<?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 primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED
  control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">
<!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_positions,
  seed,
  hsfrac,
  searchsize,
  maxsize,
  norand,
  csites,
  strands,
  brief,
  psp_file,
  priors_file,
  reason_for_stopping,
  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_positions (#PCDATA)*>
<!ELEMENT seed (#PCDATA)*>
<!ELEMENT hsfrac (#PCDATA)*>
<!ELEMENT searchsize (#PCDATA)*>
<!ELEMENT maxsize (#PCDATA)*>
<!ELEMENT norand (#PCDATA)*>
<!ELEMENT csites (#PCDATA)*>
<!ELEMENT strands (#PCDATA)*>
<!ELEMENT brief (#PCDATA)*>
<!ELEMENT psp_file (#PCDATA)*>
<!ELEMENT priors_file (#PCDATA)*>
<!ELEMENT reason_for_stopping (#PCDATA)*>
<!ELEMENT background_frequencies (alphabet_array)>
<!ATTLIST background_frequencies source CDATA #REQUIRED
		   order 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
                ic CDATA #REQUIRED
                re CDATA #REQUIRED
                llr CDATA #REQUIRED
                p_value CDATA #REQUIRED
                e_value CDATA #REQUIRED
                bayes_threshold 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="5.3.2" release="Fri Feb 5 17:50:07 2021 -0800">
<training_set primary_sequences="common/adh.s" primary_count="33" primary_positions="9996" control_sequences="Primary sequences shuffled preserving 3-mers" control_count="33" control_positions="9996">
<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="2BHD_STREX" length="255" weight="1.000000" />
<sequence id="sequence_1" name="3BHD_COMTE" length="253" weight="1.000000" />
<sequence id="sequence_2" name="ADH_DROME" length="255" weight="1.000000" />
<sequence id="sequence_3" name="AP27_MOUSE" length="244" weight="1.000000" />
<sequence id="sequence_4" name="BA72_EUBSP" length="249" weight="1.000000" />
<sequence id="sequence_5" name="BDH_HUMAN" length="343" weight="1.000000" />
<sequence id="sequence_6" name="BPHB_PSEPS" length="275" weight="1.000000" />
<sequence id="sequence_7" name="BUDC_KLETE" length="241" weight="1.000000" />
<sequence id="sequence_8" name="DHES_HUMAN" length="327" weight="1.000000" />
<sequence id="sequence_9" name="DHGB_BACME" length="262" weight="1.000000" />
<sequence id="sequence_10" name="DHII_HUMAN" length="292" weight="1.000000" />
<sequence id="sequence_11" name="DHMA_FLAS1" length="270" weight="1.000000" />
<sequence id="sequence_12" name="ENTA_ECOLI" length="248" weight="1.000000" />
<sequence id="sequence_13" name="FIXR_BRAJA" length="278" weight="1.000000" />
<sequence id="sequence_14" name="GUTD_ECOLI" length="259" weight="1.000000" />
<sequence id="sequence_15" name="HDE_CANTR" length="906" weight="1.000000" />
<sequence id="sequence_16" name="HDHA_ECOLI" length="255" weight="1.000000" />
<sequence id="sequence_17" name="LIGD_PSEPA" length="305" weight="1.000000" />
<sequence id="sequence_18" name="NODG_RHIME" length="245" weight="1.000000" />
<sequence id="sequence_19" name="RIDH_KLEAE" length="249" weight="1.000000" />
<sequence id="sequence_20" name="YINL_LISMO" length="248" weight="1.000000" />
<sequence id="sequence_21" name="YRTP_BACSU" length="238" weight="1.000000" />
<sequence id="sequence_22" name="CSGA_MYXXA" length="166" weight="1.000000" />
<sequence id="sequence_23" name="DHB2_HUMAN" length="387" weight="1.000000" />
<sequence id="sequence_24" name="DHB3_HUMAN" length="310" weight="1.000000" />
<sequence id="sequence_25" name="DHCA_HUMAN" length="276" weight="1.000000" />
<sequence id="sequence_26" name="FABI_ECOLI" length="262" weight="1.000000" />
<sequence id="sequence_27" name="FVT1_HUMAN" length="332" weight="1.000000" />
<sequence id="sequence_28" name="HMTR_LEIMA" length="287" weight="1.000000" />
<sequence id="sequence_29" name="MAS1_AGRRA" length="476" weight="1.000000" />
<sequence id="sequence_30" name="PCR_PEA" length="399" weight="1.000000" />
<sequence id="sequence_31" name="RFBB_NEIGO" length="346" weight="1.000000" />
<sequence id="sequence_32" name="YURA_MYXXA" length="258" weight="1.000000" />
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.111</value>
<value letter_id="C">0.0121</value>
<value letter_id="D">0.0502</value>
<value letter_id="E">0.0553</value>
<value letter_id="F">0.0359</value>
<value letter_id="G">0.0898</value>
<value letter_id="H">0.0182</value>
<value letter_id="I">0.0566</value>
<value letter_id="K">0.0518</value>
<value letter_id="L">0.0919</value>
<value letter_id="M">0.0272</value>
<value letter_id="N">0.0405</value>
<value letter_id="P">0.0405</value>
<value letter_id="Q">0.0294</value>
<value letter_id="R">0.0494</value>
<value letter_id="S">0.0637</value>
<value letter_id="T">0.0565</value>
<value letter_id="V">0.083</value>
<value letter_id="W">0.0095</value>
