<?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="14974" control_sequences="Primary sequences shuffled preserving 2-mers" control_count="0" control_positions="0">
<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">0.112</value>
<value letter_id="C">0.0116</value>
<value letter_id="D">0.0518</value>
<value letter_id="E">0.0549</value>
<value letter_id="F">0.036</value>
<value letter_id="G">0.0888</value>
<value letter_id="H">0.0178</value>
<value letter_id="I">0.0589</value>
<value letter_id="K">0.0527</value>
<value letter_id="L">0.0912</value>
<value letter_id="M">0.0255</value>
<value letter_id="N">0.0413</value>
<value letter_id="P">0.0407</value>
<value letter_id="Q">0.0306</value>
<value letter_id="R">0.0484</value>
<value letter_id="S">0.061</value>
<value letter_id="T">0.0574</value>
<value letter_id="V">0.0821</value>
<value letter_id="W">0.0103</value>
<value letter_id="Y">0.0266</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme -nsites 27 common/adh.s -oc results/meme45 -mod zoops -protein -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi </command_line>
<host>Timothys-Mac-Mini.local</host>
<type>zoops</type>
<nmotifs>2</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>Noise-injected 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>74865</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_positions>14974</num_positions>
<seed>0</seed>
<hsfrac>0.5</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="LGRVDVLVNNAG" alt="MEME-1" width="12" sites="27" ic="33.8" re="29.3" llr="549" p_value="3.1e-005" e_value="3.1e-005" bayes_threshold="8.9365" elapsed_time="0.234330">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-134</value>
<value letter_id="C">-166</value>
<value letter_id="D">-406</value>
<value letter_id="E">15</value>
<value letter_id="F">218</value>
<value letter_id="G">-55</value>
<value letter_id="H">-152</value>
<value letter_id="I">-22</value>
<value letter_id="K">-323</value>
<value letter_id="L">127</value>
<value letter_id="M">-155</value>
<value letter_id="N">-319</value>
<value letter_id="P">-36</value>
<value letter_id="Q">-270</value>
<value letter_id="R">-325</value>
<value letter_id="S">-267</value>
<value letter_id="T">77</value>
<value letter_id="V">-177</value>
<value letter_id="W">169</value>
<value letter_id="Y">260</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-190</value>
<value letter_id="C">-323</value>
<value letter_id="D">-302</value>
<value letter_id="E">-54</value>
<value letter_id="F">-472</value>
<value letter_id="G">320</value>
<value letter_id="H">-327</value>
<value letter_id="I">-491</value>
<value letter_id="K">-126</value>
<value letter_id="L">-227</value>
<value letter_id="M">-59</value>
<value letter_id="N">-259</value>
<value letter_id="P">-413</value>
<value letter_id="Q">-360</value>
<value letter_id="R">-350</value>
<value letter_id="S">-282</value>
<value letter_id="T">-398</value>
<value letter_id="V">-478</value>
<value letter_id="W">-364</value>
<value letter_id="Y">-416</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-269</value>
<value letter_id="C">-316</value>
<value letter_id="D">-24</value>
<value letter_id="E">-11</value>
<value letter_id="F">-357</value>
<value letter_id="G">48</value>
<value letter_id="H">-144</value>
<value letter_id="I">-362</value>
<value letter_id="K">145</value>
<value letter_id="L">-348</value>
<value letter_id="M">-281</value>
<value letter_id="N">-152</value>
<value letter_id="P">217</value>
<value letter_id="Q">-88</value>
<value letter_id="R">216</value>
<value letter_id="S">-42</value>
<value letter_id="T">84</value>
<value letter_id="V">-354</value>
<value letter_id="W">-330</value>
<value letter_id="Y">-278</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-487</value>
<value letter_id="C">153</value>
<value letter_id="D">-691</value>
<value letter_id="E">-631</value>
<value letter_id="F">6</value>
<value letter_id="G">-682</value>
<value letter_id="H">-546</value>
<value letter_id="I">174</value>
<value letter_id="K">-609</value>
<value letter_id="L">181</value>
<value letter_id="M">-263</value>
<value letter_id="N">-594</value>
<value letter_id="P">-604</value>
<value letter_id="Q">-537</value>
<value letter_id="R">-613</value>
<value letter_id="S">-553</value>
<value letter_id="T">-417</value>
<value letter_id="V">225</value>
<value letter_id="W">-463</value>
<value letter_id="Y">-458</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-403</value>
<value letter_id="C">-326</value>
<value letter_id="D">409</value>
