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date Mon, 11 Jan 2016 13:33:25 -0500
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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 min_width,
45 max_width,
46 minic,
47 wg,
48 ws,
49 endgaps,
50 minsites,
51 maxsites,
52 wnsites,
53 prob,
54 spmap,
55 spfuzz,
56 prior,
57 beta,
58 maxiter,
59 distance,
60 num_sequences,
61 num_positions,
62 seed,
63 seqfrac,
64 strands,
65 priors_file,
66 reason_for_stopping,
67 background_frequencies
68 )>
69 <!ELEMENT command_line (#PCDATA)*>
70 <!ELEMENT host (#PCDATA)*>
71 <!ELEMENT type (#PCDATA)*>
72 <!ELEMENT nmotifs (#PCDATA)*>
73 <!ELEMENT evalue_threshold (#PCDATA)*>
74 <!ELEMENT object_function (#PCDATA)*>
75 <!ELEMENT min_width (#PCDATA)*>
76 <!ELEMENT max_width (#PCDATA)*>
77 <!ELEMENT minic (#PCDATA)*>
78 <!ELEMENT wg (#PCDATA)*>
79 <!ELEMENT ws (#PCDATA)*>
80 <!ELEMENT endgaps (#PCDATA)*>
81 <!ELEMENT minsites (#PCDATA)*>
82 <!ELEMENT maxsites (#PCDATA)*>
83 <!ELEMENT wnsites (#PCDATA)*>
84 <!ELEMENT prob (#PCDATA)*>
85 <!ELEMENT spmap (#PCDATA)*>
86 <!ELEMENT spfuzz (#PCDATA)*>
87 <!ELEMENT prior (#PCDATA)*>
88 <!ELEMENT beta (#PCDATA)*>
89 <!ELEMENT maxiter (#PCDATA)*>
90 <!ELEMENT distance (#PCDATA)*>
91 <!ELEMENT num_sequences (#PCDATA)*>
92 <!ELEMENT num_positions (#PCDATA)*>
93 <!ELEMENT seed (#PCDATA)*>
94 <!ELEMENT seqfrac (#PCDATA)*>
95 <!ELEMENT strands (#PCDATA)*>
96 <!ELEMENT priors_file (#PCDATA)*>
97 <!ELEMENT reason_for_stopping (#PCDATA)*>
98 <!ELEMENT background_frequencies (alphabet_array)>
99 <!ATTLIST background_frequencies source CDATA #REQUIRED>
100
101 <!-- Motif elements -->
102 <!ELEMENT motifs (motif*)>
103 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
104 <!ATTLIST motif id ID #REQUIRED
105 name CDATA #REQUIRED
106 width CDATA #REQUIRED
107 sites CDATA #REQUIRED
108 llr CDATA #REQUIRED
109 ic CDATA #REQUIRED
110 re CDATA #REQUIRED
111 bayes_threshold CDATA #REQUIRED
112 e_value CDATA #REQUIRED
113 elapsed_time CDATA #REQUIRED
114 url CDATA ""
115 >
116 <!ELEMENT scores (alphabet_matrix)>
117 <!ELEMENT probabilities (alphabet_matrix)>
118 <!ELEMENT regular_expression (#PCDATA)*>
119
120 <!-- Contributing site elements -->
121 <!-- Contributing sites are motif occurences found during the motif discovery phase -->
122 <!ELEMENT contributing_sites (contributing_site*)>
123 <!ELEMENT contributing_site (left_flank, site, right_flank)>
124 <!ATTLIST contributing_site sequence_id IDREF #REQUIRED
125 position CDATA #REQUIRED
126 strand (plus|minus|none) 'none'
127 pvalue CDATA #REQUIRED
128 >
129 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
130 <!ELEMENT left_flank (#PCDATA)>
131 <!-- The site contains the sequence for the motif instance -->
132 <!ELEMENT site (letter_ref*)>
133 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
134 <!ELEMENT right_flank (#PCDATA)>
135
136 <!-- Scanned site elements -->
137 <!-- Scanned sites are motif occurences found during the sequence scan phase -->
138 <!ELEMENT scanned_sites_summary (scanned_sites*)>
139 <!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
140 <!ELEMENT scanned_sites (scanned_site*)>
141 <!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
142 pvalue CDATA #REQUIRED
143 num_sites CDATA #REQUIRED>
144 <!ELEMENT scanned_site EMPTY>
145 <!ATTLIST scanned_site motif_id IDREF #REQUIRED
146 strand (plus|minus|none) 'none'
147 position CDATA #REQUIRED
148 pvalue CDATA #REQUIRED>
149
150 <!-- Utility elements -->
151 <!-- A reference to a letter in the alphabet -->
152 <!ELEMENT letter_ref EMPTY>
153 <!ATTLIST letter_ref letter_id IDREF #REQUIRED>
154 <!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
155 <!ELEMENT alphabet_array (value*)>
156 <!ELEMENT value (#PCDATA)>
157 <!ATTLIST value letter_id IDREF #REQUIRED>
158
159 <!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
160 <!ELEMENT alphabet_matrix (alphabet_array*)>
161
162 ]>
163 <!-- Begin document body -->
164 <MEME version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
165 <training_set datafile="Galaxy_FASTA_Input" length="30">
