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PlantAI-dev/.tmp_meme_parallel_test_out/meme.xml
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potaser f745ee9d7e Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00

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<?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,
min_width,
max_width,
minic,
wg,
ws,
endgaps,
minsites,
maxsites,
wnsites,
prob,
spmap,
spfuzz,
prior,
beta,
maxiter,
distance,
num_sequences,
num_positions,
seed,
seqfrac,
strands,
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 min_width (#PCDATA)*>
<!ELEMENT max_width (#PCDATA)*>
<!ELEMENT minic (#PCDATA)*>
<!ELEMENT wg (#PCDATA)*>
<!ELEMENT ws (#PCDATA)*>
<!ELEMENT endgaps (#PCDATA)*>
<!ELEMENT minsites (#PCDATA)*>
<!ELEMENT maxsites (#PCDATA)*>
<!ELEMENT wnsites (#PCDATA)*>
<!ELEMENT prob (#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 seqfrac (#PCDATA)*>
<!ELEMENT strands (#PCDATA)*>
<!ELEMENT priors_file (#PCDATA)*>
<!ELEMENT reason_for_stopping (#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
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="4.11.2" release="Mon Oct 24 12:27:06 2016 -0700">
<training_set datafile="/data/project_roots/PlantAI-dev/.tmp_meme_parallel_test.fa" length="4">
<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="seq1" length="42" weight="1.000000" />
<sequence id="sequence_1" name="seq2" length="42" weight="1.000000" />
<sequence id="sequence_2" name="seq3" length="42" weight="1.000000" />
<sequence id="sequence_3" name="seq4" length="42" weight="1.000000" />
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.048</value>
<value letter_id="C">0.000</value>
<value letter_id="D">0.071</value>
<value letter_id="E">0.000</value>
<value letter_id="F">0.071</value>
<value letter_id="G">0.024</value>
<value letter_id="H">0.048</value>
<value letter_id="I">0.095</value>
<value letter_id="K">0.071</value>
<value letter_id="L">0.048</value>
<value letter_id="M">0.024</value>
<value letter_id="N">0.024</value>
<value letter_id="P">0.024</value>
<value letter_id="Q">0.119</value>
<value letter_id="R">0.048</value>
<value letter_id="S">0.071</value>
<value letter_id="T">0.048</value>
<value letter_id="V">0.024</value>
<value letter_id="W">0.048</value>
<value letter_id="Y">0.095</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme /data/project_roots/PlantAI-dev/.tmp_meme_parallel_test.fa -mod anr -protein -nmotifs 1 -minw 6 -maxw 12 -oc /data/project_roots/PlantAI-dev/.tmp_meme_parallel_test_out -nostatus </command_line>
<host>xialab-System-Product-Name</host>
<type>anr</type>
<nmotifs>1</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>E-value of product of p-values</object_function>
<use_llr>0</use_llr>
<min_width>6</min_width>
<max_width>12</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>pam</spmap>
<spfuzz>120</spfuzz>
<prior>megap</prior>
<beta>840</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_sequences>4</num_sequences>
<num_positions>168</num_positions>
<seed>0</seed>
<ctfrac>-1</ctfrac>
<maxwords>-1</maxwords>
<strands>none</strands>
<priors_file>prior30.plib</priors_file>
<reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
<background_frequencies source="dataset with add-one prior applied">
<alphabet_array>
<value letter_id="A">0.048</value>
<value letter_id="C">0.005</value>
<value letter_id="D">0.069</value>
<value letter_id="E">0.005</value>
<value letter_id="F">0.069</value>
<value letter_id="G">0.027</value>
<value letter_id="H">0.048</value>
<value letter_id="I">0.090</value>
<value letter_id="K">0.069</value>
<value letter_id="L">0.048</value>
<value letter_id="M">0.027</value>
<value letter_id="N">0.027</value>
<value letter_id="P">0.027</value>
<value letter_id="Q">0.112</value>
<value letter_id="R">0.048</value>
<value letter_id="S">0.069</value>
<value letter_id="T">0.048</value>
<value letter_id="V">0.027</value>
<value letter_id="W">0.048</value>
<value letter_id="Y">0.090</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="1" width="11" sites="12" ic="33.7" re="30.2" llr="251" e_value="5.1e-031" bayes_threshold="4.9542" elapsed_time="0.024795">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-180</value>
<value letter_id="C">-169</value>
<value letter_id="D">-198</value>
<value letter_id="E">145</value>
<value letter_id="F">-461</value>
<value letter_id="G">-128</value>
<value letter_id="H">258</value>
<value letter_id="I">-507</value>
<value letter_id="K">-175</value>
<value letter_id="L">-328</value>
<value letter_id="M">-368</value>
<value letter_id="N">-28</value>
<value letter_id="P">-278</value>
<value letter_id="Q">132</value>
<value letter_id="R">-178</value>
<value letter_id="S">204</value>
<value letter_id="T">-224</value>
<value letter_id="V">-259</value>
<value letter_id="W">-580</value>
<value letter_id="Y">-435</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-270</value>
<value letter_id="C">-225</value>
