Mercurial > repos > iuc > meme_meme
diff test-data/meme_output_test1.xml @ 13:57e5d9382f36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
| author | iuc |
|---|---|
| date | Thu, 17 May 2018 14:10:48 -0400 |
| parents | |
| children | 3f0dd362b755 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_test1.xml Thu May 17 14:10:48 2018 -0400 @@ -0,0 +1,1292 @@ +<?xml version='1.0' encoding='UTF-8' standalone='yes'?> +<!-- Document definition --> +<!DOCTYPE MEME[ +<!ELEMENT MEME ( + training_set, + model, + motifs, + scanned_sites_summary? +)> +<!ATTLIST MEME + version CDATA #REQUIRED + release CDATA #REQUIRED +> +<!-- Training-set elements --> +<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)> +<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED> +<!ELEMENT alphabet (letter*)> +<!ATTLIST alphabet name CDATA #REQUIRED> +<!ELEMENT ambigs (letter*)> +<!ELEMENT letter EMPTY> +<!ATTLIST letter id ID #REQUIRED> +<!ATTLIST letter symbol CDATA #REQUIRED> +<!ATTLIST letter equals CDATA #IMPLIED> +<!ATTLIST letter aliases CDATA #IMPLIED> +<!ATTLIST letter complement CDATA #IMPLIED> +<!ATTLIST letter name CDATA #IMPLIED> +<!ATTLIST letter colour CDATA #IMPLIED> +<!ELEMENT sequence EMPTY> +<!ATTLIST sequence id ID #REQUIRED + name CDATA #REQUIRED + length CDATA #REQUIRED + weight CDATA #REQUIRED +> +<!ELEMENT letter_frequencies (alphabet_array)> + +<!-- Model elements --> +<!ELEMENT model ( + command_line, + host, + type, + nmotifs, + evalue_threshold, + object_function, + spfun, + min_width, + max_width, + wg, + ws, + endgaps, + minsites, + maxsites, + wnsites, + spmap, + spfuzz, + prior, + beta, + maxiter, + distance, + num_sequences, + num_positions, + seed, + hsfrac, + maxwords, + maxsize, + csites, + strands, + priors_file, + reason_for_stopping, + back_order, + background_frequencies +)> +<!ELEMENT command_line (#PCDATA)*> +<!ELEMENT host (#PCDATA)*> +<!ELEMENT type (#PCDATA)*> +<!ELEMENT nmotifs (#PCDATA)*> +<!ELEMENT evalue_threshold (#PCDATA)*> +<!ELEMENT object_function (#PCDATA)*> +<!ELEMENT spfun (#PCDATA)*> +<!ELEMENT min_width (#PCDATA)*> +<!ELEMENT max_width (#PCDATA)*> +<!ELEMENT wg (#PCDATA)*> +<!ELEMENT ws (#PCDATA)*> +<!ELEMENT endgaps (#PCDATA)*> +<!ELEMENT minsites (#PCDATA)*> +<!ELEMENT maxsites (#PCDATA)*> +<!ELEMENT wnsites (#PCDATA)*> +<!ELEMENT spmap (#PCDATA)*> +<!ELEMENT spfuzz (#PCDATA)*> +<!ELEMENT prior (#PCDATA)*> +<!ELEMENT beta (#PCDATA)*> +<!ELEMENT maxiter (#PCDATA)*> +<!ELEMENT distance (#PCDATA)*> +<!ELEMENT num_sequences (#PCDATA)*> +<!ELEMENT num_positions (#PCDATA)*> +<!ELEMENT seed (#PCDATA)*> +<!ELEMENT hsfrac (#PCDATA)*> +<!ELEMENT maxwords (#PCDATA)*> +<!ELEMENT maxsites (#PCDATA)*> +<!ELEMENT csites (#PCDATA)*> +<!ELEMENT strands (#PCDATA)*> +<!ELEMENT priors_file (#PCDATA)*> +<!ELEMENT reason_for_stopping (#PCDATA)*> +<!ELEMENT back_order (#PCDATA)*> +<!ELEMENT background_frequencies (alphabet_array)> +<!ATTLIST background_frequencies source CDATA #REQUIRED> + +<!-- Motif elements --> +<!ELEMENT motifs (motif*)> +<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)> +<!ATTLIST motif id ID #REQUIRED + name CDATA #REQUIRED + alt CDATA "" + width CDATA #REQUIRED + sites CDATA #REQUIRED + llr CDATA #REQUIRED + ic CDATA #REQUIRED + re CDATA #REQUIRED + bayes_threshold CDATA #REQUIRED + e_value CDATA #REQUIRED + elapsed_time CDATA #REQUIRED + url CDATA "" +> +<!ELEMENT scores (alphabet_matrix)> +<!ELEMENT probabilities (alphabet_matrix)> +<!ELEMENT regular_expression (#PCDATA)*> + +<!-- Contributing site elements --> +<!-- Contributing sites are motif occurences found during the motif discovery phase --> +<!ELEMENT contributing_sites (contributing_site*)> +<!ELEMENT contributing_site (left_flank, site, right_flank)> +<!ATTLIST contributing_site sequence_id IDREF #REQUIRED + position CDATA #REQUIRED + strand (plus|minus|none) 'none' + pvalue CDATA #REQUIRED +> +<!-- The left_flank contains the sequence for 10 bases to the left of the motif start --> +<!ELEMENT left_flank (#PCDATA)> +<!-- The site contains the sequence for the motif instance --> +<!ELEMENT site (letter_ref*)> +<!-- The right_flank contains the sequence for 10 bases to the right of the motif end --> +<!ELEMENT right_flank (#PCDATA)> + +<!-- Scanned site elements --> +<!