<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Begin document body -->
<fimo version="5.5.1" release="Sun Jan 29 10:33:12 2023 -0800">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>fimo results/meme.txt nostoc.fa</command-line>
<settings>
<setting name="output directory">fimo_out</setting>
<setting name="MEME file name">results/meme.txt</setting>
<setting name="sequence file name">nostoc.fa</setting>
<setting name="background file name">--nrdb--</setting>
<setting name="allow clobber">true</setting>
<setting name="compute q-values">true</setting>
<setting name="parse genomic coord.">false</setting>
<setting name="text only">false</setting>
<setting name="scan both strands">false</setting>
<setting name="output threshold">0.0001</setting>
<setting name="threshold type">p-value</setting>
<setting name="max stored scores">100000</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">2</setting>
</settings>
<sequence-data num-sequences="85" num-residues="37805" />
<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>
<motif name="FGEBTVPY" alt="MEME-1" width="8" best-possible-match="FGEDTVPY"/>
<motif name="YRHLLGRA" alt="MEME-2" width="8" best-possible-match="YRHLLGRA"/>
<motif name="ISVREFVR" alt="MEME-3" width="8" best-possible-match="ISVREFVR"/>
<motif name="ALIDSVEY" alt="MEME-4" width="8" best-possible-match="ALIDSVEY"/>
<background source="--nrdb--">
<value letter="A">0.073</value>
<value letter="C">0.018</value>
<value letter="D">0.052</value>
<value letter="E">0.062</value>
<value letter="F">0.040</value>
<value letter="G">0.069</value>
<value letter="H">0.022</value>
<value letter="I">0.056</value>
<value letter="K">0.058</value>
<value letter="L">0.092</value>
<value letter="M">0.023</value>
<value letter="N">0.046</value>
<value letter="P">0.051</value>
<value letter="Q">0.041</value>
<value letter="R">0.052</value>
<value letter="S">0.074</value>
<value letter="T">0.059</value>
<value letter="V">0.064</value>
<value letter="W">0.013</value>
<value letter="Y">0.033</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>
