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    <!--{help/}-->
    <div class="pop_content wide" id="pop_discr">
      <dl>
        <dt>Classic mode</dt>
        <dd>
        <p>You provide <b>one</b> set of sequences MEME-ChIP reports motifs enriched
        in this set.
        MEME discovers motifs enriched relative to a random model based on
        frequencies of the letters in your sequences, or relative to the frequencies
        given in a "background model" that you may provide (see "Universal options").
        STREME discovers motifs that are enriched in your sequences relative
        to a control set of sequences that STREME creates by shuffling each of your sequences, 
        conserving dinucleotide frequencies.
        CentriMo identifies motifs enriched in a central (or uncentered, see "CentriMo options")
        region relative to the flanking regions. 
        </p>
        </dd>
        <dt>Discriminative mode</dt>
        <dd>
        <p>You provide <b>two</b> sets of sequences and MEME-ChIP reports motifs that
        are enriched in the first (primary) set relative to the second (control) set.
	MEME motifs use the classic MEME objective function with a <a href="../doc/psp-format.html">position-specific prior</a> 
	created from the primary and control sequences using using <a href="../doc/psp-gen.html">psp-gen</a>.
        <b>Note:</b>The sequences in the primary and control sets should all be the <b>same length</b>.</p>
        </dd>
        <dt>Differential Enrichment mode</dt>
        <dd>
        <p>You provide <b>two</b> sets of sequences and MEME-ChIP discovers motifs that
        are enriched in the first (primary) set relative to the second (control) set.
        In Differential Enrichment mode, MEME motifs are discovered using an objective function based on the
        hypergeometric distribution to determine the relative enrichment of sites in the
        primary sequences compared to the control sequences.
        </p>
        </dd>
      </dl>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_sequences">
      <p>The primary sequences should all be the same length.  
      The recommended length for ChIP-seq sequences is <b>500 bp</b>
      centered on the summit (or center if the summit is not known) of a peak.
      MEME-ChIP works best with sequences no longer than 2000 bp.
      <br/> <br/>
      There may be at most <b>500,000 (primary) sequences</b>
      in <a href="../doc/fasta-format.html">FASTA format</a>.  There is also
      a limit of 80,000,000 bytes for the entire contents of the input form.
      <br/> <br/>
      MEME-ChIP can analyze peak regions identified by ChIP-seq, 
      cross-linking sites identified by CLIP-seq and related assays, 
      as well as sets of genomic regions selected using other criteria (e.g., TSSs of
      differentially expressed or bound genes).</p>
      <p>See the <a href="@SITE_URL@/doc/examples/example-datasets/Klf1.fna"
      >example DNA sequences</a> which were used to create the <a 
      href="../doc/examples/memechip_example_output_files/meme-chip.html">sample output</a>.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_control_sequences">
      <p>The control sequences should all be the same length as the primary sequences.  
      The recommended length for ChIP-seq sequences is <b>500 bp</b>
      centered on the summit (or center if the summit is not known) of a peak.
      MEME-ChIP works best with sequences no longer than 2000 bp.
      <br/> <br/>
      There may be at most <b>500,000 control sequences</b>
      in <a href="../doc/fasta-format.html">FASTA format</a>.  There is also
      a limit of 80,000,000 bytes for the entire contents of the input form.
      <br/> <br/>
      If the primary sequences are ChIP-seq peak regions from a 
      transcription factor ChIP-seq experiment, similar regions 
      from a knockout cell line or organism, are a possible choice 
      for control sequences. The control sequences should be prepared 
      in exactly the same way (e.g., repeat-masking) as the primary sequences.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_motifs">
      <p>MEME-ChIP will use this set of motifs for motif enrichment analysis
      and will also report if any motifs that it discovers in your sequences
      are similar to any motifs in this set.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_width">
      <p>This is the width (number of letters in the sequence pattern) of a
      single motif. MEME and STREME choose the optimal width of each motif individually
      using a statistical heuristic function. You can choose different limits
      for the minimum and maximum motif widths that MEME and STREME will consider. The
      width of each motif that MEME and STREME report will lie within the limits you
      choose.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_dna2rna">
      <p>When your sequences are in the DNA alphabet but you want
      them to be treated as single-stranded RNA, check this box.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_background">
      <p>The background model normalizes for biased distribution of 
      letters and groups of letters in your sequences.
      A 0-order model adjusts for single letter biases, a 1-order model adjusts for
      dimer biases (e.g., GC content in DNA sequences), etc.</p>
      <p>By default MEME-ChIP will determine the background Markov model from 
      the primary sequences (or from the control sequences if you provide them). 
      You may select a Markov model order of 0 to 4.
      Alternately you may select "Upload background model" and input a file containing
      a <a href="../doc/bfile-format.html">background model</a>.</p>
      <p>The downloadable version of the MEME Suite contains a program named
      "fasta-get-markov" that you can use to create background model files in
      the correct format from FASTA sequence files.</p>
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    </div>

