<?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="common/Puf3p-20.s" length="20">
<alphabet name="RNA" like="rna">
<letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
<letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
<letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
<letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
<letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
<letter id="V" symbol="V" equals="ACG" name="Not U"/>
<letter id="H" symbol="H" equals="ACU" name="Not G"/>
<letter id="D" symbol="D" equals="AGU" name="Not C"/>
<letter id="B" symbol="B" equals="CGU" 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="AU" name="Weak"/>
<letter id="S" symbol="S" equals="CG" name="Strong"/>
<letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
<letter id="K" symbol="K" equals="GU" name="Keto"/>
</alphabet>
<sequence id="sequence_0" name="sacCer3_chrII_556467_556567_+" length="100" weight="1.000000" />
<sequence id="sequence_1" name="sacCer3_chrIX_312444_312544_+" length="100" weight="1.000000" />
<sequence id="sequence_2" name="sacCer3_chrXIV_443327_443427_-" length="100" weight="1.000000" />
<sequence id="sequence_3" name="sacCer3_chrVII_905741_905841_+" length="100" weight="1.000000" />
<sequence id="sequence_4" name="sacCer3_chrXI_356613_356713_+" length="100" weight="1.000000" />
<sequence id="sequence_5" name="sacCer3_chrI_93336_93436_+" length="100" weight="1.000000" />
<sequence id="sequence_6" name="sacCer3_chrIV_309697_309797_-" length="100" weight="1.000000" />
<sequence id="sequence_7" name="sacCer3_chrXVI_564127_564227_-" length="100" weight="1.000000" />
<sequence id="sequence_8" name="sacCer3_chrXIII_123147_123247_-" length="100" weight="1.000000" />
<sequence id="sequence_9" name="sacCer3_chrVII_559616_559716_-" length="100" weight="1.000000" />
<sequence id="sequence_10" name="sacCer3_chrVII_395909_396009_-" length="100" weight="1.000000" />
<sequence id="sequence_11" name="sacCer3_chrXI_569507_569607_+" length="100" weight="1.000000" />
<sequence id="sequence_12" name="sacCer3_chrIV_600891_600991_+" length="100" weight="1.000000" />
<sequence id="sequence_13" name="sacCer3_chrII_531780_531880_-" length="100" weight="1.000000" />
<sequence id="sequence_14" name="sacCer3_chrXVI_522715_522815_+" length="100" weight="1.000000" />
<sequence id="sequence_15" name="sacCer3_chrIV_1170148_1170248_+" length="100" weight="1.000000" />
<sequence id="sequence_16" name="sacCer3_chrXI_141677_141777_-" length="100" weight="1.000000" />
<sequence id="sequence_17" name="sacCer3_chrIV_1233184_1233284_-" length="100" weight="1.000000" />
<sequence id="sequence_18" name="sacCer3_chrXIV_582075_582175_+" length="100" weight="1.000000" />
<sequence id="sequence_19" name="sacCer3_chrIV_915979_916079_+" length="100" weight="1.000000" />
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.295</value>
<value letter_id="C">0.191</value>
<value letter_id="G">0.137</value>
<value letter_id="U">0.377</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme -oc results/motif.meme.puf3p -nostatus -rna -nmotifs 3 common/Puf3p-20.s </command_line>
<host>sh-ln04.stanford.edu</host>
<type>zoops</type>
<nmotifs>3</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>20</maxsites>
<wnsites>0.8</wnsites>
<spmap>uni</spmap>
<spfuzz>0.5</spfuzz>
<prior>dirichlet</prior>
<beta>0.01</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_sequences>20</num_sequences>
<num_positions>2000</num_positions>
<seed>0</seed>
<ctfrac>-1</ctfrac>
<maxwords>-1</maxwords>
<strands>none</strands>
<priors_file></priors_file>
<reason_for_stopping>Stopped because requested number of motifs (3) found.</reason_for_stopping>
<background_frequencies source="dataset with add-one prior applied">
<alphabet_array>
<value letter_id="A">0.295</value>
<value letter_id="C">0.191</value>
<value letter_id="G">0.137</value>
<value letter_id="U">0.377</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="RAYKKURCMARCMCMRCWKYACC" alt="MEME-1" width="23" sites="3" ic="33.1" re="37.2" llr="77" e_value="3.9e+000" bayes_threshold="8.67781" elapsed_time="0.663574">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">17</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">176</value>
<value letter_id="C">-823</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">80</value>
<value letter_id="G">-823</value>
<value letter_id="U">82</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">-823</value>
<value letter_id="G">-823</value>
<value letter_id="U">141</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">17</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">17</value>
<value letter_id="C">180</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">176</value>
<value letter_id="C">-823</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">17</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">80</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">80</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">17</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">-823</value>
<value letter_id="G">-823</value>
<value letter_id="U">-18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">-823</value>
<value letter_id="G">228</value>
<value letter_id="U">-18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">180</value>
<value letter_id="G">-823</value>
<value letter_id="U">-18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">-823</value>
<value letter_id="G">128</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-823</value>
<value letter_id="C">238</value>
<value letter_id="G">-823</value>