166 <alphabet name="DNA" like="dna">
167 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
168 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
169 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
170 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
171 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
172 <letter id="V" symbol="V" equals="ACG" name="Not T"/>
173 <letter id="H" symbol="H" equals="ACT" name="Not G"/>
174 <letter id="D" symbol="D" equals="AGT" name="Not C"/>
175 <letter id="B" symbol="B" equals="CGT" name="Not A"/>
176 <letter id="M" symbol="M" equals="AC" name="Amino"/>
177 <letter id="R" symbol="R" equals="AG" name="Purine"/>
178 <letter id="W" symbol="W" equals="AT" name="Weak"/>
179 <letter id="S" symbol="S" equals="CG" name="Strong"/>
180 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
181 <letter id="K" symbol="K" equals="GT" name="Keto"/>
182 </alphabet>
183 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
184 <sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" />
185 <sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" />
186 <sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" />
187 <sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" />
188 <sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" />
189 <sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" />
190 <sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" />
191 <sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" />
192 <sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" />
193 <sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" />
194 <sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" />
195 <sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" />
196 <sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" />
197 <sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" />
198 <sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" />
199 <sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" />
200 <sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" />
201 <sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" />
202 <sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" />
203 <sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" />
204 <sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" />
205 <sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" />
206 <sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" />
207 <sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" />
208 <sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" />
209 <sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" />
210 <sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" />
211 <sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" />
212 <sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" />
213 <letter_frequencies>
214 <alphabet_array>
215 <value letter_id="A">0.294</value>
216 <value letter_id="C">0.231</value>
217 <value letter_id="G">0.257</value>
218 <value letter_id="T">0.217</value>
219 </alphabet_array>
220 </letter_frequencies>
221 </training_set>
222 <model>
223 <command_line>meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files -nostatus -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat -spmap uni -spfuzz 0.5 </command_line>
224 <host>MacBook-Pro-2.local</host>
225 <type>zoops</type>
226 <nmotifs>1</nmotifs>
227 <evalue_threshold>inf</evalue_threshold>
228 <object_function>E-value of product of p-values</object_function>
229 <use_llr>0</use_llr>
230 <min_width>8</min_width>
231 <max_width>50</max_width>
232 <wg>11</wg>
233 <ws>1</ws>
234 <endgaps>yes</endgaps>
235 <substring>yes</substring>
236 <minsites>2</minsites>
237 <maxsites>30</maxsites>
238 <wnsites>0.8</wnsites>
239 <spmap>uni</spmap>
240 <spfuzz>0.5</spfuzz>
241 <prior>dirichlet</prior>
242 <beta>0.01</beta>
243 <maxiter>50</maxiter>
244 <distance>0.001</distance>
245 <num_sequences>30</num_sequences>
246 <num_positions>1500</num_positions>
247 <seed>0</seed>
248 <ctfrac>-1</ctfrac>
249 <maxwords>-1</maxwords>
250 <strands>forward</strands>
