<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Begin document body -->
<fimo version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>fimo --max-stored-scores 10000000000 --oc FIMO-CIS-BP-Hydra_magnipapillata-Aiptasia_pallida-1.1 /oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/motif_databases.12.18/CIS-BP/Hydra_magnipapillata.meme /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.1/sequence/GCA_001417965.1_Aiptasia_genome_1.1_genomic.fa</command-line>
<settings>
<setting name="output directory">FIMO-CIS-BP-Hydra_magnipapillata-Aiptasia_pallida-1.1</setting>
<setting name="MEME file name">/oak/stanford/groups/akundaje/marinovg/programs/meme-5.0.5/motif_databases.12.18/CIS-BP/Hydra_magnipapillata.meme</setting>
<setting name="sequence file name">/oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.1/sequence/GCA_001417965.1_Aiptasia_genome_1.1_genomic.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">true</setting>
<setting name="output threshold">0.0001</setting>
<setting name="threshold type">p-value</setting>
<setting name="max stored scores">-2147483648</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">2</setting>
</settings>
<sequence-data num-sequences="4312" num-residues="256132296" />
<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="M0104_1.02" alt="(XP_002160328.1)_(Mus_musculus)_(DBD_0.73)" width="11" best-possible-match="ATATTAATTAA"/>
<motif name="M0300_1.02" alt="(XP_002159178.1)_(Mus_musculus)_(DBD_0.71)" width="10" best-possible-match="AATGACGTCA"/>
<motif name="M0304_1.02" alt="(XP_002164910.1)_(Mus_musculus)_(DBD_0.56)" width="10" best-possible-match="ATTACGTAAT"/>
<motif name="M0305_1.02" alt="(XP_002160519.1)_(Mus_musculus)_(DBD_0.61)" width="9" best-possible-match="GCCACGTGT"/>
<motif name="M0319_1.02" alt="(XP_002162729.1)_(Mus_musculus)_(DBD_0.90)" width="10" best-possible-match="TATGACGTAA"/>
<motif name="M0402_1.02" alt="(XP_002166590.1)_(Mus_musculus)_(DBD_0.85)" width="10" best-possible-match="AGGGGGCGGG"/>
<motif name="M0405_1.02" alt="(XP_002170242.1)_(Mus_musculus)_(DBD_0.90)" width="10" best-possible-match="TGGGCGTGGC"/>
<motif name="M0424_1.02" alt="(XP_002162096.1)_(Mus_musculus)_(DBD_0.71)" width="10" best-possible-match="TTTGACAGCT"/>
<motif name="M0630_1.02" alt="(XP_002158720.1)_(Homo_sapiens)_(DBD_0.85)" width="10" best-possible-match="AATGTATCAA"/>
<motif name="M0711_1.02" alt="(XP_002153910.1)_(Tetraodon_nigroviridis)_(DBD_0.51)" width="8" best-possible-match="CCGGAAGT"/>
<motif name="M0728_1.02" alt="(XP_002158068.1)_(Mus_musculus)_(DBD_0.59)" width="12" best-possible-match="AATAAACAAACA"/>
<motif name="M0733_1.02" alt="(XP_002167754.1)_(Mus_musculus)_(DBD_0.66)" width="8" best-possible-match="GTAAACAA"/>
<motif name="M0736_1.02" alt="(XP_002157478.1)_(Mus_musculus)_(DBD_0.81)" width="8" best-possible-match="GTAAACAA"/>
<motif name="M0737_1.02" alt="(XP_002166230.1)_(Mus_musculus)_(DBD_0.62)" width="10" best-possible-match="TATGTAAACA"/>
<motif name="M0756_1.02" alt="(XP_002156863.1)_(Strongylocentrotus_purpuratus)_(DBD_0.65)" width="9" best-possible-match="GTAAACAAA"/>
<motif name="M0907_1.02" alt="(XP_002159502.1)_(Mus_musculus)_(DBD_0.82)" width="9" best-possible-match="TTAATTACC"/>
<motif name="M0928_1.02" alt="(XP_002162903.1)_(Mus_musculus)_(DBD_0.72)" width="7" best-possible-match="TAATTAG"/>
<motif name="M0943_1.02" alt="(XP_002163599.1)_(Mus_musculus)_(DBD_0.91)" width="8" best-possible-match="GCTAATTA"/>