<value letter_id="U">-823</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">1.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.666667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.333333</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="U">1.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.666667</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">1.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.666667</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.666667</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.666667</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="U">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.666667</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.666667</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.333333</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[GA]A[UC][GU][GU]U[GA]C[CA]A[GA]C[AC]C[AC][GA]C[AU][GU][CU][AG]CC
</regular_expression>
<contributing_sites>
<contributing_site sequence_id="sequence_5" position="60" strand="none" pvalue="1.21e-13" >
<left_flank>CCUCAUUUAA</left_flank>
<site>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>CAGCCCAUCG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_12" position="66" strand="none" pvalue="2.48e-13" >
<left_flank>AGAAUCCGAC</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="G"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
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</contributing_site>
<contributing_site sequence_id="sequence_18" position="64" strand="none" pvalue="1.35e-11" >
<left_flank>UUAAAUAAGA</left_flank>
<site>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>UUGAACGCCA</right_flank>
</contributing_site>
</contributing_sites>
</motif>
<motif id="motif_2" name="UGGGUCAG" alt="MEME-2" width="8" sites="4" ic="12.8" re="15.6" llr="43" e_value="4.1e+001" bayes_threshold="8.85798" elapsed_time="1.255360">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">-865</value>
<value letter_id="G">-865</value>
<value letter_id="U">141</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">39</value>
<value letter_id="G">245</value>
<value letter_id="U">-865</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">-865</value>
<value letter_id="G">287</value>
<value letter_id="U">-865</value>
</alphabet_array>
<alphabet_array>
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<value letter_id="C">39</value>
<value letter_id="G">245</value>
<value letter_id="U">-865</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">-865</value>
<value letter_id="G">87</value>
<value letter_id="U">99</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">238</value>
<value letter_id="G">-865</value>
<value letter_id="U">-865</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">134</value>
<value letter_id="C">-865</value>
<value letter_id="G">87</value>
<value letter_id="U">-865</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-865</value>
<value letter_id="C">-865</value>
<value letter_id="G">287</value>
<value letter_id="U">-865</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<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="U">1.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.250000</value>
<value letter_id="G">0.750000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.250000</value>
<value letter_id="G">0.750000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.250000</value>
<value letter_id="U">0.750000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.750000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.250000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
U[GC]G[GC][UG]C[AG]G
</regular_expression>
<contributing_sites>
<contributing_site sequence_id="sequence_18" position="25" strand="none" pvalue="3.85e-06" >
<left_flank>UCCAUUACUU</left_flank>
<site>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>CUAGUGAAAA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_16" position="76" strand="none" pvalue="5.16e-06" >
<left_flank>GGGCAUAAUU</left_flank>
<site>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>UUCAUUUUUU</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_12" position="23" strand="none" pvalue="1.35e-05" >
<left_flank>CCACUUCCUC</left_flank>
<site>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>UAACUAUCAC</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_7" position="3" strand="none" pvalue="1.35e-05" >
<left_flank>AAA</left_flank>
<site>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>ACUGGUAAGG</right_flank>
</contributing_site>
</contributing_sites>
</motif>
<motif id="motif_3" name="CUCCAAAAASC" alt="MEME-3" width="11" sites="6" ic="14.5" re="15.8" llr="66" e_value="1.1e+002" bayes_threshold="8.67275" elapsed_time="1.816281">
<scores>
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<alphabet_array>
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<value letter_id="C">212</value>
<value letter_id="G">-923</value>
<value letter_id="U">-117</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-923</value>
<value letter_id="C">-923</value>
<value letter_id="G">29</value>
<value letter_id="U">114</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-923</value>
<value letter_id="C">212</value>
<value letter_id="G">29</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-923</value>
<value letter_id="C">239</value>
<value letter_id="G">-923</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">176</value>
<value letter_id="C">-923</value>
<value letter_id="G">-923</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">-923</value>
<value letter_id="G">29</value>
<value letter_id="U">-117</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">176</value>
<value letter_id="C">-923</value>
<value letter_id="G">-923</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">117</value>