<value letter_id="D">-495</value>
<value letter_id="E">-44</value>
<value letter_id="F">-606</value>
<value letter_id="G">-278</value>
<value letter_id="H">-423</value>
<value letter_id="I">-563</value>
<value letter_id="K">-180</value>
<value letter_id="L">-386</value>
<value letter_id="M">-438</value>
<value letter_id="N">-277</value>
<value letter_id="P">-387</value>
<value letter_id="Q">-416</value>
<value letter_id="R">371</value>
<value letter_id="S">-351</value>
<value letter_id="T">265</value>
<value letter_id="V">-323</value>
<value letter_id="W">-650</value>
<value letter_id="Y">-597</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-311</value>
<value letter_id="C">-224</value>
<value letter_id="D">-491</value>
<value letter_id="E">112</value>
<value letter_id="F">-576</value>
<value letter_id="G">-354</value>
<value letter_id="H">-237</value>
<value letter_id="I">-540</value>
<value letter_id="K">-405</value>
<value letter_id="L">-298</value>
<value letter_id="M">-296</value>
<value letter_id="N">-274</value>
<value letter_id="P">-332</value>
<value letter_id="Q">305</value>
<value letter_id="R">-308</value>
<value letter_id="S">-398</value>
<value letter_id="T">-379</value>
<value letter_id="V">-334</value>
<value letter_id="W">-581</value>
<value letter_id="Y">-622</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-205</value>
<value letter_id="C">-170</value>
<value letter_id="D">213</value>
<value letter_id="E">120</value>
<value letter_id="F">-516</value>
<value letter_id="G">349</value>
<value letter_id="H">-370</value>
<value letter_id="I">169</value>
<value letter_id="K">-337</value>
<value letter_id="L">-326</value>
<value letter_id="M">-394</value>
<value letter_id="N">-55</value>
<value letter_id="P">-319</value>
<value letter_id="Q">-439</value>
<value letter_id="R">-362</value>
<value letter_id="S">-230</value>
<value letter_id="T">-263</value>
<value letter_id="V">-181</value>
<value letter_id="W">-664</value>
<value letter_id="Y">-544</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-226</value>
<value letter_id="C">-115</value>
<value letter_id="D">-510</value>
<value letter_id="E">-107</value>
<value letter_id="F">-170</value>
<value letter_id="G">-281</value>
<value letter_id="H">-334</value>
<value letter_id="I">170</value>
<value letter_id="K">-442</value>
<value letter_id="L">-165</value>
<value letter_id="M">-243</value>
<value letter_id="N">-290</value>
<value letter_id="P">-371</value>
<value letter_id="Q">-521</value>
<value letter_id="R">-389</value>
<value letter_id="S">206</value>
<value letter_id="T">-288</value>
<value letter_id="V">-81</value>
<value letter_id="W">-355</value>
<value letter_id="Y">178</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-377</value>
<value letter_id="C">-179</value>
<value letter_id="D">-645</value>
<value letter_id="E">-233</value>
<value letter_id="F">319</value>
<value letter_id="G">-450</value>
<value letter_id="H">-500</value>
<value letter_id="I">-241</value>
<value letter_id="K">-597</value>
<value letter_id="L">263</value>
<value letter_id="M">-125</value>
<value letter_id="N">-465</value>
<value letter_id="P">-443</value>
<value letter_id="Q">-625</value>
<value letter_id="R">-523</value>
<value letter_id="S">-501</value>
<value letter_id="T">-424</value>
<value letter_id="V">-128</value>
<value letter_id="W">-446</value>
<value letter_id="Y">-306</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-171</value>
<value letter_id="C">-152</value>
<value letter_id="D">203</value>
<value letter_id="E">172</value>
<value letter_id="F">-495</value>
<value letter_id="G">-190</value>
<value letter_id="H">-420</value>
<value letter_id="I">-351</value>
<value letter_id="K">-341</value>
<value letter_id="L">-283</value>
<value letter_id="M">-355</value>
<value letter_id="N">-154</value>
<value letter_id="P">361</value>
<value letter_id="Q">-428</value>
<value letter_id="R">-358</value>
<value letter_id="S">-256</value>
<value letter_id="T">-265</value>
<value letter_id="V">341</value>
<value letter_id="W">-653</value>
<value letter_id="Y">-558</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-212</value>
<value letter_id="C">-220</value>
<value letter_id="D">201</value>
<value letter_id="E">232</value>
<value letter_id="F">-496</value>
<value letter_id="G">-183</value>
<value letter_id="H">-306</value>
<value letter_id="I">-438</value>
<value letter_id="K">211</value>
<value letter_id="L">251</value>
<value letter_id="M">-315</value>
<value letter_id="N">-87</value>
<value letter_id="P">-284</value>
<value letter_id="Q">-292</value>
<value letter_id="R">-104</value>
<value letter_id="S">-245</value>
<value letter_id="T">-239</value>
<value letter_id="V">-217</value>
<value letter_id="W">-589</value>
<value letter_id="Y">-490</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-269</value>
<value letter_id="C">-221</value>
<value letter_id="D">-585</value>
<value letter_id="E">-253</value>