    <div class="pop_content" style="width:500px" id="pop_meme_dist">
      <p>This is where you tell MEME how you believe occurrences of the motifs
      are distributed among the sequences. Selecting the correct type of
      distribution improves the sensitivity and quality of the motif search.</p>
      <dl>
        <dt>Zero or one occurrence per sequence</dt>
        <dd>MEME assumes that each sequence may contain <b>at most</b> one
        occurrence of each motif. This option is useful when you suspect that
        some motifs may be missing from some of the sequences. In that case, the
        motifs found will be more accurate than using the one occurrence per
        sequence option. This option takes more computer time than the one 
        occurrence per sequence option (about twice as much) and is slightly less
        sensitive to weak motifs present in all of the sequences.</dd>
        <dt>One occurrence per sequence</dt>
        <dd>MEME assumes that each sequence in the dataset contains
        <b>exactly</b> one occurrence of each motif. This option is the fastest
        and most sensitive but the motifs returned by MEME may be "blurry" if
        any of the sequences is missing them.</dd>
        <dt>Any number of repetitions</dt>
        <dd>MEME assumes each sequence may contain <b>any number</b> of
        non-overlapping occurrences of each motif. This option is useful when
        you suspect that motifs repeat multiple times within a single sequence.
        In that case, the motifs found will be much more accurate than using one
        of the other options. This option can also be used to discover repeats
        within a single sequence. This option takes much more computer time than
        the one occurrence per sequence option (about ten times as much) and is
        somewhat less sensitive to weak motifs which do not repeat within a
        single sequence than the other two options.</dd>
      </dl>
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    <div class="pop_content" id="pop_meme_nmotifs">
      <p>MEME will keep searching until it finds this many motifs or it hits
      some other threshold like the maximum run time. Note that MEME does not
      use an p-value threhold like STREME, so you should always check the E-value
      of any found motifs.</p>
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    </div>