<value letter_id="C">-923</value>
<value letter_id="G">128</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">76</value>
<value letter_id="C">-20</value>
<value letter_id="G">29</value>
<value letter_id="U">-117</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-923</value>
<value letter_id="C">180</value>
<value letter_id="G">128</value>
<value letter_id="U">-923</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-923</value>
<value letter_id="C">212</value>
<value letter_id="G">29</value>
<value letter_id="U">-923</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.833333</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.166667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.166667</value>
<value letter_id="U">0.833333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.833333</value>
<value letter_id="G">0.166667</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
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<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
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<value letter_id="U">0.166667</value>
</alphabet_array>
<alphabet_array>
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<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
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<value letter_id="U">0.000000</value>
</alphabet_array>
<alphabet_array>
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</alphabet_array>
<alphabet_array>
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</alphabet_array>
<alphabet_array>
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<value letter_id="U">0.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
CUCCAAA[AG]A[CG]C
</regular_expression>
<contributing_sites>
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<left_flank>CAAACA</left_flank>
<site>
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<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>UUGAAUAGCA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_16" position="59" strand="none" pvalue="1.25e-06" >
<left_flank>UCAUUUCUGU</left_flank>
<site>
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<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>AUAAUUUGGG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_12" position="52" strand="none" pvalue="5.65e-06" >
<left_flank>UCUUCUGAAG</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>GACAACGGUA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_3" position="65" strand="none" pvalue="7.74e-06" >
<left_flank>UAUACGCGCU</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>GUAACUUUUU</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_9" position="64" strand="none" pvalue="8.67e-06" >
<left_flank>AUUUUAUUGG</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>UGACUUAUGU</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_5" position="33" strand="none" pvalue="1.09e-05" >
<left_flank>GUGGAUACUC</left_flank>
<site>
<letter_ref letter_id="U"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
</site>
<right_flank>AUUUUCCCUC</right_flank>
</contributing_site>
</contributing_sites>
</motif>
</motifs>
<scanned_sites_summary p_thresh="0.0001">
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<scanned_sites sequence_id="sequence_1" pvalue="8.63e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_2" pvalue="9.80e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_3" pvalue="3.26e-03" num_sites="1"><scanned_site motif_id="motif_3" strand="none" position="65" pvalue="7.74e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_4" pvalue="7.71e-01" num_sites="0"></scanned_sites>
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<scanned_site motif_id="motif_1" strand="none" position="60" pvalue="1.21e-13"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_6" pvalue="8.62e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_7" pvalue="1.23e-02" num_sites="1"><scanned_site motif_id="motif_2" strand="none" position="3" pvalue="1.35e-05"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_8" pvalue="8.76e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_9" pvalue="5.02e-03" num_sites="1"><scanned_site motif_id="motif_3" strand="none" position="64" pvalue="8.67e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_10" pvalue="9.94e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_11" pvalue="2.24e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_12" pvalue="9.83e-15" num_sites="3"><scanned_site motif_id="motif_2" strand="none" position="23" pvalue="1.35e-05"/>
<scanned_site motif_id="motif_3" strand="none" position="52" pvalue="5.65e-06"/>
<scanned_site motif_id="motif_1" strand="none" position="66" pvalue="2.48e-13"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_13" pvalue="4.95e-02" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="4.39e-05"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_14" pvalue="1.32e-03" num_sites="1"><scanned_site motif_id="motif_3" strand="none" position="6" pvalue="6.84e-07"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_15" pvalue="9.87e-01" num_sites="0"></scanned_sites>
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<scanned_site motif_id="motif_2" strand="none" position="76" pvalue="5.16e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_17" pvalue="7.91e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_18" pvalue="6.03e-11" num_sites="2"><scanned_site motif_id="motif_2" strand="none" position="25" pvalue="3.85e-06"/>
<scanned_site motif_id="motif_1" strand="none" position="64" pvalue="1.35e-11"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_19" pvalue="9.93e-01" num_sites="0"></scanned_sites>
</scanned_sites_summary>
</MEME>