<value letter_id="Y">0.027</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme -nsites 27 common/adh.s -oc results/meme24 -mod anr -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi </command_line>
<host>Timothys-Mac-Mini.local</host>
<type>anr</type>
<nmotifs>2</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>Differential Enrichment mHG</object_function>
<spfun>log likelihood ratio (LLR)</spfun>
<min_width>12</min_width>
<max_width>12</max_width>
<substring>yes</substring>
<minsites>27</minsites>
<maxsites>27</maxsites>
<wnsites>0.8</wnsites>
<spmap>pam</spmap>
<spfuzz>120</spfuzz>
<prior>megap</prior>
<beta>49975</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_positions>9996</num_positions>
<seed>0</seed>
<hsfrac>0.6</hsfrac>
<searchsize>9996</searchsize>
<maxsize>0</maxsize>
<norand>no</norand>
<strands>none</strands>
<brief>1000</brief>
<psp_file></psp_file>
<priors_file>prior30.plib</priors_file>
<reason_for_stopping>Stopped because requested number of motifs (2) found.</reason_for_stopping>
<background_frequencies source="--sequences--" order="0">
<alphabet_array>
<value letter_id="A">0.111</value>
<value letter_id="C">0.0122</value>
<value letter_id="D">0.0502</value>
<value letter_id="E">0.0553</value>
<value letter_id="F">0.0359</value>
<value letter_id="G">0.0898</value>
<value letter_id="H">0.0183</value>
<value letter_id="I">0.0566</value>
<value letter_id="K">0.0518</value>
<value letter_id="L">0.0919</value>
<value letter_id="M">0.0273</value>
<value letter_id="N">0.0405</value>
<value letter_id="P">0.0405</value>
<value letter_id="Q">0.0295</value>
<value letter_id="R">0.0494</value>
<value letter_id="S">0.0637</value>
<value letter_id="T">0.0565</value>
<value letter_id="V">0.083</value>
<value letter_id="W">0.00959</value>
<value letter_id="Y">0.0271</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="KGIRVNGVAPGA" alt="MEME-1" width="12" sites="27" ic="26.3" re="23.9" llr="447" p_value="2.3e-001" e_value="2.3e-001" bayes_threshold="8.47468" elapsed_time="0.202018">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-245</value>
<value letter_id="C">-295</value>
<value letter_id="D">50</value>
<value letter_id="E">-5</value>
<value letter_id="F">-332</value>
<value letter_id="G">-335</value>
<value letter_id="H">273</value>
<value letter_id="I">-74</value>
<value letter_id="K">193</value>
<value letter_id="L">-47</value>
<value letter_id="M">28</value>
<value letter_id="N">8</value>
<value letter_id="P">-23</value>
<value letter_id="Q">67</value>
<value letter_id="R">-14</value>
<value letter_id="S">-38</value>
<value letter_id="T">-36</value>
<value letter_id="V">-330</value>
<value letter_id="W">-308</value>
<value letter_id="Y">213</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-126</value>
<value letter_id="C">-317</value>
<value letter_id="D">-22</value>
<value letter_id="E">-138</value>
<value letter_id="F">-359</value>
<value letter_id="G">161</value>
<value letter_id="H">-145</value>
<value letter_id="I">-365</value>
<value letter_id="K">111</value>
<value letter_id="L">-351</value>
<value letter_id="M">-285</value>
<value letter_id="N">263</value>
<value letter_id="P">-295</value>
<value letter_id="Q">61</value>
<value letter_id="R">57</value>
<value letter_id="S">-180</value>
<value letter_id="T">-40</value>
<value letter_id="V">-358</value>
<value letter_id="W">-334</value>
<value letter_id="Y">30</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-504</value>
<value letter_id="C">-338</value>
<value letter_id="D">-680</value>
<value letter_id="E">-657</value>
<value letter_id="F">-435</value>
<value letter_id="G">-730</value>
<value letter_id="H">-670</value>
<value letter_id="I">358</value>
<value letter_id="K">-638</value>
<value letter_id="L">-301</value>
<value letter_id="M">-329</value>
<value letter_id="N">-619</value>
<value letter_id="P">-651</value>
<value letter_id="Q">-625</value>
<value letter_id="R">-688</value>
<value letter_id="S">-608</value>
<value letter_id="T">-431</value>
<value letter_id="V">183</value>
<value letter_id="W">-604</value>
<value letter_id="Y">-540</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-375</value>
<value letter_id="C">-350</value>
<value letter_id="D">-353</value>
<value letter_id="E">-260</value>
<value letter_id="F">-432</value>
<value letter_id="G">-453</value>
<value letter_id="H">92</value>
<value letter_id="I">-73</value>
<value letter_id="K">78</value>
<value letter_id="L">8</value>
<value letter_id="M">-336</value>
<value letter_id="N">126</value>
<value letter_id="P">-393</value>
<value letter_id="Q">-146</value>
<value letter_id="R">331</value>
<value letter_id="S">-300</value>
<value letter_id="T">25</value>
<value letter_id="V">-401</value>
<value letter_id="W">169</value>