-- Scanned sites are motif occurences found during the sequence scan phase --> +<!ELEMENT scanned_sites_summary (scanned_sites*)> +<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED> +<!ELEMENT scanned_sites (scanned_site*)> +<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED + pvalue CDATA #REQUIRED + num_sites CDATA #REQUIRED> +<!ELEMENT scanned_site EMPTY> +<!ATTLIST scanned_site motif_id IDREF #REQUIRED + strand (plus|minus|none) 'none' + position CDATA #REQUIRED + pvalue CDATA #REQUIRED> + +<!-- Utility elements --> +<!-- A reference to a letter in the alphabet --> +<!ELEMENT letter_ref EMPTY> +<!ATTLIST letter_ref letter_id IDREF #REQUIRED> +<!-- A alphabet-array contains one floating point value for each letter in an alphabet --> +<!ELEMENT alphabet_array (value*)> +<!ELEMENT value (#PCDATA)> +<!ATTLIST value letter_id IDREF #REQUIRED> + +<!-- A alphabet_matrix contains one alphabet_array for each position in a motif --> +<!ELEMENT alphabet_matrix (alphabet_array*)> + +]> +<!-- Begin document body --> +<MEME version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700"> +<training_set datafile="meme_input_1.fasta" length="30"> +<alphabet name="Protein" like="protein"> +<letter id="A" symbol="A" name="Alanine" colour="0000CC"/> +<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/> +<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/> +<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/> +<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/> +<letter id="G" symbol="G" name="Glycine" colour="FFB300"/> +<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/> +<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/> +<letter id="K" symbol="K" name="Lysine" colour="CC0000"/> +<letter id="L" symbol="L" name="Leucine" colour="0000CC"/> +<letter id="M" symbol="M" name="Methionine" colour="0000CC"/> +<letter id="N" symbol="N" name="Asparagine" colour="008000"/> +<letter id="P" symbol="P" name="Proline" colour="FFFF00"/> +<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/> +<letter id="R" symbol="R" name="Arginine" colour="CC0000"/> +<letter id="S" symbol="S" name="Serine" colour="008000"/> +<letter id="T" symbol="T" name="Threonine" colour="008000"/> +<letter id="V" symbol="V" name="Valine" colour="0000CC"/> +<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/> +<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/> +<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/> +<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/> +<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/> +<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/> +</alphabet> +<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" /> +<sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" /> +<sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" /> +<sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" /> +<sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" /> +<sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" /> +<sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" /> +<sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" /> +<sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" /> +<sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" /> +<sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" /> +<sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" /> +<sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" /> +<sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" /> +<sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" /> +<sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" /> +<sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" /> +<sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" /> +<sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" /> +<sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" /> +<sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" /> +<sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" /> +<sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" /> +<sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" /> +<sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" /> +<sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" /> +<sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" /> +<sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" /> +<sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" /> +<sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" /> +<letter_frequencies> +<alphabet_array> +<value