    <div class="pop_content" style="width:500px" id="pop_meme_sites">
      <p>This is the total number of sites in the training set where a single
      motif occurs. You can choose different limits for the minimum and maximum
      number of occurrences that MEME will consider. If you have prior knowledge
      about the number of occurrences that motifs have in your training set,
      limiting MEME's search in this way can can increase the likelihood of
      MEME finding true motifs.</p>
      <p>MEME chooses the number of occurrences to report for each motif by
      optimizing a statistical heuristic function, restricting the number of
      occurrences to the range you give here, or using defaults described below
      if you leave these fields deselected.</p>
      <table>
      <tr><th>Distribution</th><th>Minimum</th><th>Maximum</th></tr>
      <tr><td>Zero or one occurrence per sequence</td><td>sqrt(n)</td><td>n</td></tr>
      <tr><td>One occurrence per sequence</td><td>n</td><td>n</td></tr>
      <tr><td>Any number of repetitions</td><td>sqrt(n)</td><td>min(5*n, 600)</td></tr>
      </table>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_meme_pal">
      <p>Checking this box causes MEME to search only for DNA palindromes. This
      causes MEME to average the letter frequencies in corresponding motif
      columns together. For instance, if the width of the motif is 10, columns
      1 and 10, 2 and 9, 3 and 8, etc., are averaged together. The averaging
      combines the frequency of A in one column with T in the other, and the
      frequency of C in one column with G in the other. If this box is not
      checked, the columns are not averaged together.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_meme_norand">
      <p>If your (primary) sequences are sorted in order of confidence (best to worst)
      then you should select this option.  This will cause MEME not to randomize
      the the order of the (primary) sequences before sampling starting points if 
      there are more than 1000 sequences.  See the 
      <a href="../doc/meme.html?doc_type=cmd#norand">MEME documentation</a> 
      for the <span class="popt">-norand</span> option for more details.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_streme_limits">
      <p>STREME stops looking for motifs when one of these limits is met. There
      is an additional time limit which is set by the server operator.</p>
      <dl>
        <dt><i>p</i>-value threshold</dt>
        <dd>STREME stops when three consecutive motifs are found whose <i>p</i>-values exceed
        this threshold.</dd>
        <dt>Number of motifs</dt>
        <dd>STREME stops if it has found this many motifs.  By default STREME
        does not limit the number of motifs to be found.</dd>
      </dl>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_centrimo_score">
      <p>Specify a minimum score for a match to be considered. If a sequence does
      not have any matches which meet this minimum score for a given motif, then
      that sequence will not be considered for that motif.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_centrimo_maxreg">
      <p>This option limits the maximum region size that CentriMo will test.
      This option is useful if your sequences are quite long (&gt; 500 bp) or
      you are interested only in narrow regions of enrichment.
      Limiting the size of the maximum region reduces the impact of the 
      multiple testing correction, increasing the sensitivity of the analysis. 
      When this option is not supplied CentriMo will test region sizes up to 
      one less than the maximum number of places that a given motif can align to 
      the sequence.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_centrimo_ethresh">
      <p>This is the E-value threshold CentriMo uses for reporting enriched
      central regions for motifs. If multiple enriched regions overlap then the region
      with the best <i>p</i>-value and smallest size will be output.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_centrimo_local">
      <p>This option causes all regions up to the maximum region size to be
      considered even if they are not in the center. This can be useful when
      your sequences are aligned on a genomic landmark (e.g., TSS) since
      a motif might be enriched at a particular distance upstream or downstream
      of the landmark.
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_centrimo_store_ids">
      <p>This option causes CentriMo to store the identifiers (IDs) of sequences 
      that have their best match in the most enriched region for each motif. This will
      allow you to easily extract the IDs of the sequences contributing to
      the enrichment of one or more motifs in the CentriMo output. This option 
      makes the CentriMo output file much larger.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="content_box">
      <!--{header}-->
      <p>
      <!--{title}-->MEME-ChIP<!--{/title}--> - <!--{subtitle}-->Motif Analysis of Large Nucleotide Datasets<!--{/subtitle}--><br>
      <!--{logo}-->../doc/images/memechip_icon.png<!--{/logo}-->: <!--{alt}-->MEME-ChIP Logo<!--{/alt}--><br>
      <!--{blurb}--><span class="blurb" data-id="memechip"></span><!--{/blurb}-->
      </p>
      <!--{/header}-->
      <form enctype="multipart/form-data" accept-charset="utf-8"
      method="POST" action="meme-chip" id="memechip_form">
        <fieldset>
          <legend>Data Submission Form</legend>
          <p class="meme">Perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.</p> 
          <!-- mode -->
          <h2 class="meme">Select the motif discovery and enrichment mode <div class="help" data-topic="pop_discr"></div></h2>
          <div class="subcontent">
            <input type="radio" name="disc_mode" id="classic" value="classic" checked>
            <label for="classic">Classic mode</label>
            <input type="radio" name="disc_mode" id="psp" value="psp">
            <label for="psp">Discriminative mode</label>
            <input type="radio" name="disc_mode" id="de" value="de">
            <label for="de">Differential Enrichment mode</label>
          </div>
          <!-- /mode -->

          <!--{alphabet}-->
          <p style="border: 1px solid black">
          <!--{prefix}-->alphabet<!--{/prefix}--><br>
          <!--{description}-->sequence alphabet<!--{/description}-->
          <!--{register}-->register_component<!--{/register}-->
          </p>
          <!--{/alphabet}-->

          <!--{sequences}-->
          <p style="border: 1px solid black">
          <!--{prefix}-->sequences<!--{/prefix}-->
          <!--{title}-->Input the primary sequences<!--{/title}-->
          <!--{subtitle}-->Enter the (equal-length) nucleotide sequences to be analyzed.<!--{/subtitle}-->
          <!--{default}-->FILE<!--{/default}-->
          <!--{max_seq_count}-->500000<!--{/max_seq_count}-->
          <!--{max_seq_total}-->80000000<!--{/max_seq_total}-->
          <!--{register}-->register_component<!--{/register}-->
          <!--{/sequences}-->
          </p>

          <div id="discr_sequences_area" style="display:none">
          <!--{control}-->
          <p style="border: 1px solid black">
          <!--{prefix}-->control_sequences<!--{/prefix}--><br>
          <!--{description}-->control sequences<!--{/description}-->
          <!--{title}-->Input the control sequences<!--{/title}--><br>
          <!--{subtitle}-->MEME-ChIP will find motifs that are enriched relative to these sequences.<!--{/subtitle}--><br>
          <!--{default}-->FILE<!--{/default}-->
          <!--{max_seq_count}-->500000<!--{/max_seq_count}-->
          <!--{max_seq_total}-->80000000<!--{/max_seq_total}-->
          <!--{register}-->register_component<!--{/register}-->
          </p>
          <!--{/control}-->
          </div>