251 <priors_file>dataset_2577.dat</priors_file>
252 <reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
253 <background_frequencies source="dataset with add-one prior applied">
254 <alphabet_array>
255 <value letter_id="A">0.294</value>
256 <value letter_id="C">0.231</value>
257 <value letter_id="G">0.257</value>
258 <value letter_id="T">0.217</value>
259 </alphabet_array>
260 </background_frequencies>
261 </model>
262 <motifs>
263 <motif id="motif_1" name="1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.168106">
264 <scores>
265 <alphabet_matrix>
266 <alphabet_array>
267 <value letter_id="A">-14</value>
268 <value letter_id="C">-179</value>
269 <value letter_id="G">114</value>
270 <value letter_id="T">-112</value>
271 </alphabet_array>
272 <alphabet_array>
273 <value letter_id="A">3</value>
274 <value letter_id="C">-1155</value>
275 <value letter_id="G">137</value>
276 <value letter_id="T">-270</value>
277 </alphabet_array>
278 <alphabet_array>
279 <value letter_id="A">-114</value>
280 <value letter_id="C">20</value>
281 <value letter_id="G">86</value>
282 <value letter_id="T">-71</value>
283 </alphabet_array>
284 <alphabet_array>
285 <value letter_id="A">3</value>
286 <value letter_id="C">-279</value>
287 <value letter_id="G">122</value>
288 <value letter_id="T">-170</value>
289 </alphabet_array>
290 <alphabet_array>
291 <value letter_id="A">-1155</value>
292 <value letter_id="C">-1155</value>
293 <value letter_id="G">-295</value>
294 <value letter_id="T">215</value>
295 </alphabet_array>
296 <alphabet_array>
297 <value letter_id="A">156</value>
298 <value letter_id="C">-179</value>
299 <value letter_id="G">-1155</value>
300 <value letter_id="T">-170</value>
301 </alphabet_array>
302 <alphabet_array>
303 <value letter_id="A">-1155</value>
304 <value letter_id="C">-1155</value>
305 <value letter_id="G">-1155</value>
306 <value letter_id="T">220</value>
307 </alphabet_array>
308 <alphabet_array>
309 <value letter_id="A">172</value>
310 <value letter_id="C">-279</value>
311 <value letter_id="G">-1155</value>
312 <value letter_id="T">-1155</value>
313 </alphabet_array>
314 <alphabet_array>
315 <value letter_id="A">125</value>
316 <value letter_id="C">-1155</value>
317 <value letter_id="G">-1155</value>
318 <value letter_id="T">46</value>
319 </alphabet_array>
320 <alphabet_array>
321 <value letter_id="A">167</value>
322 <value letter_id="C">-179</value>
323 <value letter_id="G">-1155</value>
324 <value letter_id="T">-1155</value>
325 </alphabet_array>
326 <alphabet_array>
327 <value letter_id="A">144</value>
328 <value letter_id="C">-1155</value>
329 <value letter_id="G">-63</value>
330 <value letter_id="T">-270</value>
331 </alphabet_array>
332 </alphabet_matrix>
333 </scores>
334 <probabilities>
335 <alphabet_matrix>
336 <alphabet_array>
337 <value letter_id="A">0.266667</value>
338 <value letter_id="C">0.066667</value>
339 <value letter_id="G">0.566667</value>
340 <value letter_id="T">0.100000</value>
341 </alphabet_array>
342 <alphabet_array>
343 <value letter_id="A">0.300000</value>
344 <value letter_id="C">0.000000</value>
345 <value letter_id="G">0.666667</value>
346 <value letter_id="T">0.033333</value>
347 </alphabet_array>
348 <alphabet_array>
349 <value letter_id="A">0.133333</value>
350 <value letter_id="C">0.266667</value>
351 <value letter_id="G">0.466667</value>
352 <value letter_id="T">0.133333</value>
353 </alphabet_array>
354 <alphabet_array>
355 <value letter_id="A">0.300000</value>
356 <value letter_id="C">0.033333</value>
357 <value letter_id="G">0.600000</value>
358 <value letter_id="T">0.066667</value>
359 </alphabet_array>
360 <alphabet_array>
361 <value letter_id="A">0.000000</value>
362 <value letter_id="C">0.000000</value>
363 <value letter_id="G">0.033333</value>
364 <value letter_id="T">0.966667</value>
365 </alphabet_array>
366 <alphabet_array>
367 <value letter_id="A">0.866667</value>
368 <value letter_id="C">0.066667</value>
369 <value letter_id="G">0.000000</value>
370 <value letter_id="T">0.066667</value>
371 </alphabet_array>
372 <alphabet_array>
