ELEMENT letter_frequencies (alphabet_array)>
35
36 <!-- Model elements -->
37 <!ELEMENT model (
38 command_line,
39 host,
40 type,
41 nmotifs,
42 evalue_threshold,
43 object_function,
44 spfun,
45 min_width,
46 max_width,
47 wg,
48 ws,
49 endgaps,
50 minsites,
51 maxsites,
52 wnsites,
53 spmap,
54 spfuzz,
55 prior,
56 beta,
57 maxiter,
58 distance,
59 num_sequences,
60 num_positions,
61 seed,
62 hsfrac,
63 maxwords,
64 maxsize,
65 csites,
66 strands,
67 priors_file,
68 reason_for_stopping,
69 back_order,
70 background_frequencies
71 )>
72 <!ELEMENT command_line (#PCDATA)*>
73 <!ELEMENT host (#PCDATA)*>
74 <!ELEMENT type (#PCDATA)*>
75 <!ELEMENT nmotifs (#PCDATA)*>
76 <!ELEMENT evalue_threshold (#PCDATA)*>
77 <!ELEMENT object_function (#PCDATA)*>
78 <!ELEMENT spfun (#PCDATA)*>
79 <!ELEMENT min_width (#PCDATA)*>
80 <!ELEMENT max_width (#PCDATA)*>
81 <!ELEMENT wg (#PCDATA)*>
82 <!ELEMENT ws (#PCDATA)*>
83 <!ELEMENT endgaps (#PCDATA)*>
84 <!ELEMENT minsites (#PCDATA)*>
85 <!ELEMENT maxsites (#PCDATA)*>
86 <!ELEMENT wnsites (#PCDATA)*>
87 <!ELEMENT spmap (#PCDATA)*>
88 <!ELEMENT spfuzz (#PCDATA)*>
89 <!ELEMENT prior (#PCDATA)*>
90 <!ELEMENT beta (#PCDATA)*>
91 <!ELEMENT maxiter (#PCDATA)*>
92 <!ELEMENT distance (#PCDATA)*>
93 <!ELEMENT num_sequences (#PCDATA)*>
94 <!ELEMENT num_positions (#PCDATA)*>
95 <!ELEMENT seed (#PCDATA)*>
96 <!ELEMENT hsfrac (#PCDATA)*>
97 <!ELEMENT maxwords (#PCDATA)*>
98 <!ELEMENT maxsites (#PCDATA)*>
99 <!ELEMENT csites (#PCDATA)*>
100 <!ELEMENT strands (#PCDATA)*>
101 <!ELEMENT priors_file (#PCDATA)*>
102 <!ELEMENT reason_for_stopping (#PCDATA)*>
103 <!ELEMENT back_order (#PCDATA)*>
104 <!ELEMENT background_frequencies (alphabet_array)>
105 <!ATTLIST background_frequencies source CDATA #REQUIRED>
106
107 <!-- Motif elements -->
108 <!ELEMENT motifs (motif*)>
109 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
110 <!ATTLIST motif id ID #REQUIRED
111 name CDATA #REQUIRED
112 alt CDATA ""
113 width CDATA #REQUIRED
114 sites CDATA #REQUIRED
115 llr CDATA #REQUIRED
116 ic CDATA #REQUIRED
117 re CDATA #REQUIRED
118 bayes_threshold CDATA #REQUIRED
119 e_value CDATA #REQUIRED
120 elapsed_time CDATA #REQUIRED
121 url CDATA ""
122 >
123 <!ELEMENT scores (alphabet_matrix)>
124 <!ELEMENT probabilities (alphabet_matrix)>
125 <!ELEMENT regular_expression (#PCDATA)*>
126
127 <!-- Contributing site elements -->
128 <!-- Contributing sites are motif occurences found during the motif discovery phase -->
129 <!ELEMENT contributing_sites (contributing_site*)>
130 <!ELEMENT contributing_site (left_flank, site, right_flank)>
131 <!ATTLIST contributing_site sequence_id IDREF #REQUIRED
132 position CDATA #REQUIRED
133 strand (plus|minus|none) 'none'
134 pvalue CDATA #REQUIRED
135 >
136 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
137 <!ELEMENT left_flank (#PCDATA)>
138 <!-- The site contains the sequence for the motif instance -->
139 <!ELEMENT site (letter_ref*)>
140 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
141 <!ELEMENT right_flank (#PCDATA)>
142
143 <!-- Scanned site elements -->
144 <!-- Scanned sites are motif occurences found during the sequence scan phase -->
145 <!ELEMENT scanned_sites_summary (scanned_sites*)>
146 <!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
147 <!ELEMENT scanned_sites (scanned_site*)>
148 <!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
149 pvalue CDATA #REQUIRED
150 num_sites CDATA #REQUIRED>
151 <!ELEMENT scanned_site EMPTY>
152 <!ATTLIST scanned_site motif_id IDREF #REQUIRED
153 strand (plus|minus|none) 'none'
154 position CDATA #REQUIRED
155 pvalue CDATA #REQUIRED>
156
157 <!-- Utility elements -->
158 <!-- A reference to a letter in the alphabet -->
159 <!ELEMENT letter_ref EMPTY>
160 <!ATTLIST letter_ref letter_id IDREF #REQUIRED>
161 <!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
162 <!ELEMENT alphabet_array (value*)>
163 <!ELEMENT value (#PCDATA)>
164 <!ATTLIST value letter_id IDREF #REQUIRED>
165
166 <!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
167 <!ELEMENT alphabet_matrix (alphabet_array*)>
168
169 ]>
170 <!-- Begin document body -->
171 <MEME version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
172 <training_set datafile="meme_input_1.fasta" length="30">
173 <alphabet name="Protein" like="protein">
174 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
175 <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
