Mercurial > repos > iuc > meme_psp_gen
diff test-data/meme_output_test1.xml @ 3:ff2f53a32d0e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:04:34 -0500 |
| parents | b48e673af4e8 |
| children | 5f95d385a33c |
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--- a/test-data/meme_output_test1.xml Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test1.xml Wed Dec 11 18:04:34 2019 -0500 @@ -10,136 +10,29 @@ <!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*)> @@ -153,7 +46,6 @@ 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> @@ -162,643 +54,44 @@ <!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"> +<MEME version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700"> <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> -<value letter_id="N">0.000000</value> -<value letter_id="P">0.000000</value> -<value letter_id="Q">0.000000</value> -<value letter_id="R">0.000000</value> -<value letter_id="S">0.000000</value> -<value letter_id="T">0.080000</value> -<value letter_id="V">0.000000</value> -<value letter_id="W">0.000000</value> -<value letter_id="Y">0.000000</value> -</alphabet_array> -<alphabet_array> <value letter_id="A">0.280000</value> -<value letter_id="C">0.000000</value> -<value letter_id="D">0.000000</value> -<value letter_id="E">0.000000</value> -<value 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letter_id="T">0.040000</value> -<value letter_id="V">0.000000</value> -<value letter_id="W">0.000000</value> -<value letter_id="Y">0.000000</value> -</alphabet_array> </alphabet_matrix> </probabilities> <regular_expression> @@ -809,484 +102,17 @@ <left_flank>AAGGCCAGGA</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="A"/> -<letter_ref letter_id="A"/> </site> <right_flank>GCCTGAGAGC</right_flank> </contributing_site> <contributing_site sequence_id="sequence_25" position="36" strand="none" pvalue="3.41e-06" > <left_flank>ACAGGCCCTG</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="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>GCC</right_flank> </contributing_site> <contributing_site sequence_id="sequence_19" position="9" strand="none" pvalue="3.41e-06" > <left_flank>CAGGCCCTG</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="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>GCCCCAGCAG</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_9" position="13" strand="none" pvalue="3.41e-06" > -<left_flank>GATTCACTGA</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="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>GGCCCTCTGC</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_21" position="7" strand="none" pvalue="4.00e-06" > -<left_flank>CCAAGGA</left_flank> -<site> -<letter_ref letter_id="G"/> -<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="A"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>GCCCCACAAA</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_13" position="13" strand="none" pvalue="5.01e-06" > -<left_flank>CCACCAGCTT</left_flank> -<site> -<letter_ref letter_id="G"/> -<letter_ref letter_id="A"/> -<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="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>AGCCCTGTAC</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_23" position="15" strand="none" pvalue="6.06e-06" > -<left_flank>ATACCCAGGG</left_flank> -<site> -<letter_ref letter_id="A"/> -<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="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>CCTCAGCAGC</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_15" position="21" strand="none" pvalue="8.67e-06" > -<left_flank>AATCACTGAG</left_flank> -<site> -<letter_ref letter_id="G"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="T"/> -<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="A"/> -</site> -<right_flank>GTCCCAGGGA</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_12" position="18" strand="none" pvalue="8.67e-06" > -<left_flank>CACCAGAGCT</left_flank> -<site> -<letter_ref letter_id="G"/> -<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="T"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="T"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>AGAAGGTTCT</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_11" position="16" strand="none" pvalue="8.67e-06" > -<left_flank>CACTATTGAA</left_flank> -<site> -<letter_ref letter_id="G"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="T"/> -<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="A"/> -</site> -<right_flank>TTTCATTTGC</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_22" position="2" strand="none" pvalue="1.21e-05" > -<left_flank>GA</left_flank> -<site> -<letter_ref letter_id="G"/> -<letter_ref letter_id="A"/> -<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="A"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>GCCAACATCC</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_28" position="32" strand="none" pvalue="1.59e-05" > -<left_flank>CCGGCGGGGC</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="A"/> -<letter_ref letter_id="G"/> -</site> -<right_flank>GGGGCGG</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_20" position="4" strand="none" pvalue="1.59e-05" > -<left_flank>CAGA</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="A"/> -<letter_ref letter_id="G"/> -</site> -<right_flank>GTTCCGACCA</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_6" position="15" strand="none" pvalue="1.68e-05" > -<left_flank>CCCACTACTT</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="A"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>TCATTCTGAG</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_14" position="19" strand="none" pvalue="2.03e-05" > -<left_flank>CACCAGCAAG</left_flank> -<site> -<letter_ref letter_id="G"/> -<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"/> -<letter_ref letter_id="A"/> -<letter_ref letter_id="A"/> -</site> -<right_flank>GCTCAGGAGT</right_flank> -</contributing_site> -<contributing_site sequence_id="sequence_4" position="12" strand="none" pvalue="3.06e-05" > -<left_flank>CAGGTCTAAG</left_flank> -<site> -<letter_ref 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>