Mercurial > repos > iuc > meme_meme
diff test-data/meme_output_test2.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_test2.xml Thu May 17 14:10:48 2018 -0400 @@ -0,0 +1,984 @@ +<?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="Galaxy_FASTA_Input" length="30"> +<alphabet name="DNA" like="dna"> +<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> +<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/> +<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/> +<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/> +<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/> +<letter id="V" symbol="V" equals="ACG" name="Not T"/> +<letter id="H" symbol="H" equals="ACT" name="Not G"/> +<letter id="D" symbol="D" equals="AGT" name="Not C"/> +<letter id="B" symbol="B" equals="CGT" name="Not A"/> +<letter id="M" symbol="M" equals="AC" name="Amino"/> +<letter id="R" symbol="R" equals="AG" name="Purine"/> +<letter id="W" symbol="W" equals="AT" name="Weak"/> +<letter id="S" symbol="S" equals="CG" name="Strong"/> +<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/> +<letter id="K" symbol="K" equals="GT" name="Keto"/> +</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="G">0.257</value> +<value letter_id="T">0.217</value> +</alphabet_array> +</letter_frequencies> +</training_set> +<model> +<command_line>meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -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 prior30.plib -spmap uni -spfuzz 0.5 </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>uni</spmap> +<spfuzz>0.5</spfuzz> +<prior>dirichlet</prior> +<beta>0.01</beta> +<maxiter>50</maxiter> +<distance>0.001</distance> +<num_sequences>30</num_sequences> +<num_positions>1500</num_positions> +<seed>0</seed> +<ctfrac>-1</ctfrac> +<maxwords>-1</maxwords> +<strands>forward</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">0.294</value> +<value letter_id="C">0.231</value> +<value letter_id="G">0.257</value> +<value letter_id="T">0.217</value> +</alphabet_array> +</background_frequencies> +</model> +<motifs> +<motif id="motif_1" name="GGSRTATAAAA" alt="MEME-1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.376000"> +<scores> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">-14</value> +<value letter_id="C">-179</value> +<value letter_id="G">114</value> +<value letter_id="T">-112</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">3</value> +<value letter_id="C">-1155</value> +<value letter_id="G">137</value> +<value letter_id="T">-270</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-114</value> +<value letter_id="C">20</value> +<value letter_id="G">86</value> +<value letter_id="T">-71</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">3</value> +<value letter_id="C">-279</value> +<value letter_id="G">122</value> +<value letter_id="T">-170</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-1155</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-295</value> +<value letter_id="T">215</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">156</value> +<value letter_id="C">-179</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-170</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-1155</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-1155</value> +<value letter_id="T">220</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">172</value> +<value letter_id="C">-279</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-1155</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">125</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-1155</value> +<value letter_id="T">46</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">167</value> +<value letter_id="C">-179</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-1155</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">144</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-63</value> +<value letter_id="T">-270</value> +</alphabet_array> +</alphabet_matrix> +</scores> +<probabilities> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">0.266667</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.566667</value> +<value letter_id="T">0.100000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.300000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.666667</value> +<value letter_id="T">0.033333</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.133333</value> +<value letter_id="C">0.266667</value> +<value letter_id="G">0.466667</value> +<value letter_id="T">0.133333</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.300000</value> +<value letter_id="C">0.033333</value> +<value letter_id="G">0.600000</value> +<value letter_id="T">0.066667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.000000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.033333</value> +<value letter_id="T">0.966667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.866667</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.066667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.000000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">1.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.966667</value> +<value letter_id="C">0.033333</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.700000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.300000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.933333</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.800000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.166667</value> +<value letter_id="T">0.033333</value> +</alphabet_array> +</alphabet_matrix> +</probabilities> +<regular_expression> +[GA][GA][GC][GA]TATA[AT]AA +</regular_expression> +<contributing_sites> +<contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" > +<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_23" position="15" strand="plus" pvalue="2.22e-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_13" position="13" strand="plus" pvalue="2.74e-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_25" position="36" strand="plus" pvalue="4.86e-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_21" position="7" strand="plus" pvalue="4.86e-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_19" position="9" strand="plus" pvalue="4.86e-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="plus" pvalue="4.86e-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_28" position="32" strand="plus" pvalue="6.48e-06" > +<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="plus" pvalue="6.48e-06" > +<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_12" position="18" strand="plus" pvalue="6.48e-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_15" position="21" strand="plus" pvalue="1.38e-05" > +<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_11" position="16" strand="plus" pvalue="1.38e-05" > +<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_0" position="39" strand="plus" pvalue="1.41e-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_6" position="15" strand="plus" pvalue="1.61e-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_22" position="2" strand="plus" pvalue="1.95e-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_14" position="17" strand="plus" pvalue="1.95e-05" > +<left_flank>CCCACCAGCA</left_flank> +<site> +<letter_ref letter_id="A"/> +<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>AAGCTCAGGA</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-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_29" position="30" strand="plus" pvalue="3.04e-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_4" position="12" strand="plus" pvalue="3.04e-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_5" position="0" strand="plus" pvalue="3.67e-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_1" position="27" strand="plus" pvalue="3.93e-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_7" position="4" strand="plus" pvalue="5.65e-05" > +<left_flank>TCAG</left_flank> +<site> +<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"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ATGTTCCTGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-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="plus" pvalue="7.15e-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_27" position="36" strand="plus" pvalue="1.39e-04" > +<left_flank>TGCCTGGGTC</left_flank> +<site> +<letter_ref letter_id="C"/> +<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="G"/> +</site> +<right_flank>GCT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" > +<left_flank>TGCCTGGGCC</left_flank> +<site> +<letter_ref letter_id="C"/> +<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="G"/> +</site> +<right_flank>GC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" > +<left_flank>ga</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<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"/> +</site> +<right_flank>ggggcctcac</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-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_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" > +<left_flank>aaactta</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<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>acttaaaact</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" > +<left_flank>GGTGGGGGTG</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="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +</site> +<right_flank>GGTCCACTAT</right_flank> +</contributing_site> +</contributing_sites> +</motif> +</motifs> +<scanned_sites_summary p_thresh="0.0001"> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites> +<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"/> +</scanned_sites> +<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"/> +</scanned_sites> +</scanned_sites_summary> +</MEME>