176 <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
177 <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
178 <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
179 <letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
180 <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
181 <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
182 <letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
183 <letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
184 <letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
185 <letter id="N" symbol="N" name="Asparagine" colour="008000"/>
186 <letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
187 <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
188 <letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
189 <letter id="S" symbol="S" name="Serine" colour="008000"/>
190 <letter id="T" symbol="T" name="Threonine" colour="008000"/>
191 <letter id="V" symbol="V" name="Valine" colour="0000CC"/>
192 <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
193 <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
194 <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
195 <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
196 <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
197 <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
198 </alphabet>
199 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
200 <sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" />
201 <sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" />
202 <sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" />
203 <sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" />
204 <sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" />
205 <sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" />
206 <sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" />
207 <sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" />
208 <sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" />
209 <sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" />
210 <sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" />
211 <sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" />
212 <sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" />
213 <sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" />
214 <sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" />
215 <sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" />
216 <sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" />
217 <sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" />
218 <sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" />
219 <sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" />
220 <sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" />
221 <sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" />
222 <sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" />
223 <sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" />
224 <sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" />
225 <sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" />
226 <sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" />
227 <sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" />
228 <sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" />
229 <letter_frequencies>
230 <alphabet_array>
231 <value letter_id="A">0.294</value>
232 <value letter_id="C">0.231</value>
233 <value letter_id="D">0.000</value>
234 <value letter_id="E">0.000</value>
235 <value letter_id="F">0.000</value>
236 <value letter_id="G">0.257</value>
237 <value letter_id="H">0.000</value>
238 <value letter_id="I">0.000</value>
239 <value letter_id="K">0.000</value>
240 <value letter_id="L">0.000</value>
241 <value letter_id="M">0.000</value>
242 <value letter_id="N">0.000</value>
243 <value letter_id="P">0.000</value>
244 <value letter_id="Q">0.000</value>
245 <value letter_id="R">0.000</value>
246 <value letter_id="S">0.000</value>
247 <value letter_id="T">0.217</value>
248 <value letter_id="V">0.000</value>
249 <value letter_id="W">0.000</value>
250 <value letter_id="Y">0.000</value>
251 </alphabet_array>
252 </letter_frequencies>
253 </training_set>
254 <model>
255 <command_line>meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 </command_line>
256 <host>ThinkPad-T450s</host>
257 <type>zoops</type>
258 <nmotifs>1</nmotifs>