<value letter_id="F">-436</value>
<value letter_id="G">-293</value>
<value letter_id="H">-549</value>
<value letter_id="I">-658</value>
<value letter_id="K">-599</value>
<value letter_id="L">-457</value>
<value letter_id="M">-542</value>
<value letter_id="N">-412</value>
<value letter_id="P">-435</value>
<value letter_id="Q">-680</value>
<value letter_id="R">-533</value>
<value letter_id="S">221</value>
<value letter_id="T">-413</value>
<value letter_id="V">-382</value>
<value letter_id="W">375</value>
<value letter_id="Y">-441</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-222</value>
<value letter_id="C">-148</value>
<value letter_id="D">-357</value>
<value letter_id="E">92</value>
<value letter_id="F">-296</value>
<value letter_id="G">-238</value>
<value letter_id="H">256</value>
<value letter_id="I">162</value>
<value letter_id="K">-147</value>
<value letter_id="L">-160</value>
<value letter_id="M">-233</value>
<value letter_id="N">-171</value>
<value letter_id="P">-321</value>
<value letter_id="Q">132</value>
<value letter_id="R">-139</value>
<value letter_id="S">-291</value>
<value letter_id="T">-252</value>
<value letter_id="V">-115</value>
<value letter_id="W">-462</value>
<value letter_id="Y">-314</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-452</value>
<value letter_id="C">-230</value>
<value letter_id="D">-587</value>
<value letter_id="E">-209</value>
<value letter_id="F">222</value>
<value letter_id="G">-415</value>
<value letter_id="H">-290</value>
<value letter_id="I">-491</value>
<value letter_id="K">-540</value>
<value letter_id="L">-276</value>
<value letter_id="M">-379</value>
<value letter_id="N">346</value>
<value letter_id="P">-456</value>
<value letter_id="Q">-571</value>
<value letter_id="R">-449</value>
<value letter_id="S">-468</value>
<value letter_id="T">-457</value>
<value letter_id="V">-302</value>
<value letter_id="W">-299</value>
<value letter_id="Y">190</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="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.333333</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.333333</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.333333</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.666667</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.333333</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">1.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.333333</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.333333</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.333333</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.333333</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.333333</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.666667</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.333333</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.333333</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.333333</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.333333</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.333333</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.333333</value>
<value letter_id="L">0.333333</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.333333</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.666667</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.333333</value>
<value letter_id="I">0.333333</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.000000</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.333333</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="D">0.000000</value>
<value letter_id="E">0.000000</value>
<value letter_id="F">0.333333</value>
<value letter_id="G">0.000000</value>
<value letter_id="H">0.000000</value>
<value letter_id="I">0.000000</value>
<value letter_id="K">0.000000</value>
<value letter_id="L">0.000000</value>
<value letter_id="M">0.000000</value>
<value letter_id="N">0.333333</value>
<value letter_id="P">0.000000</value>
<value letter_id="Q">0.000000</value>
<value letter_id="R">0.000000</value>
<value letter_id="S">0.000000</value>
<value letter_id="T">0.000000</value>
<value letter_id="V">0.000000</value>
<value letter_id="W">0.000000</value>
<value letter_id="Y">0.333333</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[HQS][RT]Q[DGI][ISY][FL][DPV][DKL][WS][HIQ][FNY]
</regular_expression>
<contributing_sites>
<contributing_site sequence_id="sequence_3" position="30" strand="none" pvalue="8.89e-12" >
<left_flank>RQDILDLWIY</left_flank>
<site>
<letter_ref letter_id="H"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="Y"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="P"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="N"/>
</site>
<right_flank>Y</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_2" position="30" strand="none" pvalue="8.89e-12" >
<left_flank>RQDILDLWIY</left_flank>
<site>
<letter_ref letter_id="H"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="Y"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="P"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="N"/>