373 <value letter_id="A">0.000000</value>
374 <value letter_id="C">0.000000</value>
375 <value letter_id="G">0.000000</value>
376 <value letter_id="T">1.000000</value>
377 </alphabet_array>
378 <alphabet_array>
379 <value letter_id="A">0.966667</value>
380 <value letter_id="C">0.033333</value>
381 <value letter_id="G">0.000000</value>
382 <value letter_id="T">0.000000</value>
383 </alphabet_array>
384 <alphabet_array>
385 <value letter_id="A">0.700000</value>
386 <value letter_id="C">0.000000</value>
387 <value letter_id="G">0.000000</value>
388 <value letter_id="T">0.300000</value>
389 </alphabet_array>
390 <alphabet_array>
391 <value letter_id="A">0.933333</value>
392 <value letter_id="C">0.066667</value>
393 <value letter_id="G">0.000000</value>
394 <value letter_id="T">0.000000</value>
395 </alphabet_array>
396 <alphabet_array>
397 <value letter_id="A">0.800000</value>
398 <value letter_id="C">0.000000</value>
399 <value letter_id="G">0.166667</value>
400 <value letter_id="T">0.033333</value>
401 </alphabet_array>
402 </alphabet_matrix>
403 </probabilities>
404 <regular_expression>
405 [GA][GA][GC][GA]TATA[AT]AA
406 </regular_expression>
407 <contributing_sites>
408 <contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
409 <left_flank>AAGGCCAGGA</left_flank>
410 <site>
411 <letter_ref letter_id="G"/>
412 <letter_ref letter_id="G"/>
413 <letter_ref letter_id="G"/>
414 <letter_ref letter_id="G"/>
415 <letter_ref letter_id="T"/>
416 <letter_ref letter_id="A"/>
417 <letter_ref letter_id="T"/>
418 <letter_ref letter_id="A"/>
419 <letter_ref letter_id="A"/>
420 <letter_ref letter_id="A"/>
421 <letter_ref letter_id="A"/>
422 </site>
423 <right_flank>GCCTGAGAGC</right_flank>
424 </contributing_site>
425 <contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
426 <left_flank>ATACCCAGGG</left_flank>
427 <site>
428 <letter_ref letter_id="A"/>
429 <letter_ref letter_id="G"/>
430 <letter_ref letter_id="G"/>
431 <letter_ref letter_id="G"/>
432 <letter_ref letter_id="T"/>
433 <letter_ref letter_id="A"/>
434 <letter_ref letter_id="T"/>
435 <letter_ref letter_id="A"/>
436 <letter_ref letter_id="A"/>
437 <letter_ref letter_id="A"/>
438 <letter_ref letter_id="A"/>
439 </site>
440 <right_flank>CCTCAGCAGC</right_flank>
441 </contributing_site>
442 <contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
443 <left_flank>CCACCAGCTT</left_flank>
444 <site>
445 <letter_ref letter_id="G"/>
446 <letter_ref letter_id="A"/>
447 <letter_ref letter_id="G"/>
448 <letter_ref letter_id="G"/>
449 <letter_ref letter_id="T"/>
450 <letter_ref letter_id="A"/>
451 <letter_ref letter_id="T"/>
452 <letter_ref letter_id="A"/>
453 <letter_ref letter_id="A"/>
454 <letter_ref letter_id="A"/>
455 <letter_ref letter_id="A"/>
456 </site>
457 <right_flank>AGCCCTGTAC</right_flank>
458 </contributing_site>
459 <contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
460 <left_flank>ACAGGCCCTG</left_flank>
461 <site>
462 <letter_ref letter_id="G"/>
463 <letter_ref letter_id="G"/>
464 <letter_ref letter_id="C"/>
465 <letter_ref letter_id="A"/>
466 <letter_ref letter_id="T"/>
467 <letter_ref letter_id="A"/>
468 <letter_ref letter_id="T"/>
469 <letter_ref letter_id="A"/>
470 <letter_ref letter_id="A"/>
471 <letter_ref letter_id="A"/>
472 <letter_ref letter_id="A"/>
473 </site>
474 <right_flank>GCC</right_flank>
475 </contributing_site>
476 <contributing_site sequence_id="sequence_21" position="7" strand="plus" pvalue="4.86e-06" >
477 <left_flank>CCAAGGA</left_flank>
478 <site>
479 <letter_ref letter_id="G"/>
480 <letter_ref letter_id="G"/>
481 <letter_ref letter_id="A"/>
482 <letter_ref letter_id="G"/>
483 <letter_ref letter_id="T"/>
484 <letter_ref letter_id="A"/>
485 <letter_ref letter_id="T"/>
486 <letter_ref letter_id="A"/>
487 <letter_ref letter_id="A"/>
488 <letter_ref letter_id="A"/>
489 <letter_ref letter_id="A"/>
490 </site>
491 <right_flank>GCCCCACAAA</right_flank>
492 </contributing_site>
493 <contributing_site sequence_id="sequence_19" position="9" strand="plus" pvalue="4.86e-06" >
494 <left_flank>CAGGCCCTG</left_flank>
495 <site>
