<?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/farntrans5.s" primary_count="5" primary_positions="1900" control_sequences="--none--" 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="RAM1_YEAST" length="431" weight="1.000000" />
<sequence id="sequence_1" name="PFTB_RAT" length="437" weight="1.000000" />
<sequence id="sequence_2" name="BET2_YEAST" length="325" weight="1.000000" />
<sequence id="sequence_3" name="RATRABGERB" length="331" weight="1.000000" />
<sequence id="sequence_4" name="CAL1_YEAST" length="376" weight="1.000000" />
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.0611</value>
<value letter_id="C">0.0368</value>
<value letter_id="D">0.0616</value>
<value letter_id="E">0.0605</value>
<value letter_id="F">0.0437</value>
<value letter_id="G">0.0753</value>
<value letter_id="H">0.03</value>
<value letter_id="I">0.0526</value>
<value letter_id="K">0.0505</value>
<value letter_id="L">0.114</value>
<value letter_id="M">0.0205</value>
<value letter_id="N">0.0337</value>
<value letter_id="P">0.0411</value>
<value letter_id="Q">0.0384</value>
<value letter_id="R">0.0405</value>
<value letter_id="S">0.0779</value>
<value letter_id="T">0.0458</value>
<value letter_id="V">0.0574</value>
<value letter_id="W">0.0179</value>
<value letter_id="Y">0.0411</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme common/farntrans5.s -oc results/meme13 -mod oops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi </command_line>
<host>Timothys-Mac-Mini.local</host>
<type>oops</type>
<nmotifs>2</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>E-value of product of p-values</object_function>
<spfun>E-value of product of p-values</spfun>
<min_width>8</min_width>
<max_width>50</max_width>
<wg>11</wg>
<ws>1</ws>
<endgaps>yes</endgaps>
<substring>yes</substring>
<minsites>5</minsites>
<maxsites>5</maxsites>
<wnsites>0.8</wnsites>
<spmap>pam</spmap>
<spfuzz>120</spfuzz>
<prior>dmix</prior>
<beta>0</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_positions>1900</num_positions>
<seed>0</seed>
<hsfrac>0</hsfrac>
<searchsize>1900</searchsize>
<maxsize>0</maxsize>
<norand>no</norand>
<csites>1000</csites>
<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">0.0609</value>
<value letter_id="C">0.037</value>
<value letter_id="D">0.0615</value>
<value letter_id="E">0.0604</value>
<value letter_id="F">0.0437</value>
<value letter_id="G">0.075</value>
<value letter_id="H">0.0302</value>
<value letter_id="I">0.0526</value>
<value letter_id="K">0.0505</value>
<value letter_id="L">0.113</value>
<value letter_id="M">0.0208</value>
<value letter_id="N">0.0339</value>
<value letter_id="P">0.0411</value>
<value letter_id="Q">0.0385</value>
<value letter_id="R">0.0406</value>
<value letter_id="S">0.0776</value>
<value letter_id="T">0.0458</value>
<value letter_id="V">0.0573</value>
<value letter_id="W">0.0182</value>
<value letter_id="Y">0.0411</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="EGGFQGRPNKLPDVCYSFWV" alt="MEME-1" width="20" sites="5" ic="71.7" re="71.2" llr="247" p_value="3.9e-043" e_value="2.3e-030" bayes_threshold="8.49185" elapsed_time="0.166056">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-174</value>
<value letter_id="C">-549</value>
<value letter_id="D">101</value>
<value letter_id="E">341</value>
<value letter_id="F">-468</value>
<value letter_id="G">-299</value>
<value letter_id="H">-249</value>
<value letter_id="I">-379</value>
<value letter_id="K">-137</value>
<value letter_id="L">-418</value>
<value letter_id="M">-292</value>
<value letter_id="N">-106</value>
<value letter_id="P">-278</value>
<value letter_id="Q">-80</value>
<value letter_id="R">-220</value>
<value letter_id="S">24</value>
<value letter_id="T">-207</value>
<value letter_id="V">-314</value>
<value letter_id="W">-499</value>
<value letter_id="Y">-405</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-159</value>
<value letter_id="C">-414</value>
<value letter_id="D">-264</value>
<value letter_id="E">-305</value>
<value letter_id="F">-433</value>
<value letter_id="G">350</value>
<value letter_id="H">-327</value>
<value letter_id="I">-413</value>
<value letter_id="K">-255</value>
<value letter_id="L">-492</value>
<value letter_id="M">-331</value>
<value letter_id="N">-164</value>
<value letter_id="P">-347</value>
<value letter_id="Q">-318</value>
<value letter_id="R">10</value>
<value letter_id="S">-242</value>
<value letter_id="T">-294</value>