</site>
<right_flank>Y</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_1" position="30" strand="none" pvalue="8.89e-12" >
<left_flank>RQDILDLWIY</left_flank>
<site>
<letter_ref letter_id="H"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="Y"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="P"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="N"/>
</site>
<right_flank>Y</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_0" position="30" strand="none" pvalue="8.89e-12" >
<left_flank>RQDILDLWIY</left_flank>
<site>
<letter_ref letter_id="H"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="Y"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="P"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="N"/>
</site>
<right_flank>Y</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_3" position="8" strand="none" pvalue="5.96e-10" >
<left_flank>MKTAYIAK</left_flank>
<site>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="V"/>
<letter_ref letter_id="K"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="H"/>
<letter_ref letter_id="F"/>
</site>
<right_flank>SRQDILDLWI</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_2" position="8" strand="none" pvalue="5.96e-10" >
<left_flank>MKTAYIAK</left_flank>
<site>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="V"/>
<letter_ref letter_id="K"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="H"/>
<letter_ref letter_id="F"/>
</site>
<right_flank>SRQDILDLWI</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_1" position="8" strand="none" pvalue="5.96e-10" >
<left_flank>MKTAYIAK</left_flank>
<site>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="V"/>
<letter_ref letter_id="K"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="H"/>
<letter_ref letter_id="F"/>
</site>
<right_flank>SRQDILDLWI</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_0" position="8" strand="none" pvalue="5.96e-10" >
<left_flank>MKTAYIAK</left_flank>
<site>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="F"/>
<letter_ref letter_id="V"/>
<letter_ref letter_id="K"/>
<letter_ref letter_id="S"/>
<letter_ref letter_id="H"/>
<letter_ref letter_id="F"/>
</site>
<right_flank>SRQDILDLWI</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_3" position="19" strand="none" pvalue="7.58e-10" >
<left_flank>RQISFVKSHF</left_flank>
<site>
<letter_ref letter_id="S"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="Y"/>
</site>
<right_flank>HTQGYFPDWQ</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_2" position="19" strand="none" pvalue="7.58e-10" >
<left_flank>RQISFVKSHF</left_flank>
<site>
<letter_ref letter_id="S"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="Y"/>
</site>
<right_flank>HTQGYFPDWQ</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_1" position="19" strand="none" pvalue="7.58e-10" >
<left_flank>RQISFVKSHF</left_flank>
<site>
<letter_ref letter_id="S"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="Y"/>
</site>
<right_flank>HTQGYFPDWQ</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_0" position="19" strand="none" pvalue="7.58e-10" >
<left_flank>RQISFVKSHF</left_flank>
<site>
<letter_ref letter_id="S"/>
<letter_ref letter_id="R"/>
<letter_ref letter_id="Q"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="D"/>
<letter_ref letter_id="L"/>
<letter_ref letter_id="W"/>
<letter_ref letter_id="I"/>
<letter_ref letter_id="Y"/>
</site>
<right_flank>HTQGYFPDWQ</right_flank>
</contributing_site>
</contributing_sites>
</motif>
</motifs>
<scanned_sites_summary p_thresh="0.0001">
<scanned_sites sequence_id="sequence_0" pvalue="2.84e-10" num_sites="3"><scanned_site motif_id="motif_1" strand="none" position="8" pvalue="5.96e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="19" pvalue="7.58e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="30" pvalue="8.89e-12"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_1" pvalue="2.84e-10" num_sites="3"><scanned_site motif_id="motif_1" strand="none" position="8" pvalue="5.96e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="19" pvalue="7.58e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="30" pvalue="8.89e-12"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_2" pvalue="2.84e-10" num_sites="3"><scanned_site motif_id="motif_1" strand="none" position="8" pvalue="5.96e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="19" pvalue="7.58e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="30" pvalue="8.89e-12"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_3" pvalue="2.84e-10" num_sites="3"><scanned_site motif_id="motif_1" strand="none" position="8" pvalue="5.96e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="19" pvalue="7.58e-10"/>
<scanned_site motif_id="motif_1" strand="none" position="30" pvalue="8.89e-12"/>
</scanned_sites>
</scanned_sites_summary>
</MEME>
Reference in New Issue View Git Blame Copy Permalink