<motif name="M0970_1.02" alt="(XP_002158205.1)_(Mus_musculus)_(DBD_0.70)" width="9" best-possible-match="TTAATCCCC"/>
<motif name="M0972_1.02" alt="(XP_002156720.1)_(Mus_musculus)_(DBD_0.70)" width="8" best-possible-match="TTAATTAA"/>
<motif name="M1000_1.02" alt="(XP_002160816.1)_(Mus_musculus)_(DBD_0.86)" width="8" best-possible-match="TTAATTAG"/>
<motif name="M1016_1.02" alt="(XP_002162399.1)_(Mus_musculus)_(DBD_0.86)" width="7" best-possible-match="GTGATAC"/>
<motif name="M1024_1.02" alt="(XP_002153848.1)_(Mus_musculus)_(DBD_0.81)" width="9" best-possible-match="ATAATTGCC"/>
<motif name="M1097_1.02" alt="(XP_002156835.1)_(Drosophila_melanogaster)_(DBD_0.72)" width="10" best-possible-match="ATTAATTAAT"/>
<motif name="M1205_1.02" alt="(XP_002164563.1)_(Nematostella_vectensis)_(DBD_0.79)" width="8" best-possible-match="CTAATTAC"/>
<motif name="M1499_1.02" alt="(XP_002155904.1)_(Danio_rerio)_(DBD_0.78)" width="10" best-possible-match="CAGTCAAGCG"/>
<motif name="M1528_1.02" alt="(XP_002167174.1)_(Mus_musculus)_(DBD_0.58)" width="10" best-possible-match="CCATGGCAAC"/>
<motif name="M1529_1.02" alt="(XP_002167798.1)_(Mus_musculus)_(DBD_0.55)" width="10" best-possible-match="CCATAGCAAC"/>
<motif name="M1539_1.02" alt="XP_002157607.1" width="10" best-possible-match="CCATGGCAAC"/>
<motif name="M1837_1.02" alt="(XP_002165633.1)_(Mus_musculus)_(DBD_0.75)" width="11" best-possible-match="AAACCACAGAC"/>
<motif name="M1936_1.02" alt="(XP_002159483.1)_(Homo_sapiens)_(DBD_0.74)" width="15" best-possible-match="CTGGACTTTGAACTC"/>
<motif name="M2003_1.02" alt="(XP_002155267.1)_(Drosophila_melanogaster)_(DBD_0.70)" width="7" best-possible-match="TTAATTA"/>
<motif name="M2017_1.02" alt="(XP_002168027.1)_(Drosophila_melanogaster)_(DBD_0.81)" width="7" best-possible-match="TAATTAA"/>
<motif name="M2041_1.02" alt="(XP_002166749.1)_(Drosophila_melanogaster)_(DBD_0.85)" width="5" best-possible-match="AAACA"/>
<motif name="M2042_1.02" alt="(XP_002157088.1)_(Drosophila_melanogaster)_(DBD_0.82)" width="6" best-possible-match="TAATCC"/>
<motif name="M2269_1.02" alt="(XP_002159031.1)_(Mus_musculus)_(DBD_0.74)" width="11" best-possible-match="CTAATCCTCTT"/>
<motif name="M2276_1.02" alt="(XP_002170865.1)_(Mus_musculus)_(DBD_0.68)" width="11" best-possible-match="ACAGGAAGTGG"/>
<motif name="M2283_1.02" alt="(XP_002164110.1)_(Homo_sapiens)_(DBD_0.69)" width="15" best-possible-match="CAAAAGTAAACAAAG"/>
<motif name="M2289_1.02" alt="(XP_002157179.1)_(Homo_sapiens)_(DBD_0.59)" width="13" best-possible-match="AAGATGATGTCAT"/>
<motif name="M2302_1.02" alt="(XP_002156512.1)_(Mus_musculus)_(DBD_0.72)" width="11" best-possible-match="AGCCACTCAAG"/>
<motif name="M2317_1.02" alt="(XP_002153906.1)_(Mus_musculus)_(DBD_0.81)" width="11" best-possible-match="AACAGCTGCAG"/>
<motif name="M4466_1.02" alt="(XP_002156532.1)_(Homo_sapiens)_(DBD_0.92)" width="15" best-possible-match="ATGCCAAAAATAGAA"/>
<motif name="M4477_1.02" alt="(XP_002156545.1)_(Homo_sapiens)_(DBD_0.96)" width="19" best-possible-match="CTATGGCCATATAAGGCAA"/>
<motif name="M4481_1.02" alt="(XP_002162281.1)_(Homo_sapiens)_(DBD_0.68)" width="15" best-possible-match="GGTCACGTGGCCCGG"/>
<motif name="M4537_1.02" alt="(XP_002154174.1)_(Homo_sapiens)_(DBD_0.94)" width="15" best-possible-match="GGCGGGAAATTTGAA"/>
<motif name="M4577_1.02" alt="(XP_002164692.1)_(Homo_sapiens)_(DBD_0.96)" width="18" best-possible-match="CATGCCCATATAAGGCAA"/>