496 <letter_ref letter_id="G"/>
497 <letter_ref letter_id="G"/>
498 <letter_ref letter_id="C"/>
499 <letter_ref letter_id="A"/>
500 <letter_ref letter_id="T"/>
501 <letter_ref letter_id="A"/>
502 <letter_ref letter_id="T"/>
503 <letter_ref letter_id="A"/>
504 <letter_ref letter_id="A"/>
505 <letter_ref letter_id="A"/>
506 <letter_ref letter_id="A"/>
507 </site>
508 <right_flank>GCCCCAGCAG</right_flank>
509 </contributing_site>
510 <contributing_site sequence_id="sequence_9" position="13" strand="plus" pvalue="4.86e-06" >
511 <left_flank>GATTCACTGA</left_flank>
512 <site>
513 <letter_ref letter_id="G"/>
514 <letter_ref letter_id="G"/>
515 <letter_ref letter_id="C"/>
516 <letter_ref letter_id="A"/>
517 <letter_ref letter_id="T"/>
518 <letter_ref letter_id="A"/>
519 <letter_ref letter_id="T"/>
520 <letter_ref letter_id="A"/>
521 <letter_ref letter_id="A"/>
522 <letter_ref letter_id="A"/>
523 <letter_ref letter_id="A"/>
524 </site>
525 <right_flank>GGCCCTCTGC</right_flank>
526 </contributing_site>
527 <contributing_site sequence_id="sequence_28" position="32" strand="plus" pvalue="6.48e-06" >
528 <left_flank>CCGGCGGGGC</left_flank>
529 <site>
530 <letter_ref letter_id="G"/>
531 <letter_ref letter_id="G"/>
532 <letter_ref letter_id="G"/>
533 <letter_ref letter_id="G"/>
534 <letter_ref letter_id="T"/>
535 <letter_ref letter_id="A"/>
536 <letter_ref letter_id="T"/>
537 <letter_ref letter_id="A"/>
538 <letter_ref letter_id="A"/>
539 <letter_ref letter_id="A"/>
540 <letter_ref letter_id="G"/>
541 </site>
542 <right_flank>GGGGCGG</right_flank>
543 </contributing_site>
544 <contributing_site sequence_id="sequence_20" position="4" strand="plus" pvalue="6.48e-06" >
545 <left_flank>CAGA</left_flank>
546 <site>
547 <letter_ref letter_id="G"/>
548 <letter_ref letter_id="G"/>
549 <letter_ref letter_id="G"/>
550 <letter_ref letter_id="G"/>
551 <letter_ref letter_id="T"/>
552 <letter_ref letter_id="A"/>
553 <letter_ref letter_id="T"/>
554 <letter_ref letter_id="A"/>
555 <letter_ref letter_id="A"/>
556 <letter_ref letter_id="A"/>
557 <letter_ref letter_id="G"/>
558 </site>
559 <right_flank>GTTCCGACCA</right_flank>
560 </contributing_site>
561 <contributing_site sequence_id="sequence_12" position="18" strand="plus" pvalue="6.48e-06" >
562 <left_flank>CACCAGAGCT</left_flank>
563 <site>
564 <letter_ref letter_id="G"/>
565 <letter_ref letter_id="G"/>
566 <letter_ref letter_id="G"/>
567 <letter_ref letter_id="A"/>
568 <letter_ref letter_id="T"/>
569 <letter_ref letter_id="A"/>
570 <letter_ref letter_id="T"/>
571 <letter_ref letter_id="A"/>
572 <letter_ref letter_id="T"/>
573 <letter_ref letter_id="A"/>
574 <letter_ref letter_id="A"/>
575 </site>
576 <right_flank>AGAAGGTTCT</right_flank>
577 </contributing_site>
578 <contributing_site sequence_id="sequence_15" position="21" strand="plus" pvalue="1.38e-05" >
579 <left_flank>AATCACTGAG</left_flank>
580 <site>
581 <letter_ref letter_id="G"/>
582 <letter_ref letter_id="A"/>
583 <letter_ref letter_id="T"/>
584 <letter_ref letter_id="G"/>
585 <letter_ref letter_id="T"/>
586 <letter_ref letter_id="A"/>
587 <letter_ref letter_id="T"/>
588 <letter_ref letter_id="A"/>
589 <letter_ref letter_id="A"/>
590 <letter_ref letter_id="A"/>
591 <letter_ref letter_id="A"/>
592 </site>
593 <right_flank>GTCCCAGGGA</right_flank>
594 </contributing_site>
595 <contributing_site sequence_id="sequence_11" position="16" strand="plus" pvalue="1.38e-05" >
596 <left_flank>CACTATTGAA</left_flank>
597 <site>
598 <letter_ref letter_id="G"/>
599 <letter_ref letter_id="A"/>
600 <letter_ref letter_id="T"/>
601 <letter_ref letter_id="G"/>
602 <letter_ref letter_id="T"/>
603 <letter_ref letter_id="A"/>
604 <letter_ref letter_id="T"/>
605 <letter_ref letter_id="A"/>
606 <letter_ref letter_id="A"/>
607 <letter_ref letter_id="A"/>
608 <letter_ref letter_id="A"/>
609 </site>
610 <right_flank>TTTCATTTGC</right_flank>
611 </contributing_site>
612 <contributing_site sequence_id="sequence_0" position="39" strand="plus" pvalue="1.41e-05" >
613 <left_flank>CCTCGGGACG</left_flank>
614 <site>
615 <letter_ref letter_id="T"/>
616 <letter_ref letter_id="G"/>