letter_id="A">0.294</value> +<value letter_id="C">0.231</value> +<value letter_id="D">0.000</value> +<value letter_id="E">0.000</value> +<value letter_id="F">0.000</value> +<value letter_id="G">0.257</value> +<value letter_id="H">0.000</value> +<value letter_id="I">0.000</value> +<value letter_id="K">0.000</value> +<value letter_id="L">0.000</value> +<value letter_id="M">0.000</value> +<value letter_id="N">0.000</value> +<value letter_id="P">0.000</value> +<value letter_id="Q">0.000</value> +<value letter_id="R">0.000</value> +<value letter_id="S">0.000</value> +<value letter_id="T">0.217</value> +<value letter_id="V">0.000</value> +<value letter_id="W">0.000</value> +<value letter_id="Y">0.000</value> +</alphabet_array> +</letter_frequencies> +</training_set> +<model> +<command_line>meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 </command_line> +<host>ThinkPad-T450s</host> +<type>zoops</type> +<nmotifs>1</nmotifs> +<evalue_threshold>inf</evalue_threshold> +<object_function>E-value of product of p-values</object_function> +<use_llr>0</use_llr> +<min_width>8</min_width> +<max_width>50</max_width> +<wg>11</wg> +<ws>1</ws> +<endgaps>yes</endgaps> +<substring>yes</substring> +<minsites>2</minsites> +<maxsites>30</maxsites> +<wnsites>0.8</wnsites> +<spmap>pam</spmap> +<spfuzz>120</spfuzz> +<prior>megap</prior> +<beta>7500</beta> +<maxiter>50</maxiter> +<distance>1e-05</distance> +<num_sequences>30</num_sequences> +<num_positions>1500</num_positions> +<seed>0</seed> +<ctfrac>-1</ctfrac> +<maxwords>-1</maxwords> +<strands>none</strands> +<priors_file>prior30.plib</priors_file> +<reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping> +<background_frequencies source="dataset with add-one prior applied"> +<alphabet_array> +<value letter_id="A">0.291</value> +<value letter_id="C">0.229</value> +<value letter_id="D">0.001</value> +<value letter_id="E">0.001</value> +<value letter_id="F">0.001</value> +<value letter_id="G">0.255</value> +<value letter_id="H">0.001</value> +<value letter_id="I">0.001</value> +<value letter_id="K">0.001</value> +<value letter_id="L">0.001</value> +<value letter_id="M">0.001</value> +<value letter_id="N">0.001</value> +<value letter_id="P">0.001</value> +<value letter_id="Q">0.001</value> +<value letter_id="R">0.001</value> +<value letter_id="S">0.001</value> +<value letter_id="T">0.215</value> +<value letter_id="V">0.001</value> +<value letter_id="W">0.001</value> +<value letter_id="Y">0.001</value> +</alphabet_array> +</background_frequencies> +</model> +<motifs> +<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"> +<scores> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">-32</value> +<value letter_id="C">-680</value> +<value letter_id="D">91</value> +<value letter_id="E">77</value> +<value letter_id="F">7</value> +<value letter_id="G">138</value> +<value letter_id="H">-20</value> +<value letter_id="I">55</value> +<value letter_id="K">64</value> +<value letter_id="L">107</value> +<value letter_id="M">11</value> +<value letter_id="N">150</value> +<value letter_id="P">142</value> +<value letter_id="Q">72</value> +<value letter_id="R">87</value> +<value letter_id="S">396</value> +<value letter_id="T">-148</value> +<value letter_id="V">221</value> +<value letter_id="W">-140</value> +<value letter_id="Y">-36</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-11</value> +<value letter_id="C">-680</value> +<value letter_id="D">89</value> +<value letter_id="E">76</value> +<value letter_id="F">7</value> +<value letter_id="G">137</value> +<value letter_id="H">-21</value> +<value letter_id="I">55</value> +<value letter_id="K">63</value> +<value letter_id="L">107</value> +<value letter_id="M">10</value> +<value letter_id="N">149</value> +<value letter_id="P">141</value> +<value letter_id="Q">71</value> +<value letter_id="R">87</value> +<value letter_id="S">396</value> +<value letter_id="T">-239</value> +<value letter_id="V">220</value> +<value letter_id="W">-140</value> +<value letter_id="Y">-36</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-79</value> +<value letter_id="C">41</value> +<value letter_id="D">4</value> +<value letter_id="E">21</value> +<value letter_id="F">-7</value> +<value letter_id="G">44</value> +<value