259 <evalue_threshold>inf</evalue_threshold>
260 <object_function>E-value of product of p-values</object_function>
261 <use_llr>0</use_llr>
262 <min_width>8</min_width>
263 <max_width>50</max_width>
264 <wg>11</wg>
265 <ws>1</ws>
266 <endgaps>yes</endgaps>
267 <substring>yes</substring>
268 <minsites>2</minsites>
269 <maxsites>30</maxsites>
270 <wnsites>0.8</wnsites>
271 <spmap>pam</spmap>
272 <spfuzz>120</spfuzz>
273 <prior>megap</prior>
274 <beta>7500</beta>
275 <maxiter>50</maxiter>
276 <distance>1e-05</distance>
277 <num_sequences>30</num_sequences>
278 <num_positions>1500</num_positions>
279 <seed>0</seed>
280 <ctfrac>-1</ctfrac>
281 <maxwords>-1</maxwords>
282 <strands>none</strands>
283 <priors_file>prior30.plib</priors_file>
284 <reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
285 <background_frequencies source="dataset with add-one prior applied">
286 <alphabet_array>
287 <value letter_id="A">0.291</value>
288 <value letter_id="C">0.229</value>
289 <value letter_id="D">0.001</value>
290 <value letter_id="E">0.001</value>
291 <value letter_id="F">0.001</value>
292 <value letter_id="G">0.255</value>
293 <value letter_id="H">0.001</value>
294 <value letter_id="I">0.001</value>
295 <value letter_id="K">0.001</value>
296 <value letter_id="L">0.001</value>
297 <value letter_id="M">0.001</value>
298 <value letter_id="N">0.001</value>
299 <value letter_id="P">0.001</value>
300 <value letter_id="Q">0.001</value>
301 <value letter_id="R">0.001</value>
302 <value letter_id="S">0.001</value>
303 <value letter_id="T">0.215</value>
304 <value letter_id="V">0.001</value>
305 <value letter_id="W">0.001</value>
306 <value letter_id="Y">0.001</value>
307 </alphabet_array>
308 </background_frequencies>
309 </model>
310 <motifs>
311 <motif id="motif_1" name="GGGGTATAAAA" alt="MEME-1" width="11" sites="25" ic="40.0" re="13.8" llr="239" e_value="2.4e-011" bayes_threshold="5.33554" elapsed_time="0.772000">
312 <scores>
313 <alphabet_matrix>
314 <alphabet_array>
315 <value letter_id="A">-32</value>
316 <value letter_id="C">-680</value>
317 <value letter_id="D">91</value>
318 <value letter_id="E">77</value>
319 <value letter_id="F">7</value>
320 <value letter_id="G">138</value>
321 <value letter_id="H">-20</value>
322 <value letter_id="I">55</value>
323 <value letter_id="K">64</value>
324 <value letter_id="L">107</value>
325 <value letter_id="M">11</value>
326 <value letter_id="N">150</value>
327 <value letter_id="P">142</value>
328 <value letter_id="Q">72</value>
329 <value letter_id="R">87</value>
330 <value letter_id="S">396</value>
331 <value letter_id="T">-148</value>
332 <value letter_id="V">221</value>
333 <value letter_id="W">-140</value>
334 <value letter_id="Y">-36</value>
335 </alphabet_array>
336 <alphabet_array>
337 <value letter_id="A">-11</value>
338 <value letter_id="C">-680</value>
339 <value letter_id="D">89</value>
340 <value letter_id="E">76</value>
341 <value letter_id="F">7</value>
342 <value letter_id="G">137</value>
343 <value letter_id="H">-21</value>
344 <value letter_id="I">55</value>
345 <value letter_id="K">63</value>
346 <value letter_id="L">107</value>
347 <value letter_id="M">10</value>
348 <value letter_id="N">149</value>
349 <value letter_id="P">141</value>
350 <value letter_id="Q">71</value>
351 <value letter_id="R">87</value>
352 <value letter_id="S">396</value>
353 <value letter_id="T">-239</value>
354 <value letter_id="V">220</value>
355 <value letter_id="W">-140</value>
356 <value letter_id="Y">-36</value>
357 </alphabet_array>
358 <alphabet_array>
359 <value letter_id="A">-79</value>
360 <value letter_id="C">41</value>
361 <value letter_id="D">4</value>
362 <value letter_id="E">21</value>
363 <value letter_id="F">-7</value>
364 <value letter_id="G">44</value>
365 <value letter_id="H">-62</value>
366 <value letter_id="I">42</value>
367 <value letter_id="K">-5</value>
368 <value letter_id="L">99</value>
369 <value letter_id="M">0</value>
370 <value letter_id="N">99</value>
371 <value letter_id="P">138</value>
372 <value letter_id="Q">52</value>
373 <value letter_id="R">42</value>
374 <value letter_id="S">399</value>
375 <value letter_id="T">-46</value>
376 <value letter_id="V">223</value>
377 <value letter_id="W">-173</value>
378 <value letter_id="Y">-68</value>
379 </alphabet_array>
380 <alphabet_array>
381 <value letter_id="A">11</value>
382 <value letter_id="C">-677</value>