617 <letter_ref letter_id="G"/>
618 <letter_ref letter_id="G"/>
619 <letter_ref letter_id="T"/>
620 <letter_ref letter_id="A"/>
621 <letter_ref letter_id="T"/>
622 <letter_ref letter_id="A"/>
623 <letter_ref letter_id="T"/>
624 <letter_ref letter_id="A"/>
625 <letter_ref letter_id="A"/>
626 </site>
627 <right_flank></right_flank>
628 </contributing_site>
629 <contributing_site sequence_id="sequence_6" position="15" strand="plus" pvalue="1.61e-05" >
630 <left_flank>CCCACTACTT</left_flank>
631 <site>
632 <letter_ref letter_id="A"/>
633 <letter_ref letter_id="G"/>
634 <letter_ref letter_id="A"/>
635 <letter_ref letter_id="G"/>
636 <letter_ref letter_id="T"/>
637 <letter_ref letter_id="A"/>
638 <letter_ref letter_id="T"/>
639 <letter_ref letter_id="A"/>
640 <letter_ref letter_id="A"/>
641 <letter_ref letter_id="A"/>
642 <letter_ref letter_id="A"/>
643 </site>
644 <right_flank>TCATTCTGAG</right_flank>
645 </contributing_site>
646 <contributing_site sequence_id="sequence_22" position="2" strand="plus" pvalue="1.95e-05" >
647 <left_flank>GA</left_flank>
648 <site>
649 <letter_ref letter_id="G"/>
650 <letter_ref letter_id="A"/>
651 <letter_ref letter_id="C"/>
652 <letter_ref letter_id="A"/>
653 <letter_ref letter_id="T"/>
654 <letter_ref letter_id="A"/>
655 <letter_ref letter_id="T"/>
656 <letter_ref letter_id="A"/>
657 <letter_ref letter_id="A"/>
658 <letter_ref letter_id="A"/>
659 <letter_ref letter_id="A"/>
660 </site>
661 <right_flank>GCCAACATCC</right_flank>
662 </contributing_site>
663 <contributing_site sequence_id="sequence_14" position="17" strand="plus" pvalue="1.95e-05" >
664 <left_flank>CCCACCAGCA</left_flank>
665 <site>
666 <letter_ref letter_id="A"/>
667 <letter_ref letter_id="G"/>
668 <letter_ref letter_id="G"/>
669 <letter_ref letter_id="A"/>
670 <letter_ref letter_id="T"/>
671 <letter_ref letter_id="A"/>
672 <letter_ref letter_id="T"/>
673 <letter_ref letter_id="A"/>
674 <letter_ref letter_id="T"/>
675 <letter_ref letter_id="A"/>
676 <letter_ref letter_id="A"/>
677 </site>
678 <right_flank>AAGCTCAGGA</right_flank>
679 </contributing_site>
680 <contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-05" >
681 <left_flank>CGTGGTCGCG</left_flank>
682 <site>
683 <letter_ref letter_id="G"/>
684 <letter_ref letter_id="G"/>
685 <letter_ref letter_id="G"/>
686 <letter_ref letter_id="G"/>
687 <letter_ref letter_id="T"/>
688 <letter_ref letter_id="A"/>
689 <letter_ref letter_id="T"/>
690 <letter_ref letter_id="A"/>
691 <letter_ref letter_id="A"/>
692 <letter_ref letter_id="C"/>
693 <letter_ref letter_id="A"/>
694 </site>
695 <right_flank>GC</right_flank>
696 </contributing_site>
697 <contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
698 <left_flank>GCTGCCGGTG</left_flank>
699 <site>
700 <letter_ref letter_id="A"/>
701 <letter_ref letter_id="G"/>
702 <letter_ref letter_id="C"/>
703 <letter_ref letter_id="G"/>
704 <letter_ref letter_id="T"/>
705 <letter_ref letter_id="A"/>
706 <letter_ref letter_id="T"/>
707 <letter_ref letter_id="A"/>
708 <letter_ref letter_id="A"/>
709 <letter_ref letter_id="A"/>
710 <letter_ref letter_id="G"/>
711 </site>
712 <right_flank>GCCCTGGCG</right_flank>
713 </contributing_site>
714 <contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
715 <left_flank>CAGGTCTAAG</left_flank>
716 <site>
717 <letter_ref letter_id="A"/>
718 <letter_ref letter_id="G"/>
719 <letter_ref letter_id="C"/>
720 <letter_ref letter_id="A"/>
721 <letter_ref letter_id="T"/>
722 <letter_ref letter_id="A"/>
723 <letter_ref letter_id="T"/>
724 <letter_ref letter_id="A"/>
725 <letter_ref letter_id="T"/>
726 <letter_ref letter_id="A"/>
727 <letter_ref letter_id="A"/>
728 </site>
729 <right_flank>CTTGGAGTCC</right_flank>
730 </contributing_site>
731 <contributing_site sequence_id="sequence_5" position="0" strand="plus" pvalue="3.67e-05" >
732 <left_flank></left_flank>
733 <site>
734 <letter_ref letter_id="A"/>
735 <letter_ref letter_id="A"/>
736 <letter_ref letter_id="C"/>
737 <letter_ref letter_id="G"/>
738 <letter_ref letter_id="T"/>
739 <letter_ref letter_id="A"/>
740 <letter_ref letter_id="T"/>