letter_id="H">-62</value> +<value letter_id="I">42</value> +<value letter_id="K">-5</value> +<value letter_id="L">99</value> +<value letter_id="M">0</value> +<value letter_id="N">99</value> +<value letter_id="P">138</value> +<value letter_id="Q">52</value> +<value letter_id="R">42</value> +<value letter_id="S">399</value> +<value letter_id="T">-46</value> +<value letter_id="V">223</value> +<value letter_id="W">-173</value> +<value letter_id="Y">-68</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">11</value> +<value letter_id="C">-677</value> +<value letter_id="D">48</value> +<value letter_id="E">47</value> +<value letter_id="F">-2</value> +<value letter_id="G">127</value> +<value letter_id="H">-43</value> +<value letter_id="I">46</value> +<value letter_id="K">27</value> +<value letter_id="L">101</value> +<value letter_id="M">3</value> +<value letter_id="N">124</value> +<value letter_id="P">138</value> +<value letter_id="Q">60</value> +<value letter_id="R">62</value> +<value letter_id="S">397</value> +<value letter_id="T">-235</value> +<value letter_id="V">220</value> +<value letter_id="W">-160</value> +<value letter_id="Y">-55</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-596</value> +<value letter_id="C">-820</value> +<value letter_id="D">12</value> +<value letter_id="E">-21</value> +<value letter_id="F">-53</value> +<value letter_id="G">-267</value> +<value letter_id="H">-74</value> +<value letter_id="I">37</value> +<value letter_id="K">16</value> +<value letter_id="L">44</value> +<value letter_id="M">-37</value> +<value letter_id="N">98</value> +<value letter_id="P">31</value> +<value letter_id="Q">9</value> +<value letter_id="R">19</value> +<value letter_id="S">319</value> +<value letter_id="T">212</value> +<value letter_id="V">127</value> +<value letter_id="W">-193</value> +<value letter_id="Y">-95</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">165</value> +<value letter_id="C">-261</value> +<value letter_id="D">70</value> +<value letter_id="E">110</value> +<value letter_id="F">77</value> +<value letter_id="G">-521</value> +<value letter_id="H">-4</value> +<value letter_id="I">147</value> +<value letter_id="K">95</value> +<value letter_id="L">201</value> +<value letter_id="M">90</value> +<value letter_id="N">121</value> +<value letter_id="P">124</value> +<value letter_id="Q">91</value> +<value letter_id="R">107</value> +<value letter_id="S">425</value> +<value letter_id="T">-527</value> +<value letter_id="V">314</value> +<value letter_id="W">-95</value> +<value letter_id="Y">8</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-838</value> +<value letter_id="C">-990</value> +<value letter_id="D">-89</value> +<value letter_id="E">-149</value> +<value letter_id="F">-151</value> +<value letter_id="G">-841</value> +<value letter_id="H">-161</value> +<value letter_id="I">-117</value> +<value letter_id="K">-113</value> +<value letter_id="L">-66</value> +<value letter_id="M">-209</value> +<value letter_id="N">-68</value> +<value letter_id="P">-69</value> +<value letter_id="Q">-129</value> +<value letter_id="R">-91</value> +<value letter_id="S">111</value> +<value letter_id="T">221</value> +<value letter_id="V">-55</value> +<value letter_id="W">-255</value> +<value letter_id="Y">-173</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">176</value> +<value letter_id="C">-858</value> +<value letter_id="D">-79</value> +<value letter_id="E">-103</value> +<value letter_id="F">-115</value> +<value letter_id="G">-717</value> +<value letter_id="H">-148</value> +<value letter_id="I">-95</value> +<value letter_id="K">-108</value> +<value letter_id="L">-17</value> +<value letter_id="M">-162</value> +<value letter_id="N">-61</value> +<value letter_id="P">-12</value> +<value letter_id="Q">-95</value> +<value letter_id="R">-69</value> +<value letter_id="S">193</value> +<value letter_id="T">-737</value> +<value letter_id="V">52</value> +<value letter_id="W">-240</value> +<value letter_id="Y">-153</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">134</value> +<value letter_id="C">-686</value> +<value letter_id="D">0</value> +<value letter_id="E">16</value> +<value letter_id="F">-12</value> +<value letter_id="G">-553</value> +<value letter_id="H">-68</value> +<value letter_id="I">44</value> +<value letter_id="K">-8</value> +<value letter_id="L">96</value> +<value