383 <value letter_id="D">48</value>
384 <value letter_id="E">47</value>
385 <value letter_id="F">-2</value>
386 <value letter_id="G">127</value>
387 <value letter_id="H">-43</value>
388 <value letter_id="I">46</value>
389 <value letter_id="K">27</value>
390 <value letter_id="L">101</value>
391 <value letter_id="M">3</value>
392 <value letter_id="N">124</value>
393 <value letter_id="P">138</value>
394 <value letter_id="Q">60</value>
395 <value letter_id="R">62</value>
396 <value letter_id="S">397</value>
397 <value letter_id="T">-235</value>
398 <value letter_id="V">220</value>
399 <value letter_id="W">-160</value>
400 <value letter_id="Y">-55</value>
401 </alphabet_array>
402 <alphabet_array>
403 <value letter_id="A">-596</value>
404 <value letter_id="C">-820</value>
405 <value letter_id="D">12</value>
406 <value letter_id="E">-21</value>
407 <value letter_id="F">-53</value>
408 <value letter_id="G">-267</value>
409 <value letter_id="H">-74</value>
410 <value letter_id="I">37</value>
411 <value letter_id="K">16</value>
412 <value letter_id="L">44</value>
413 <value letter_id="M">-37</value>
414 <value letter_id="N">98</value>
415 <value letter_id="P">31</value>
416 <value letter_id="Q">9</value>
417 <value letter_id="R">19</value>
418 <value letter_id="S">319</value>
419 <value letter_id="T">212</value>
420 <value letter_id="V">127</value>
421 <value letter_id="W">-193</value>
422 <value letter_id="Y">-95</value>
423 </alphabet_array>
424 <alphabet_array>
425 <value letter_id="A">165</value>
426 <value letter_id="C">-261</value>
427 <value letter_id="D">70</value>
428 <value letter_id="E">110</value>
429 <value letter_id="F">77</value>
430 <value letter_id="G">-521</value>
431 <value letter_id="H">-4</value>
432 <value letter_id="I">147</value>
433 <value letter_id="K">95</value>
434 <value letter_id="L">201</value>
435 <value letter_id="M">90</value>
436 <value letter_id="N">121</value>
437 <value letter_id="P">124</value>
438 <value letter_id="Q">91</value>
439 <value letter_id="R">107</value>
440 <value letter_id="S">425</value>
441 <value letter_id="T">-527</value>
442 <value letter_id="V">314</value>
443 <value letter_id="W">-95</value>
444 <value letter_id="Y">8</value>
445 </alphabet_array>
446 <alphabet_array>
447 <value letter_id="A">-838</value>
448 <value letter_id="C">-990</value>
449 <value letter_id="D">-89</value>
450 <value letter_id="E">-149</value>
451 <value letter_id="F">-151</value>
452 <value letter_id="G">-841</value>
453 <value letter_id="H">-161</value>
454 <value letter_id="I">-117</value>
455 <value letter_id="K">-113</value>
456 <value letter_id="L">-66</value>
457 <value letter_id="M">-209</value>
458 <value letter_id="N">-68</value>
459 <value letter_id="P">-69</value>
460 <value letter_id="Q">-129</value>
461 <value letter_id="R">-91</value>
462 <value letter_id="S">111</value>
463 <value letter_id="T">221</value>
464 <value letter_id="V">-55</value>
465 <value letter_id="W">-255</value>
466 <value letter_id="Y">-173</value>
467 </alphabet_array>
468 <alphabet_array>
469 <value letter_id="A">176</value>
470 <value letter_id="C">-858</value>
471 <value letter_id="D">-79</value>
472 <value letter_id="E">-103</value>
473 <value letter_id="F">-115</value>
474 <value letter_id="G">-717</value>
475 <value letter_id="H">-148</value>
476 <value letter_id="I">-95</value>
477 <value letter_id="K">-108</value>
478 <value letter_id="L">-17</value>
479 <value letter_id="M">-162</value>
480 <value letter_id="N">-61</value>
481 <value letter_id="P">-12</value>
482 <value letter_id="Q">-95</value>
483 <value letter_id="R">-69</value>
484 <value letter_id="S">193</value>
485 <value letter_id="T">-737</value>
486 <value letter_id="V">52</value>
487 <value letter_id="W">-240</value>
488 <value letter_id="Y">-153</value>
489 </alphabet_array>
490 <alphabet_array>
491 <value letter_id="A">134</value>
492 <value letter_id="C">-686</value>
493 <value letter_id="D">0</value>
494 <value letter_id="E">16</value>
495 <value letter_id="F">-12</value>
496 <value letter_id="G">-553</value>
497 <value letter_id="H">-68</value>
498 <value letter_id="I">44</value>
499 <value letter_id="K">-8</value>
500 <value letter_id="L">96</value>
501 <value letter_id="M">-9</value>
502 <value letter_id="N">88</value>
503 <value letter_id="P">124</value>
504 <value letter_id="Q">41</value>
505 <value letter_id="R">36</value>