741 <letter_ref letter_id="A"/>
742 <letter_ref letter_id="T"/>
743 <letter_ref letter_id="A"/>
744 <letter_ref letter_id="A"/>
745 </site>
746 <right_flank>ATGGTCCTGT</right_flank>
747 </contributing_site>
748 <contributing_site sequence_id="sequence_1" position="27" strand="plus" pvalue="3.93e-05" >
749 <left_flank>AGTCACAAGT</left_flank>
750 <site>
751 <letter_ref letter_id="G"/>
752 <letter_ref letter_id="A"/>
753 <letter_ref letter_id="G"/>
754 <letter_ref letter_id="T"/>
755 <letter_ref letter_id="T"/>
756 <letter_ref letter_id="A"/>
757 <letter_ref letter_id="T"/>
758 <letter_ref letter_id="A"/>
759 <letter_ref letter_id="A"/>
760 <letter_ref letter_id="A"/>
761 <letter_ref letter_id="A"/>
762 </site>
763 <right_flank>GGGTCGCACG</right_flank>
764 </contributing_site>
765 <contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="5.65e-05" >
766 <left_flank>TCAG</left_flank>
767 <site>
768 <letter_ref letter_id="A"/>
769 <letter_ref letter_id="G"/>
770 <letter_ref letter_id="T"/>
771 <letter_ref letter_id="A"/>
772 <letter_ref letter_id="T"/>
773 <letter_ref letter_id="A"/>
774 <letter_ref letter_id="T"/>
775 <letter_ref letter_id="A"/>
776 <letter_ref letter_id="T"/>
777 <letter_ref letter_id="A"/>
778 <letter_ref letter_id="A"/>
779 </site>
780 <right_flank>ATGTTCCTGT</right_flank>
781 </contributing_site>
782 <contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-05" >
783 <left_flank>CCCAGGTTTC</left_flank>
784 <site>
785 <letter_ref letter_id="T"/>
786 <letter_ref letter_id="G"/>
787 <letter_ref letter_id="A"/>
788 <letter_ref letter_id="G"/>
789 <letter_ref letter_id="T"/>
790 <letter_ref letter_id="A"/>
791 <letter_ref letter_id="T"/>
792 <letter_ref letter_id="A"/>
793 <letter_ref letter_id="T"/>
794 <letter_ref letter_id="A"/>
795 <letter_ref letter_id="A"/>
796 </site>
797 <right_flank>TCGCCGCACC</right_flank>
798 </contributing_site>
799 <contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" >
800 <left_flank>AGTTTCAGTT</left_flank>
801 <site>
802 <letter_ref letter_id="G"/>
803 <letter_ref letter_id="G"/>
804 <letter_ref letter_id="C"/>
805 <letter_ref letter_id="A"/>
806 <letter_ref letter_id="T"/>
807 <letter_ref letter_id="C"/>
808 <letter_ref letter_id="T"/>
809 <letter_ref letter_id="A"/>
810 <letter_ref letter_id="A"/>
811 <letter_ref letter_id="A"/>
812 <letter_ref letter_id="A"/>
813 </site>
814 <right_flank>attatataac</right_flank>
815 </contributing_site>
816 <contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" >
817 <left_flank>TGCCTGGGTC</left_flank>
818 <site>
819 <letter_ref letter_id="C"/>
820 <letter_ref letter_id="A"/>
821 <letter_ref letter_id="G"/>
822 <letter_ref letter_id="G"/>
823 <letter_ref letter_id="T"/>
824 <letter_ref letter_id="A"/>
825 <letter_ref letter_id="T"/>
826 <letter_ref letter_id="A"/>
827 <letter_ref letter_id="A"/>
828 <letter_ref letter_id="A"/>
829 <letter_ref letter_id="G"/>
830 </site>
831 <right_flank>GCT</right_flank>
832 </contributing_site>
833 <contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" >
834 <left_flank>TGCCTGGGCC</left_flank>
835 <site>
836 <letter_ref letter_id="C"/>
837 <letter_ref letter_id="A"/>
838 <letter_ref letter_id="G"/>
839 <letter_ref letter_id="G"/>
840 <letter_ref letter_id="T"/>
841 <letter_ref letter_id="A"/>
842 <letter_ref letter_id="T"/>
843 <letter_ref letter_id="A"/>
844 <letter_ref letter_id="A"/>
845 <letter_ref letter_id="A"/>
846 <letter_ref letter_id="G"/>
847 </site>
848 <right_flank>GC</right_flank>
849 </contributing_site>
850 <contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" >
851 <left_flank>ga</left_flank>
852 <site>
853 <letter_ref letter_id="T"/>
854 <letter_ref letter_id="G"/>
855 <letter_ref letter_id="G"/>
856 <letter_ref letter_id="T"/>
857 <letter_ref letter_id="T"/>
858 <letter_ref letter_id="T"/>
859 <letter_ref letter_id="T"/>
860 <letter_ref letter_id="A"/>
861 <letter_ref letter_id="T"/>
862 <letter_ref letter_id="A"/>
863 <letter_ref letter_id="A"/>
864 </site>
865 <right_flank>ggggcctcac</right_flank>
866 </contributing_site>