letter_id="M">-9</value> +<value letter_id="N">88</value> +<value letter_id="P">124</value> +<value letter_id="Q">41</value> +<value letter_id="R">36</value> +<value letter_id="S">384</value> +<value letter_id="T">11</value> +<value letter_id="V">216</value> +<value letter_id="W">-177</value> +<value letter_id="Y">-71</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">165</value> +<value letter_id="C">-261</value> +<value letter_id="D">70</value> +<value letter_id="E">110</value> +<value letter_id="F">77</value> +<value letter_id="G">-521</value> +<value letter_id="H">-4</value> +<value letter_id="I">147</value> +<value letter_id="K">95</value> +<value letter_id="L">201</value> +<value letter_id="M">90</value> +<value letter_id="N">121</value> +<value letter_id="P">124</value> +<value letter_id="Q">91</value> +<value letter_id="R">107</value> +<value letter_id="S">425</value> +<value letter_id="T">-527</value> +<value letter_id="V">314</value> +<value letter_id="W">-95</value> +<value letter_id="Y">8</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">147</value> +<value letter_id="C">-614</value> +<value letter_id="D">89</value> +<value letter_id="E">129</value> +<value letter_id="F">93</value> +<value letter_id="G">-121</value> +<value letter_id="H">12</value> +<value letter_id="I">160</value> +<value letter_id="K">113</value> +<value letter_id="L">217</value> +<value letter_id="M">108</value> +<value letter_id="N">144</value> +<value letter_id="P">144</value> +<value letter_id="Q">111</value> +<value letter_id="R">125</value> +<value letter_id="S">447</value> +<value letter_id="T">-241</value> +<value letter_id="V">332</value> +<value letter_id="W">-81</value> +<value letter_id="Y">22</value> +</alphabet_array> +</alphabet_matrix> +</scores> +<probabilities> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">0.240000</value> +<value letter_id="C">0.000000</value> +<value letter_id="D">0.000000</value> +<value letter_id="E">0.000000</value> +<value letter_id="F">0.000000</value> +<value letter_id="G">0.680000</value> +<value letter_id="H">0.000000</value> +<value letter_id="I">0.000000</value> +<value letter_id="K">0.000000</value> +<value letter_id="L">0.000000</value> +<value letter_id="M">0.000000</value> 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letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>CTTGGAGTCC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_0" position="39" strand="none" pvalue="3.06e-05" > +<left_flank>CCTCGGGACG</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank></right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_18" position="37" strand="none" pvalue="3.82e-05" > +<left_flank>CGTGGTCGCG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_5" position="0" strand="none" pvalue="3.82e-05" > +<left_flank></left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ATGGTCCTGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_29" position="30" strand="none" pvalue="4.02e-05" > +<left_flank>GCTGCCGGTG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GCCCTGGCG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_1" position="27" strand="none" pvalue="5.52e-05" > +<left_flank>AGTCACAAGT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GGGTCGCACG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_3" position="14" strand="none" pvalue="5.94e-05" > +<left_flank>CCCAGGTTTC</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TCGCCGCACC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_16" position="22" strand="none" pvalue="6.78e-05" > +<left_flank>AGTTTCAGTT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>attatataac</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_7" position="2" strand="none" pvalue="2.08e-04" > +<left_flank>TC</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +</site> +<right_flank>AAATGTTCCT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_8" position="13" strand="none" pvalue="4.05e-04" > +<left_flank>TATAACTCAG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TAATTTGTAC</right_flank> +</contributing_site> +</contributing_sites> +</motif> +</motifs> +<scanned_sites_summary p_thresh="0.0001"> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_2" pvalue="7.29e-01" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +</scanned_sites_summary> +</MEME>