506 <value letter_id="S">384</value>
507 <value letter_id="T">11</value>
508 <value letter_id="V">216</value>
509 <value letter_id="W">-177</value>
510 <value letter_id="Y">-71</value>
511 </alphabet_array>
512 <alphabet_array>
513 <value letter_id="A">165</value>
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521 <value letter_id="K">95</value>
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532 <value letter_id="Y">8</value>
533 </alphabet_array>
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543 <value letter_id="K">113</value>
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552 <value letter_id="V">332</value>
553 <value letter_id="W">-81</value>
554 <value letter_id="Y">22</value>
555 </alphabet_array>
556 </alphabet_matrix>
557 </scores>
558 <probabilities>
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603 </alphabet_array>
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625 </alphabet_array>
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647 </alphabet_array>
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801 </alphabet_array>
802 </alphabet_matrix>
803 </probabilities>
804 <regular_expression>
805 [GA][GA][GC][GA]TATA[AT]AA
806 </regular_expression>
807 <contributing_sites>
808 <contributing_site sequence_id="sequence_24" position="12" strand="none" pvalue="1.06e-06" >
809 <left_flank>AAGGCCAGGA</left_flank>
810 <site>
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812 <letter_ref letter_id="G"/>
813 <letter_ref letter_id="G"/>
814 <letter_ref letter_id="G"/>
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819 <letter_ref letter_id="A"/>
820 <letter_ref letter_id="A"/>
821 <letter_ref letter_id="A"/>
822 </site>
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824 </contributing_site>
825 <contributing_site sequence_id="sequence_25" position="36" strand="none" pvalue="3.41e-06" >
826 <left_flank>ACAGGCCCTG</left_flank>
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829 <letter_ref letter_id="G"/>
830 <letter_ref letter_id="C"/>
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836 <letter_ref letter_id="A"/>
837 <letter_ref letter_id="A"/>
838 <letter_ref letter_id="A"/>
839 </site>
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841 </contributing_site>
842 <contributing_site sequence_id="sequence_19" position="9" strand="none" pvalue="3.41e-06" >
843 <left_flank>CAGGCCCTG</left_flank>
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846 <letter_ref letter_id="G"/>
847 <letter_ref letter_id="C"/>
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853 <letter_ref letter_id="A"/>
854 <letter_ref letter_id="A"/>
855 <letter_ref letter_id="A"/>
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858 </contributing_site>
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860 <left_flank>GATTCACTGA</left_flank>
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863 <letter_ref letter_id="G"/>
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871 <letter_ref letter_id="A"/>
872 <letter_ref letter_id="A"/>
873 </site>
874 <right_flank>GGCCCTCTGC</right_flank>
875 </contributing_site>
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877 <left_flank>CCAAGGA</left_flank>
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882 <letter_ref letter_id="G"/>
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887 <letter_ref letter_id="A"/>
888 <letter_ref letter_id="A"/>
889 <letter_ref letter_id="A"/>
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892 </contributing_site>
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894 <left_flank>CCACCAGCTT</left_flank>
895 <site>
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897 <letter_ref letter_id="A"/>
898 <letter_ref letter_id="G"/>
899 <letter_ref letter_id="G"/>
900 <letter_ref letter_id="T"/>
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902 <letter_ref letter_id="T"/>
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904 <letter_ref letter_id="A"/>
905 <letter_ref letter_id="A"/>
906 <letter_ref letter_id="A"/>
907 </site>
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909 </contributing_site>
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915 <letter_ref letter_id="G"/>
916 <letter_ref letter_id="G"/>
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921 <letter_ref letter_id="A"/>
922 <letter_ref letter_id="A"/>