<value letter_id="Y">-356</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-141</value>
<value letter_id="C">71</value>
<value letter_id="D">-391</value>
<value letter_id="E">-356</value>
<value letter_id="F">-301</value>
<value letter_id="G">-464</value>
<value letter_id="H">-292</value>
<value letter_id="I">-37</value>
<value letter_id="K">-364</value>
<value letter_id="L">-95</value>
<value letter_id="M">-242</value>
<value letter_id="N">-377</value>
<value letter_id="P">-345</value>
<value letter_id="Q">-335</value>
<value letter_id="R">-339</value>
<value letter_id="S">-340</value>
<value letter_id="T">-198</value>
<value letter_id="V">324</value>
<value letter_id="W">-367</value>
<value letter_id="Y">-405</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-427</value>
<value letter_id="C">-326</value>
<value letter_id="D">-205</value>
<value letter_id="E">-342</value>
<value letter_id="F">-435</value>
<value letter_id="G">-167</value>
<value letter_id="H">-137</value>
<value letter_id="I">-419</value>
<value letter_id="K">-90</value>
<value letter_id="L">-491</value>
<value letter_id="M">-430</value>
<value letter_id="N">413</value>
<value letter_id="P">-402</value>
<value letter_id="Q">-257</value>
<value letter_id="R">-369</value>
<value letter_id="S">-82</value>
<value letter_id="T">104</value>
<value letter_id="V">-174</value>
<value letter_id="W">-370</value>
<value letter_id="Y">-378</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">90</value>
<value letter_id="C">244</value>
<value letter_id="D">-470</value>
<value letter_id="E">-413</value>
<value letter_id="F">-273</value>
<value letter_id="G">216</value>
<value letter_id="H">-322</value>
<value letter_id="I">-32</value>
<value letter_id="K">-387</value>
<value letter_id="L">-254</value>
<value letter_id="M">47</value>
<value letter_id="N">-22</value>
<value letter_id="P">-404</value>
<value letter_id="Q">-326</value>
<value letter_id="R">-390</value>
<value letter_id="S">71</value>
<value letter_id="T">-260</value>
<value letter_id="V">-77</value>
<value letter_id="W">-306</value>
<value letter_id="Y">-299</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-77</value>
<value letter_id="C">109</value>
<value letter_id="D">-418</value>
<value letter_id="E">-369</value>
<value letter_id="F">-36</value>
<value letter_id="G">-181</value>
<value letter_id="H">-284</value>
<value letter_id="I">189</value>
<value letter_id="K">-360</value>
<value letter_id="L">-111</value>
<value letter_id="M">-190</value>
<value letter_id="N">-363</value>
<value letter_id="P">-358</value>
<value letter_id="Q">-315</value>
<value letter_id="R">-344</value>
<value letter_id="S">-316</value>
<value letter_id="T">-206</value>
<value letter_id="V">271</value>
<value letter_id="W">-300</value>
<value letter_id="Y">-305</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">137</value>
<value letter_id="C">236</value>
<value letter_id="D">-421</value>
<value letter_id="E">-349</value>
<value letter_id="F">5</value>
<value letter_id="G">45</value>
<value letter_id="H">174</value>
<value letter_id="I">48</value>
<value letter_id="K">-323</value>
<value letter_id="L">-80</value>
<value letter_id="M">49</value>
<value letter_id="N">-28</value>
<value letter_id="P">-377</value>
<value letter_id="Q">-269</value>
<value letter_id="R">-333</value>
<value letter_id="S">64</value>
<value letter_id="T">-45</value>
<value letter_id="V">-168</value>
<value letter_id="W">-251</value>
<value letter_id="Y">34</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-83</value>
<value letter_id="C">-324</value>
<value letter_id="D">-360</value>
<value letter_id="E">-333</value>
<value letter_id="F">-415</value>
<value letter_id="G">-433</value>
<value letter_id="H">-306</value>
<value letter_id="I">-411</value>
<value letter_id="K">5</value>
<value letter_id="L">-394</value>
<value letter_id="M">-396</value>
<value letter_id="N">33</value>
<value letter_id="P">415</value>
<value letter_id="Q">-264</value>
<value letter_id="R">-344</value>
<value letter_id="S">-91</value>
<value letter_id="T">-305</value>
<value letter_id="V">-405</value>
<value letter_id="W">134</value>
<value letter_id="Y">-441</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-311</value>
<value letter_id="C">-323</value>
<value letter_id="D">-112</value>
<value letter_id="E">-361</value>
<value letter_id="F">-471</value>
<value letter_id="G">317</value>
<value letter_id="H">4</value>
<value letter_id="I">-490</value>
<value letter_id="K">-126</value>
<value letter_id="L">-226</value>
<value letter_id="M">-58</value>
<value letter_id="N">-257</value>
<value letter_id="P">-412</value>
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<value letter_id="F">-507</value>
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