<value letter_id="V">-356</value>
<value letter_id="W">-392</value>
<value letter_id="Y">-408</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-176</value>
<value letter_id="C">-427</value>
<value letter_id="D">-286</value>
<value letter_id="E">-332</value>
<value letter_id="F">-447</value>
<value letter_id="G">358</value>
<value letter_id="H">-350</value>
<value letter_id="I">-433</value>
<value letter_id="K">-298</value>
<value letter_id="L">-511</value>
<value letter_id="M">-353</value>
<value letter_id="N">-188</value>
<value letter_id="P">-360</value>
<value letter_id="Q">-351</value>
<value letter_id="R">-277</value>
<value letter_id="S">-261</value>
<value letter_id="T">-315</value>
<value letter_id="V">-375</value>
<value letter_id="W">-406</value>
<value letter_id="Y">-425</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-295</value>
<value letter_id="C">-345</value>
<value letter_id="D">-493</value>
<value letter_id="E">-448</value>
<value letter_id="F">386</value>
<value letter_id="G">-479</value>
<value letter_id="H">-353</value>
<value letter_id="I">-101</value>
<value letter_id="K">-421</value>
<value letter_id="L">103</value>
<value letter_id="M">-36</value>
<value letter_id="N">-379</value>
<value letter_id="P">-389</value>
<value letter_id="Q">-380</value>
<value letter_id="R">-389</value>
<value letter_id="S">-376</value>
<value letter_id="T">-313</value>
<value letter_id="V">-158</value>
<value letter_id="W">-218</value>
<value letter_id="Y">-95</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-108</value>
<value letter_id="C">135</value>
<value letter_id="D">-103</value>
<value letter_id="E">-92</value>
<value letter_id="F">-294</value>
<value letter_id="G">-198</value>
<value letter_id="H">-86</value>
<value letter_id="I">-250</value>
<value letter_id="K">-50</value>
<value letter_id="L">-292</value>
<value letter_id="M">-163</value>
<value letter_id="N">312</value>
<value letter_id="P">-221</value>
<value letter_id="Q">296</value>
<value letter_id="R">-75</value>
<value letter_id="S">-115</value>
<value letter_id="T">-99</value>
<value letter_id="V">-213</value>
<value letter_id="W">-328</value>
<value letter_id="Y">-256</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-176</value>
<value letter_id="C">-427</value>
<value letter_id="D">-286</value>
<value letter_id="E">-332</value>
<value letter_id="F">-447</value>
<value letter_id="G">358</value>
<value letter_id="H">-350</value>
<value letter_id="I">-433</value>
<value letter_id="K">-298</value>
<value letter_id="L">-511</value>
<value letter_id="M">-353</value>
<value letter_id="N">-188</value>
<value letter_id="P">-360</value>
<value letter_id="Q">-351</value>
<value letter_id="R">-277</value>
<value letter_id="S">-261</value>
<value letter_id="T">-315</value>
<value letter_id="V">-375</value>
<value letter_id="W">-406</value>
<value letter_id="Y">-425</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-313</value>
<value letter_id="C">-372</value>
<value letter_id="D">-445</value>
<value letter_id="E">-422</value>
<value letter_id="F">-458</value>
<value letter_id="G">-408</value>
<value letter_id="H">-222</value>
<value letter_id="I">-384</value>
<value letter_id="K">-97</value>
<value letter_id="L">-421</value>
<value letter_id="M">-338</value>
<value letter_id="N">-267</value>
<value letter_id="P">-326</value>
<value letter_id="Q">-213</value>
<value letter_id="R">447</value>
<value letter_id="S">-368</value>
<value letter_id="T">-328</value>
<value letter_id="V">-436</value>
<value letter_id="W">-331</value>
<value letter_id="Y">-424</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-63</value>
<value letter_id="C">97</value>
<value letter_id="D">-195</value>
<value letter_id="E">61</value>
<value letter_id="F">-293</value>
<value letter_id="G">-240</value>
<value letter_id="H">-195</value>
<value letter_id="I">-245</value>
<value letter_id="K">-109</value>
<value letter_id="L">-282</value>
<value letter_id="M">-182</value>
<value letter_id="N">-111</value>
<value letter_id="P">361</value>
<value letter_id="Q">-114</value>
<value letter_id="R">-134</value>
<value letter_id="S">40</value>
<value letter_id="T">-105</value>
<value letter_id="V">-195</value>
<value letter_id="W">-363</value>
<value letter_id="Y">-300</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-188</value>
<value letter_id="C">-396</value>
<value letter_id="D">-78</value>