923 <letter_ref letter_id="A"/>
924 </site>
925 <right_flank>CCTCAGCAGC</right_flank>
926 </contributing_site>
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928 <left_flank>AATCACTGAG</left_flank>
929 <site>
930 <letter_ref letter_id="G"/>
931 <letter_ref letter_id="A"/>
932 <letter_ref letter_id="T"/>
933 <letter_ref letter_id="G"/>
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938 <letter_ref letter_id="A"/>
939 <letter_ref letter_id="A"/>
940 <letter_ref letter_id="A"/>
941 </site>
942 <right_flank>GTCCCAGGGA</right_flank>
943 </contributing_site>
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945 <left_flank>CACCAGAGCT</left_flank>
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948 <letter_ref letter_id="G"/>
949 <letter_ref letter_id="G"/>
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955 <letter_ref letter_id="T"/>
956 <letter_ref letter_id="A"/>
957 <letter_ref letter_id="A"/>
958 </site>
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960 </contributing_site>
961 <contributing_site sequence_id="sequence_11" position="16" strand="none" pvalue="8.67e-06" >
962 <left_flank>CACTATTGAA</left_flank>
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966 <letter_ref letter_id="T"/>
967 <letter_ref letter_id="G"/>
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972 <letter_ref letter_id="A"/>
973 <letter_ref letter_id="A"/>
974 <letter_ref letter_id="A"/>
975 </site>
976 <right_flank>TTTCATTTGC</right_flank>
977 </contributing_site>
978 <contributing_site sequence_id="sequence_22" position="2" strand="none" pvalue="1.21e-05" >
979 <left_flank>GA</left_flank>
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983 <letter_ref letter_id="C"/>
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989 <letter_ref letter_id="A"/>
990 <letter_ref letter_id="A"/>
991 <letter_ref letter_id="A"/>
992 </site>
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994 </contributing_site>
995 <contributing_site sequence_id="sequence_28" position="32" strand="none" pvalue="1.59e-05" >
996 <left_flank>CCGGCGGGGC</left_flank>
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999 <letter_ref letter_id="G"/>
1000 <letter_ref letter_id="G"/>
1001 <letter_ref letter_id="G"/>
1002 <letter_ref letter_id="T"/>
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1004 <letter_ref letter_id="T"/>
1005 <letter_ref letter_id="A"/>
1006 <letter_ref letter_id="A"/>
1007 <letter_ref letter_id="A"/>
1008 <letter_ref letter_id="G"/>
1009 </site>
1010 <right_flank>GGGGCGG</right_flank>
1011 </contributing_site>
1012 <contributing_site sequence_id="sequence_20" position="4" strand="none" pvalue="1.59e-05" >
1013 <left_flank>CAGA</left_flank>
1014 <site>
1015 <letter_ref letter_id="G"/>
1016 <letter_ref letter_id="G"/>
1017 <letter_ref letter_id="G"/>
1018 <letter_ref letter_id="G"/>
1019 <letter_ref letter_id="T"/>
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1021 <letter_ref letter_id="T"/>
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1023 <letter_ref letter_id="A"/>
1024 <letter_ref letter_id="A"/>
1025 <letter_ref letter_id="G"/>
1026 </site>
1027 <right_flank>GTTCCGACCA</right_flank>
1028 </contributing_site>
1029 <contributing_site sequence_id="sequence_6" position="15" strand="none" pvalue="1.68e-05" >
1030 <left_flank>CCCACTACTT</left_flank>
1031 <site>
1032 <letter_ref letter_id="A"/>
1033 <letter_ref letter_id="G"/>
1034 <letter_ref letter_id="A"/>
1035 <letter_ref letter_id="G"/>
1036 <letter_ref letter_id="T"/>
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1038 <letter_ref letter_id="T"/>
1039 <letter_ref letter_id="A"/>
1040 <letter_ref letter_id="A"/>
1041 <letter_ref letter_id="A"/>
1042 <letter_ref letter_id="A"/>
1043 </site>
1044 <right_flank>TCATTCTGAG</right_flank>
1045 </contributing_site>
1046 <contributing_site sequence_id="sequence_14" position="19" strand="none" pvalue="2.03e-05" >
1047 <left_flank>CACCAGCAAG</left_flank>
1048 <site>
1049 <letter_ref letter_id="G"/>
1050 <letter_ref letter_id="A"/>
1051 <letter_ref letter_id="T"/>
1052 <letter_ref letter_id="A"/>
1053 <letter_ref letter_id="T"/>
1054 <letter_ref letter_id="A"/>
1055 <letter_ref letter_id="T"/>
1056 <letter_ref letter_id="A"/>
1057 <letter_ref letter_id="A"/>
1058 <letter_ref letter_id="A"/>
1059 <letter_ref letter_id="A"/>
1060 </site>
1061 <right_flank>GCTCAGGAGT</right_flank>
