--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_test2.xml	Thu May 17 14:10:48 2018 -0400
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Begin document body -->
+<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
+>
+<command-line>fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa</command-line>
+<settings>
+<setting name="output directory">fimo_test2_out</setting>
+<setting name="MEME file name">dreme_fimo_input_1.xml</setting>
+<setting name="sequence file name">hsa_chrM.fa</setting>
+<setting name="background file name">fimo_background_probs_hsa_chrM.txt</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">true</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="1" num-residues="16569" />
+<alphabet name="DNA" like="dna">
+<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
+<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
+<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
+<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
+<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
+<letter id="V" symbol="V" equals="ACG" name="Not T"/>
+<letter id="H" symbol="H" equals="ACT" name="Not G"/>
+<letter id="D" symbol="D" equals="AGT" name="Not C"/>
+<letter id="B" symbol="B" equals="CGT" name="Not A"/>
+<letter id="M" symbol="M" equals="AC" name="Amino"/>
+<letter id="R" symbol="R" equals="AG" name="Purine"/>
+<letter id="W" symbol="W" equals="AT" name="Weak"/>
+<letter id="S" symbol="S" equals="CG" name="Strong"/>
+<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
+<letter id="K" symbol="K" equals="GT" name="Keto"/>
+</alphabet>
+<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/>
+<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/>
+<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/>
+<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/>
+<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/>
+<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/>
+<background source="fimo_background_probs_hsa_chrM.txt">
+<value letter="A">0.278</value>
+<value letter="C">0.222</value>
+<value letter="G">0.222</value>
+<value letter="T">0.278</value>
+</background>
+<cisml-file>cisml.xml</cisml-file>
+</fimo>