<value letter_id="E">-104</value>
<value letter_id="F">-416</value>
<value letter_id="G">-264</value>
<value letter_id="H">-47</value>
<value letter_id="I">-425</value>
<value letter_id="K">-379</value>
<value letter_id="L">-458</value>
<value letter_id="M">-414</value>
<value letter_id="N">5</value>
<value letter_id="P">-445</value>
<value letter_id="Q">-307</value>
<value letter_id="R">-390</value>
<value letter_id="S">-320</value>
<value letter_id="T">-383</value>
<value letter_id="V">-440</value>
<value letter_id="W">-362</value>
<value letter_id="Y">-359</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-10</value>
<value letter_id="C">-172</value>
<value letter_id="D">-470</value>
<value letter_id="E">-398</value>
<value letter_id="F">-219</value>
<value letter_id="G">-51</value>
<value letter_id="H">-288</value>
<value letter_id="I">184</value>
<value letter_id="K">-369</value>
<value letter_id="L">30</value>
<value letter_id="M">50</value>
<value letter_id="N">-360</value>
<value letter_id="P">-387</value>
<value letter_id="Q">-308</value>
<value letter_id="R">-363</value>
<value letter_id="S">-303</value>
<value letter_id="T">-46</value>
<value letter_id="V">222</value>
<value letter_id="W">-262</value>
<value letter_id="Y">-253</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-421</value>
<value letter_id="C">-266</value>
<value letter_id="D">-504</value>
<value letter_id="E">-417</value>
<value letter_id="F">-36</value>
<value letter_id="G">-550</value>
<value letter_id="H">-339</value>
<value letter_id="I">2</value>
<value letter_id="K">-395</value>
<value letter_id="L">306</value>
<value letter_id="M">95</value>
<value letter_id="N">-432</value>
<value letter_id="P">-397</value>
<value letter_id="Q">-292</value>
<value letter_id="R">-364</value>
<value letter_id="S">-404</value>
<value letter_id="T">-128</value>
<value letter_id="V">-127</value>
<value letter_id="W">-291</value>
<value letter_id="Y">-315</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-208</value>
<value letter_id="C">-140</value>
<value letter_id="D">-389</value>
<value letter_id="E">-351</value>
<value letter_id="F">-74</value>
<value letter_id="G">-217</value>
<value letter_id="H">3</value>
<value letter_id="I">145</value>
<value letter_id="K">-353</value>
<value letter_id="L">-230</value>
<value letter_id="M">-218</value>
<value letter_id="N">-364</value>
<value letter_id="P">-340</value>
<value letter_id="Q">-320</value>
<value letter_id="R">-331</value>
<value letter_id="S">-326</value>
<value letter_id="T">-193</value>
<value letter_id="V">303</value>
<value letter_id="W">-331</value>
<value letter_id="Y">-348</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-238</value>
<value letter_id="C">-32</value>
<value letter_id="D">-218</value>
<value letter_id="E">-399</value>
<value letter_id="F">-362</value>
<value letter_id="G">-402</value>
<value letter_id="H">-64</value>
<value letter_id="I">-331</value>
<value letter_id="K">-305</value>
<value letter_id="L">-284</value>
<value letter_id="M">-356</value>
<value letter_id="N">437</value>
<value letter_id="P">-188</value>
<value letter_id="Q">-227</value>
<value letter_id="R">-345</value>
<value letter_id="S">-175</value>
<value letter_id="T">-261</value>
<value letter_id="V">-412</value>
<value letter_id="W">-285</value>
<value letter_id="Y">-134</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-285</value>
<value letter_id="C">-11</value>
<value letter_id="D">-224</value>
<value letter_id="E">-404</value>
<value letter_id="F">-370</value>
<value letter_id="G">-259</value>
<value letter_id="H">-72</value>
<value letter_id="I">-340</value>
<value letter_id="K">-312</value>
<value letter_id="L">-431</value>
<value letter_id="M">-364</value>
<value letter_id="N">440</value>
<value letter_id="P">-372</value>
<value letter_id="Q">-234</value>
<value letter_id="R">-352</value>
<value letter_id="S">-120</value>
<value letter_id="T">-265</value>
<value letter_id="V">-418</value>
<value letter_id="W">-293</value>
<value letter_id="Y">-334</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">295</value>
<value letter_id="C">-130</value>
<value letter_id="D">-466</value>
<value letter_id="E">-425</value>
<value letter_id="F">-400</value>
<value letter_id="G">-307</value>
<value letter_id="H">-399</value>
<value letter_id="I">-377</value>
<value letter_id="K">-427</value>
<value letter_id="L">-401</value>
<value letter_id="M">-340</value>
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</scanned_sites_summary>
</MEME>