867 <contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" >
868 <left_flank>TATAACTCAG</left_flank>
869 <site>
870 <letter_ref letter_id="G"/>
871 <letter_ref letter_id="T"/>
872 <letter_ref letter_id="T"/>
873 <letter_ref letter_id="G"/>
874 <letter_ref letter_id="G"/>
875 <letter_ref letter_id="A"/>
876 <letter_ref letter_id="T"/>
877 <letter_ref letter_id="A"/>
878 <letter_ref letter_id="A"/>
879 <letter_ref letter_id="A"/>
880 <letter_ref letter_id="A"/>
881 </site>
882 <right_flank>TAATTTGTAC</right_flank>
883 </contributing_site>
884 <contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" >
885 <left_flank>aaactta</left_flank>
886 <site>
887 <letter_ref letter_id="A"/>
888 <letter_ref letter_id="A"/>
889 <letter_ref letter_id="A"/>
890 <letter_ref letter_id="C"/>
891 <letter_ref letter_id="T"/>
892 <letter_ref letter_id="C"/>
893 <letter_ref letter_id="T"/>
894 <letter_ref letter_id="A"/>
895 <letter_ref letter_id="T"/>
896 <letter_ref letter_id="A"/>
897 <letter_ref letter_id="A"/>
898 </site>
899 <right_flank>acttaaaact</right_flank>
900 </contributing_site>
901 <contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" >
902 <left_flank>GGTGGGGGTG</left_flank>
903 <site>
904 <letter_ref letter_id="G"/>
905 <letter_ref letter_id="G"/>
906 <letter_ref letter_id="G"/>
907 <letter_ref letter_id="G"/>
908 <letter_ref letter_id="T"/>
909 <letter_ref letter_id="T"/>
910 <letter_ref letter_id="T"/>
911 <letter_ref letter_id="C"/>
912 <letter_ref letter_id="A"/>
913 <letter_ref letter_id="C"/>
914 <letter_ref letter_id="T"/>
915 </site>
916 <right_flank>GGTCCACTAT</right_flank>
917 </contributing_site>
918 </contributing_sites>
919 </motif>
920 </motifs>
921 <scanned_sites_summary p_thresh="0.0001">
922 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/>
923 </scanned_sites>
924 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/>
925 </scanned_sites>
926 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
927 <scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
928 </scanned_sites>
929 <scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
930 </scanned_sites>
931 <scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
932 </scanned_sites>
933 <scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
934 </scanned_sites>
935 <scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
936 </scanned_sites>
937 <scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
938 <scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
939 </scanned_sites>
940 <scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
941 <scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
942 </scanned_sites>
943 <scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
944 </scanned_sites>
945 <scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
946 </scanned_sites>
947 <scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
948 </scanned_sites>
949 <scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
950 </scanned_sites>
951 <scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
952 </scanned_sites>
953 <scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
954 <scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
955 </scanned_sites>
956 <scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
957 </scanned_sites>
958 <scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
959 </scanned_sites>
960 <scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
961 </scanned_sites>
962 <scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
963 </scanned_sites>
964 <scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
965 </scanned_sites>
966 <scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
967 </scanned_sites>
968 <scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
969 </scanned_sites>
970 <scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
971 <scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
972 <scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
973 </scanned_sites>
974 <scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
975 </scanned_sites>
976 </scanned_sites_summary>
977 </MEME>