<motif name="M4616_1.02" alt="(XP_002155290.1)_(Homo_sapiens)_(DBD_0.89)" width="20" best-possible-match="TGCGTGGGCGGGGGGGGGGG"/>
<motif name="M4674_1.02" alt="(XP_002159183.1)_(Drosophila_melanogaster)_(DBD_0.83)" width="18" best-possible-match="ATTTTGTGATAAGGGGGT"/>
<motif name="M4702_1.02" alt="(XP_002159396.1)_(Homo_sapiens)_(DBD_0.86)" width="8" best-possible-match="TGACCTTT"/>
<motif name="M4708_1.02" alt="(XP_002160884.1)_(Homo_sapiens)_(DBD_0.92)" width="10" best-possible-match="TATGCAAATA"/>
<motif name="M4951_1.02" alt="(XP_002163608.1)_(Drosophila_melanogaster)_(DBD_0.89)" width="8" best-possible-match="CCGGAAAT"/>
<motif name="M4952_1.02" alt="(XP_002166140.1)_(Drosophila_melanogaster)_(DBD_0.80)" width="11" best-possible-match="ACCGGAAGTAC"/>
<motif name="M5000_1.02" alt="(XP_002163595.1)_(Drosophila_melanogaster)_(DBD_0.88)" width="8" best-possible-match="GTTAATTA"/>
<motif name="M5043_1.02" alt="(XP_002155451.1)_(Drosophila_melanogaster)_(DBD_0.79)" width="9" best-possible-match="TACTAATTA"/>
<motif name="M5133_1.02" alt="(XP_002153782.1)_(Drosophila_melanogaster)_(DBD_0.77)" width="12" best-possible-match="CAGCGGGGGGTC"/>
<motif name="M5191_1.02" alt="(XP_002156969.1)_(Drosophila_melanogaster)_(DBD_0.70)" width="9" best-possible-match="ATTTGATAC"/>
<motif name="M5743_1.02" alt="(XP_002158636.1)_(Homo_sapiens)_(DBD_0.88)" width="16" best-possible-match="ATGCATAATTAATGAG"/>
<motif name="M6139_1.02" alt="(XP_002161735.1)_(Homo_sapiens)_(DBD_0.76)" width="9" best-possible-match="GCACGCAAC"/>
<motif name="M6164_1.02" alt="(XP_002164912.1)_(Homo_sapiens)_(DBD_0.76)" width="25" best-possible-match="ACATAGTGACACCTAGGTGTGAAAT"/>
<motif name="M6207_1.02" alt="(XP_002161852.1)_(Homo_sapiens)_(DBD_0.59)" width="9" best-possible-match="ACCGGAAGT"/>
<motif name="M6208_1.02" alt="(XP_002161884.1)_(Homo_sapiens)_(DBD_0.50)" width="12" best-possible-match="CCCAGGAAGTGC"/>
<motif name="M6235_1.02" alt="(XP_002167983.1)_(Homo_sapiens)_(DBD_0.85)" width="15" best-possible-match="CTTAAGTAAACAATG"/>
<motif name="M6238_1.02" alt="(XP_002159677.1)_(Homo_sapiens)_(DBD_0.49)" width="11" best-possible-match="AAAATAAACAT"/>
<motif name="M6344_1.02" alt="(XP_002162967.1)_(Homo_sapiens)_(DBD_0.88)" width="13" best-possible-match="TGACAGCTGTCAA"/>
<motif name="M6345_1.02" alt="(XP_002158833.1)_(Homo_sapiens)_(DBD_0.73)" width="10" best-possible-match="ATCACATGAC"/>
<motif name="M6400_1.02" alt="(XP_002161581.1)_(Homo_sapiens)_(DBD_0.84)" width="8" best-possible-match="CTAATCCT"/>
<motif name="M6413_1.02" alt="(XP_002159231.1)_(Homo_sapiens)_(DBD_0.88)" width="15" best-possible-match="CCATCAATCAATTTA"/>
<motif name="M6463_1.02" alt="(XP_002160208.1)_(Homo_sapiens)_(DBD_0.83)" width="12" best-possible-match="AGCCTGTCTGCC"/>
<motif name="M6465_1.02" alt="(XP_002157279.1)_(Homo_sapiens)_(DBD_0.76)" width="10" best-possible-match="GTGTCTGGCC"/>
<motif name="M6466_1.02" alt="(XP_002161797.1)_(Homo_sapiens)_(DBD_0.89)" width="9" best-possible-match="TGTCTGGCC"/>
<motif name="M6537_1.02" alt="(XP_002154000.1)_(Homo_sapiens)_(DBD_0.87)" width="11" best-possible-match="GGGGATTGGCC"/>
<motif name="M6549_1.02" alt="(XP_002159358.1)_(Homo_sapiens)_(DBD_0.72)" width="9" best-possible-match="GGGGTGGTC"/>
<background source="--nrdb--">
<value letter="A">0.275</value>
<value letter="C">0.225</value>
<value letter="G">0.225</value>
<value letter="T">0.275</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>