1062 </contributing_site>
1063 <contributing_site sequence_id="sequence_4" position="12" strand="none" pvalue="3.06e-05" >
1064 <left_flank>CAGGTCTAAG</left_flank>
1065 <site>
1066 <letter_ref letter_id="A"/>
1067 <letter_ref letter_id="G"/>
1068 <letter_ref letter_id="C"/>
1069 <letter_ref letter_id="A"/>
1070 <letter_ref letter_id="T"/>
1071 <letter_ref letter_id="A"/>
1072 <letter_ref letter_id="T"/>
1073 <letter_ref letter_id="A"/>
1074 <letter_ref letter_id="T"/>
1075 <letter_ref letter_id="A"/>
1076 <letter_ref letter_id="A"/>
1077 </site>
1078 <right_flank>CTTGGAGTCC</right_flank>
1079 </contributing_site>
1080 <contributing_site sequence_id="sequence_0" position="39" strand="none" pvalue="3.06e-05" >
1081 <left_flank>CCTCGGGACG</left_flank>
1082 <site>
1083 <letter_ref letter_id="T"/>
1084 <letter_ref letter_id="G"/>
1085 <letter_ref letter_id="G"/>
1086 <letter_ref letter_id="G"/>
1087 <letter_ref letter_id="T"/>
1088 <letter_ref letter_id="A"/>
1089 <letter_ref letter_id="T"/>
1090 <letter_ref letter_id="A"/>
1091 <letter_ref letter_id="T"/>
1092 <letter_ref letter_id="A"/>
1093 <letter_ref letter_id="A"/>
1094 </site>
1095 <right_flank></right_flank>
1096 </contributing_site>
1097 <contributing_site sequence_id="sequence_18" position="37" strand="none" pvalue="3.82e-05" >
1098 <left_flank>CGTGGTCGCG</left_flank>
1099 <site>
1100 <letter_ref letter_id="G"/>
1101 <letter_ref letter_id="G"/>
1102 <letter_ref letter_id="G"/>
1103 <letter_ref letter_id="G"/>
1104 <letter_ref letter_id="T"/>
1105 <letter_ref letter_id="A"/>
1106 <letter_ref letter_id="T"/>
1107 <letter_ref letter_id="A"/>
1108 <letter_ref letter_id="A"/>
1109 <letter_ref letter_id="C"/>
1110 <letter_ref letter_id="A"/>
1111 </site>
1112 <right_flank>GC</right_flank>
1113 </contributing_site>
1114 <contributing_site sequence_id="sequence_5" position="0" strand="none" pvalue="3.82e-05" >
1115 <left_flank></left_flank>
1116 <site>
1117 <letter_ref letter_id="A"/>
1118 <letter_ref letter_id="A"/>
1119 <letter_ref letter_id="C"/>
1120 <letter_ref letter_id="G"/>
1121 <letter_ref letter_id="T"/>
1122 <letter_ref letter_id="A"/>
1123 <letter_ref letter_id="T"/>
1124 <letter_ref letter_id="A"/>
1125 <letter_ref letter_id="T"/>
1126 <letter_ref letter_id="A"/>
1127 <letter_ref letter_id="A"/>
1128 </site>
1129 <right_flank>ATGGTCCTGT</right_flank>
1130 </contributing_site>
1131 <contributing_site sequence_id="sequence_29" position="30" strand="none" pvalue="4.02e-05" >
1132 <left_flank>GCTGCCGGTG</left_flank>
1133 <site>
1134 <letter_ref letter_id="A"/>
1135 <letter_ref letter_id="G"/>
1136 <letter_ref letter_id="C"/>
1137 <letter_ref letter_id="G"/>
1138 <letter_ref letter_id="T"/>
1139 <letter_ref letter_id="A"/>
1140 <letter_ref letter_id="T"/>
1141 <letter_ref letter_id="A"/>
1142 <letter_ref letter_id="A"/>
1143 <letter_ref letter_id="A"/>
1144 <letter_ref letter_id="G"/>
1145 </site>
1146 <right_flank>GCCCTGGCG</right_flank>
1147 </contributing_site>
1148 <contributing_site sequence_id="sequence_1" position="27" strand="none" pvalue="5.52e-05" >
1149 <left_flank>AGTCACAAGT</left_flank>
1150 <site>
1151 <letter_ref letter_id="G"/>
1152 <letter_ref letter_id="A"/>
1153 <letter_ref letter_id="G"/>
1154 <letter_ref letter_id="T"/>
1155 <letter_ref letter_id="T"/>
1156 <letter_ref letter_id="A"/>
1157 <letter_ref letter_id="T"/>
1158 <letter_ref letter_id="A"/>
1159 <letter_ref letter_id="A"/>
1160 <letter_ref letter_id="A"/>
1161 <letter_ref letter_id="A"/>
1162 </site>
1163 <right_flank>GGGTCGCACG</right_flank>
1164 </contributing_site>
1165 <contributing_site sequence_id="sequence_3" position="14" strand="none" pvalue="5.94e-05" >
1166 <left_flank>CCCAGGTTTC</left_flank>
1167 <site>
1168 <letter_ref letter_id="T"/>
1169 <letter_ref letter_id="G"/>
1170 <letter_ref letter_id="A"/>
1171 <letter_ref letter_id="G"/>
1172 <letter_ref letter_id="T"/>
1173 <letter_ref letter_id="A"/>
1174 <letter_ref letter_id="T"/>
1175 <letter_ref letter_id="A"/>
1176 <letter_ref letter_id="T"/>
1177 <letter_ref letter_id="A"/>
1178 <letter_ref letter_id="A"/>
1179 </site>
1180 <right_flank>TCGCCGCACC</right_flank>
1181 </contributing_site>
1182 <contributing_site sequence_id="sequence_16" position="22" strand="none" pvalue="6.78e-05" >
1183 <left_flank>AGTTTCAGTT</left_flank>
1184 <site>
1185 <letter_ref letter_id="G"/>
1186 <letter_ref letter_id="G"/>