          <div id="dna2rna_area" style="display:none">
            <p>
	    <h3 class="meme top">Convert DNA sequences to RNA?
              &nbsp;<img src="../images/new_icon.png" alt="NEW" id="new_3"></h3>
	    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<input type="checkbox" value="1" id="dna2rna" name="dna2rna">
	    <label for="dna2rna">Convert DNA to RNA</label>
	    <div class="help" data-topic="pop_dna2rna"></div>
            </p>
          </div>

          <!--{motifs}-->
          <!--{prefix}-->motifs<!--{/prefix}-->
          <!--{title}-->Input the motifs<!--{/title}-->
          <!--{subtitle}-->Select, upload or enter a set of known motifs.<!--{/subtitle}-->
          <!--{alphabets}-->DNA RNA<!--{/alphabets}-->
          <!--{default}-->DATABASE<!--{/default}-->
          <!--{enable_db/}-->
          <!--{register}-->register_component<!--{/register}-->
          <!--{/motifs}-->

          <!--{job_details/}-->

	  <!-- Advanced Options -->
          <div style="margin-top:5px; margin-bottom: 5px; width:80%;">

	  <!--{universal_opts}-->
	    <!--{prefix}-->universal_opts<!--{/prefix}-->
            <!--{title}-->Universal options &nbsp;<img src='../images/new_icon.png' alt='NEW' id='new_4'><!--{/title}-->
	    <!--{change_fn}-->general_changed<!--{/change_fn}-->
	    <!--{reset_fn}-->general_reset<!--{/reset_fn}-->
	  <!--{/universal_opts}-->
	  <div>
	    <!--{bfile}-->
	      <!--{prefix}-->background<!--{/prefix}-->
	      <!--{alphabets}-->DNA<!--{/alphabets}-->
	      <!--{enable_zero_order/}-->
	      <!--{enable_first_order/}-->
	      <!--{enable_high_order/}-->
	      <!--{enable_upload/}-->
	      <!--{selected}-->high<!--{/selected}-->
	      <!--{register}-->register_component<!--{/register}-->
	    <!--{/bfile}-->

            <h3 class="meme">What width motifs should MEME and STREME find?
              &nbsp;<img src="../images/new_icon.png" alt="NEW" id="new_1"></h3>
            <span class="pad">
            <label for="minw">Minimum width:</label>
            <input class="meme intonly sz2" type="number" name="minw" value="6"
            step="1" min="3" max="30" size="2" id="minw">
            </span>
            <label for="maxw">Maximum width:</label>
            <input class="meme intonly sz2" type="number" name="maxw" value="15"
            step="1" min="3" max="30"  size="2" id="maxw">
            <div class="help" data-topic="pop_width"></div>
	  </div>

          <!--{meme_opts}-->
            <!--{prefix}-->meme_opts<!--{/prefix}-->
            <!--{title}-->MEME options<!--{/title}-->
            <!--{change_fn}-->meme_changed<!--{/change_fn}-->
            <!--{reset_fn}-->meme_reset<!--{/reset_fn}-->
          <!--{/meme_opts}-->
          <div>
            <h3 class="meme top">What is the expected motif site distribution?</h3>
            <select class="meme" name="meme_dist" id="meme_dist">
              <option value="zoops" selected><b>Zero or one</b> occurrence per sequence</option>
              <option value="oops" ><b>One</b> occurrence per sequence</option>
              <option value="anr" ><b>Any number</b> of repetitions</option>
            </select> 
            <div class="help" data-topic="pop_meme_dist"></div>

            <h3 class="meme">How many motifs should MEME find?</h3>
            <label for="meme_nmotifs">Number of motifs:</label>
            <input class="meme intonly sz3" type="number" name="meme_nmotifs" value="3"
            step="1" min="0" size="2" id="meme_nmotifs">
            <div class="help" data-topic="pop_meme_nmotifs"></div>

