|
6
|
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>
|