1187 <letter_ref letter_id="C"/>
1188 <letter_ref letter_id="A"/>
1189 <letter_ref letter_id="T"/>
1190 <letter_ref letter_id="C"/>
1191 <letter_ref letter_id="T"/>
1192 <letter_ref letter_id="A"/>
1193 <letter_ref letter_id="A"/>
1194 <letter_ref letter_id="A"/>
1195 <letter_ref letter_id="A"/>
1196 </site>
1197 <right_flank>attatataac</right_flank>
1198 </contributing_site>
1199 <contributing_site sequence_id="sequence_7" position="2" strand="none" pvalue="2.08e-04" >
1200 <left_flank>TC</left_flank>
1201 <site>
1202 <letter_ref letter_id="A"/>
1203 <letter_ref letter_id="G"/>
1204 <letter_ref letter_id="A"/>
1205 <letter_ref letter_id="G"/>
1206 <letter_ref letter_id="T"/>
1207 <letter_ref letter_id="A"/>
1208 <letter_ref letter_id="T"/>
1209 <letter_ref letter_id="A"/>
1210 <letter_ref letter_id="T"/>
1211 <letter_ref letter_id="A"/>
1212 <letter_ref letter_id="T"/>
1213 </site>
1214 <right_flank>AAATGTTCCT</right_flank>
1215 </contributing_site>
1216 <contributing_site sequence_id="sequence_8" position="13" strand="none" pvalue="4.05e-04" >
1217 <left_flank>TATAACTCAG</left_flank>
1218 <site>
1219 <letter_ref letter_id="G"/>
1220 <letter_ref letter_id="T"/>
1221 <letter_ref letter_id="T"/>
1222 <letter_ref letter_id="G"/>
1223 <letter_ref letter_id="G"/>
1224 <letter_ref letter_id="A"/>
1225 <letter_ref letter_id="T"/>
1226 <letter_ref letter_id="A"/>
1227 <letter_ref letter_id="A"/>
1228 <letter_ref letter_id="A"/>
1229 <letter_ref letter_id="A"/>
1230 </site>
1231 <right_flank>TAATTTGTAC</right_flank>
1232 </contributing_site>
1233 </contributing_sites>
1234 </motif>
1235 </motifs>
1236 <scanned_sites_summary p_thresh="0.0001">
1237 <scanned_sites sequence_id="sequence_0" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="39" pvalue="3.06e-05"/>
1238 </scanned_sites>
1239 <scanned_sites sequence_id="sequence_1" pvalue="2.21e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="27" pvalue="5.52e-05"/>
1240 </scanned_sites>
1241 <scanned_sites sequence_id="sequence_2" pvalue="7.29e-01" num_sites="0"></scanned_sites>
1242 <scanned_sites sequence_id="sequence_3" pvalue="2.37e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="14" pvalue="5.94e-05"/>
1243 </scanned_sites>
1244 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="3.06e-05"/>
1245 </scanned_sites>
1246 <scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>
1247 </scanned_sites>
1248 <scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>
1249 </scanned_sites>
1250 <scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>
1251 </scanned_sites>
1252 <scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>
1253 <scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>
1254 </scanned_sites>
1255 <scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>
1256 <scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>
1257 </scanned_sites>
1258 <scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>
1259 </scanned_sites>
1260 <scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>
1261 </scanned_sites>
1262 <scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>
1263 </scanned_sites>
1264 <scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>
1265 </scanned_sites>
1266 <scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>
1267 </scanned_sites>
1268 <scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>
1269 <scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>
1270 </scanned_sites>
1271 <scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>
1272 </scanned_sites>
1273 <scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>
1274 </scanned_sites>
1275 <scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>
1276 </scanned_sites>
1277 <scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>
1278 </scanned_sites>
1279 <scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>
1280 </scanned_sites>
1281 <scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>
1282 </scanned_sites>
1283 <scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>
1284 </scanned_sites>
1285 <scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>
1286 <scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>
1287 <scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>
1288 </scanned_sites>
1289 <scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>
1290 </scanned_sites>
1291 </scanned_sites_summary>
1292 </MEME>