            <div id="meme_sites">
              <h3 class="meme">How many sites per motif is acceptable?</h3>
              <span class="enabopt pad">
              <input type="checkbox" value="1" name="meme_minsites_enable" id="meme_minsites_enable">
              <label for="meme_minsites">Minimum sites:</label>
              <input class="meme intonly sz2" type="number" id="meme_minsites" 
              name="meme_minsites" value="2" step="1" min="2" max="600" size="2">
              </span>
              <span class="enabopt">
              <input type="checkbox" value="1" name="meme_maxsites_enable" id="meme_maxsites_enable">
              <label for="meme_maxsites">Maximum sites:</label>
              <input class="meme intonly sz3" type="number" id="meme_maxsites" 
              name="meme_maxsites" value="600" step="1" min="2" max="600" size="3">
              </span>
              <div class="help" data-topic="pop_meme_sites"></div>
            </div>
            
            <h3 class="meme">Should MEME restrict the search to palindromes?</h3>
            <input class="meme" type="checkbox" name="meme_pal" value="1" id="meme_pal">
            <label for="meme_pal">Look for palindromes only.</label>
            <div class="help" data-topic="pop_meme_pal"></div>

            <h3 class="meme">Should MEME randomize the sequence order?</h3>
            <input type="checkbox" value="1" id="meme_norand" name="meme_norand">
            <label for="meme_norand">Don't randomize sequence order before sampling starting points.</label>
            <div class="help" data-topic="pop_meme_norand"></div>

          </div>

          <!--{streme_opts}-->
            <!--{prefix}-->streme_opts<!--{/prefix}-->
            <!--{title}-->STREME options &nbsp;<img src='../images/new_icon.png' alt='NEW' id='new_2'><!--{/title}-->
            <!--{change_fn}-->streme_changed<!--{/change_fn}-->
            <!--{reset_fn}-->streme_reset<!--{/reset_fn}-->
          <!--{/streme_opts}-->
          <div>
            <h3 class="meme top">How should STREME limit its search?</h3>
            <span class="selectopt pad">
              <input type="radio" name="streme_srch_limit" id="streme_enable_pthresh" value="streme_enable_pthresh" checked>
              <label for="streme_pthresh"><i>p</i>-value &le;</label>
              <input class="meme numonly sz4" type="text" name="streme_pthresh" id="streme_pthresh" value="0.05" step="any" min="0" size="4">
              <input type="radio" name="streme_srch_limit" id="streme_enable_nmotifs" value="streme_enable_nmotifs">
              <label for="streme_nmotifs">Number of motifs:</label>
              <input class="meme intonly sz2" type="number" name="streme_nmotifs" id="streme_nmotifs" value="5" step="1" min="0" size="2">
            </span>
            <div class="help" data-topic="pop_streme_limits"></div>
          </div>
          <!--{centrimo_opts}-->
            <!--{prefix}-->centrimo_opts<!--{/prefix}-->
            <!--{title}-->CentriMo options<!--{/title}-->
            <!--{change_fn}-->centrimo_changed<!--{/change_fn}-->
            <!--{reset_fn}-->centrimo_reset<!--{/reset_fn}-->
          <!--{/centrimo_opts}-->
          <div>
            <h3 class="meme">What is the threshold for a motif match (bits)?</h3>
            <label for="centrimo_score">Score &ge;</label>
            <input class="meme numonly sz3" type="text" id="centrimo_score"
            name="centrimo_score" size="3" value="5" step="any">
            <div class="help" data-topic="pop_centrimo_score"></div>

            <h3 class="meme">What is the maximum allowed width of an enriched region?</h3>
            <span class="enabopt">
            <input type="checkbox" value="1" name="centrimo_maxreg_enable" id="centrimo_maxreg_enable">
            <label for="centrimo_maxreg">Region width &le;</label>
            <input class="meme intonly sz5" type="number" id="centrimo_maxreg"
            name="centrimo_maxreg" value="200" step="1" min="1" size="5">
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            <h3 class="meme">What is the <i>E</i>-value threshold for an enriched region?</h3>
            <label for="centrimo_ethresh"><i>E</i>-value &le;</label>
            <input class="meme numonly sz5" type="text" id="centrimo_ethresh"
            name="centrimo_ethresh" value="10" step="any" min="0.00000001" size="5">
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            <h3 class="meme">Should CentriMo find non-central enriched regions?</h3>
            <input type="checkbox" value="1" name="centrimo_local" id="centrimo_local">
            <label for="centrimo_local">Run CentriMo in local mode to find non-central enriched regions.</label>
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            <h3 class="meme">Should CentriMo output include the IDs of sequences with a motif match?</h3>
            <input type="checkbox" value="1" name="centrimo_store_ids" id="centrimo_store_ids" checked>
            <label for="centrimo_store_ids">Include a list of matching sequence IDs for each enriched motif.</label>
            <div class="help" data-topic="pop_centrimo_store_ids"></div>
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