<value letter_id="E">72</value>
<value letter_id="F">-356</value>
<value letter_id="G">-209</value>
<value letter_id="H">-114</value>
<value letter_id="I">-319</value>
<value letter_id="K">-131</value>
<value letter_id="L">-393</value>
<value letter_id="M">-266</value>
<value letter_id="N">416</value>
<value letter_id="P">-262</value>
<value letter_id="Q">-129</value>
<value letter_id="R">-176</value>
<value letter_id="S">44</value>
<value letter_id="T">-137</value>
<value letter_id="V">-306</value>
<value letter_id="W">-374</value>
<value letter_id="Y">-308</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-318</value>
<value letter_id="C">-451</value>
<value letter_id="D">-472</value>
<value letter_id="E">-400</value>
<value letter_id="F">-523</value>
<value letter_id="G">-459</value>
<value letter_id="H">-377</value>
<value letter_id="I">-378</value>
<value letter_id="K">416</value>
<value letter_id="L">-489</value>
<value letter_id="M">-351</value>
<value letter_id="N">-290</value>
<value letter_id="P">-406</value>
<value letter_id="Q">-335</value>
<value letter_id="R">-3</value>
<value letter_id="S">-426</value>
<value letter_id="T">-332</value>
<value letter_id="V">-427</value>
<value letter_id="W">-439</value>
<value letter_id="Y">-479</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-275</value>
<value letter_id="C">-363</value>
<value letter_id="D">-497</value>
<value letter_id="E">-397</value>
<value letter_id="F">107</value>
<value letter_id="G">-473</value>
<value letter_id="H">-349</value>
<value letter_id="I">-47</value>
<value letter_id="K">-357</value>
<value letter_id="L">273</value>
<value letter_id="M">40</value>
<value letter_id="N">-362</value>
<value letter_id="P">-358</value>
<value letter_id="Q">-288</value>
<value letter_id="R">-300</value>
<value letter_id="S">-390</value>
<value letter_id="T">-255</value>
<value letter_id="V">-107</value>
<value letter_id="W">-288</value>
<value letter_id="Y">-248</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">110</value>
<value letter_id="C">-266</value>
<value letter_id="D">-305</value>
<value letter_id="E">-241</value>
<value letter_id="F">-261</value>
<value letter_id="G">-248</value>
<value letter_id="H">-272</value>
<value letter_id="I">-112</value>
<value letter_id="K">-216</value>
<value letter_id="L">-236</value>
<value letter_id="M">-143</value>
<value letter_id="N">-212</value>
<value letter_id="P">334</value>
<value letter_id="Q">-208</value>
<value letter_id="R">-214</value>
<value letter_id="S">-157</value>
<value letter_id="T">-116</value>
<value letter_id="V">217</value>
<value letter_id="W">-356</value>
<value letter_id="Y">-320</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-291</value>
<value letter_id="C">-459</value>
<value letter_id="D">383</value>
<value letter_id="E">-92</value>
<value letter_id="F">-417</value>
<value letter_id="G">-370</value>
<value letter_id="H">-283</value>
<value letter_id="I">-390</value>
<value letter_id="K">-349</value>
<value letter_id="L">-461</value>
<value letter_id="M">-350</value>
<value letter_id="N">-37</value>
<value letter_id="P">-416</value>
<value letter_id="Q">-318</value>
<value letter_id="R">-335</value>
<value letter_id="S">-325</value>
<value letter_id="T">-328</value>
<value letter_id="V">-362</value>
<value letter_id="W">-427</value>
<value letter_id="Y">-393</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-22</value>
<value letter_id="C">-224</value>
<value letter_id="D">-301</value>
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[EDS][GR]G[FL][NQC]GR[PCES][NES]K[LF][PVA]D[GVT]CY[SA][FW]W[VCQ]
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</motif>
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<scanned_sites sequence_id="sequence_3" pvalue="2.71e-44" num_sites="4"><scanned_site motif_id="motif_2" strand="none" position="76" pvalue="5.22e-05"/>
<scanned_site motif_id="motif_1" strand="none" position="129" pvalue="5.77e-05"/>
<scanned_site motif_id="motif_1" strand="none" position="225" pvalue="4.66e-22"/>
<scanned_site motif_id="motif_2" strand="none" position="269" pvalue="5.81e-30"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_4" pvalue="4.35e-30" num_sites="2"><scanned_site motif_id="motif_1" strand="none" position="273" pvalue="6.15e-20"/>
<scanned_site motif_id="motif_2" strand="none" position="320" pvalue="7.81e-18"/>
</scanned_sites>
</scanned_sites_summary>
</MEME>
