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<h1 style="line-height: 1.15; margin-top: 20px;">Multiple Comparative Genome Viewer</h1>
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MCGV is a graphical display for whole genome multiple sequence alignments.
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Currently you are viewing
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<span id="descr_epo33" class="about_details">a eutherian mammals EPO alignment from <a class="usa-link" target="_blank" href="https://mart.ensembl.org/info/genome/compara/mlss.html?mlss=2072">Ensembl</a>. </span>
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<span id="descr_primates8" class="about_details">an eight-way primate alignment from <a class="usa-link" target="_blank" href="https://cglgenomics.ucsc.edu/february-2024-t2t-apes/">NHGRI</a>. </span>
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<label for="chroms">Navigate to a chromosome on anchor assembly human GRCh38.p14</label>
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Chromosome overview of aligned assemblies
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Sequence conservation
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<div style="padding-bottom:1px;"><i>Not available at this zoom level. Zoom in below 1Mbp to view sequence conservation.</i></div>
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<span>Chromosome name</span>
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Assembly alignments
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S12.9,2.9,9.3,2.9z M10,5.7v2.9h2.9V10H10v2.9H8.6V10H5.7V8.6h2.9V5.7H10z"></path>
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|
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<li class="usa-button-group__item" style="margin-left:0;">
|
||
<button class="zoomOut usa-button usa-button--outline mcgv-btn" title="Zoom out (control + mouse wheel)" disabled>
|
||
<svg viewBox="-3 -4 30 30" height="28">
|
||
<path fill="currentColor" d="M17.9,15.7h-1.1l-0.4-0.4c1.4-1.6,2.2-3.7,2.2-6c0-5.1-4.2-9.3-9.3-9.3S0,4.2,0,9.3s4.2,9.3,9.3,9.3
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||
c2.3,0,4.4-0.8,6-2.2l0.4,0.4v1.1l7.1,7.1l2.1-2.1L17.9,15.7z M9.3,15.7c-3.6,0-6.4-2.9-6.4-6.4s2.9-6.4,6.4-6.4s6.4,2.9,6.4,6.4
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||
S12.9,15.7,9.3,15.7z M5.7,8.6h7.1V10H5.7V8.6z"></path>
|
||
</svg>
|
||
</button>
|
||
</li>
|
||
<li class="usa-button-group__item" style="margin-right:0;">
|
||
<button class="panLeft usa-button usa-button--outline mcgv-btn" title="Pan left" disabled>
|
||
<svg viewBox="-2 -4 30 30" height="28">
|
||
<path fill="currentColor" d="M0,12.5L13.5,0v7.1H25v10.7H13.5V25L0,12.5z"></path>
|
||
</svg>
|
||
</button>
|
||
</li>
|
||
<li class="usa-button-group__item" style="margin-left:0;">
|
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<button class="panRight usa-button usa-button--outline mcgv-btn" title="Pan right" disabled>
|
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<svg viewBox="-2 -4 30 30" height="28">
|
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<path fill="currentColor" d="M25,12.5L11.5,25v-7.1H0V7.1h11.5V0L25,12.5z"></path>
|
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|
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|
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|
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<li style="display:inline;margin-left:auto;margin-right:auto;margin-top:20px;">
|
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<div class="usa-radio" style="display:inline;">
|
||
<input class="coloration usa-radio__input" type="radio" id="identityColor" name="coloration" value="0" checked="">
|
||
<label class="coloration usa-radio__label" for="identityColor">Color by Identity</label>
|
||
</div>
|
||
<div class="usa-radio" style="display:inline;">
|
||
<input class="coloration usa-radio__input" type="radio" id="orientationColor" name="coloration" value="1">
|
||
<label class="coloration usa-radio__label" for="orientationColor">Color by Orientation</label>
|
||
</div>
|
||
<div class="usa-checkbox" style="display:inline;">
|
||
<input class="showLegend usa-checkbox__input" type="checkbox" id="showLegend"/>
|
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<label class="showLegend usa-checkbox__label" for="showLegend">Show legend</label>
|
||
</div>
|
||
</li>
|
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<li style="display:inline;margin-top:20px;margin-right: 50px;font-size:15px; font-weight:400;line-height: 17.58px;font-family:'Roboto'">
|
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<div class="legend-subcont">
|
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<svg class="usa-icon" aria-hidden="true" focusable="false" role="img" style="width:24px;height:24px; margin-right:7px">
|
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<use xlink:href="/mcgv/static/django_uswds/uswds/img/sprite.svg#filter_list"></use>
|
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</svg>
|
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<!-- hack to trigger the opening of the modal from a button, but display a link-->
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<a href="#filter-modal" class="usa-button hidden-filter-btn" style="display:none;" aria-controls="filter-modal" data-open-modal>Placeholder</a>
|
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<a href="#" class="usa-link" style="display: inline;cursor: pointer;" onclick="MCGV.showFilterDialog(event)">Filter assemblies</a>
|
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</div>
|
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</li>
|
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<li style="display:inline-flex;justify-content: center; align-items: flex-end;margin-top:20px;font-size:15px; font-weight:400;line-height: 17.58px;font-family:'Roboto';">
|
||
<p style="margin-bottom: 3px;">Showing <span class="alnNumber"></span> assemblies <a class="usa-link cgv-navbtn" style="cursor:pointer;">Show all</a></p>
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|
||
</ul>
|
||
</div>
|
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<div id="colorLegend" class="usa-row usa-button-group" style="border-top:1px solid #D6D7D9;height:45px;display:none;">
|
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<div class="coloration-legend">
|
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<div style="display:inherit;">
|
||
<div class="legend-subcont" style="padding-right:40px;">
|
||
<p style="font-size:16px;margin: 0 15px;"><b>% Identity</b></p>
|
||
<div class="legend-rect-long" style="background-color:#112E51;"></div><div class="legend-tick"></div>
|
||
<div class="legend-ctext">95</div>
|
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<div class="legend-rect-long" style="background-color:#205493;"></div><div class="legend-tick"></div>
|
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<div class="legend-ctext">90</div>
|
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<div class="legend-rect-long" style="background-color:#0071BC;"></div><div class="legend-tick"></div>
|
||
<div class="legend-ctext">75</div>
|
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<div class="legend-rect-long" style="background-color:#00A6D2;"></div><div class="legend-tick"></div>
|
||
<div class="legend-ctext">50</div>
|
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<div class="legend-rect-long" style="background-color:#02BFE7;"></div><div class="legend-tick"></div>
|
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<div class="legend-ctext">25</div>
|
||
<div class="legend-rect-long" style="background-color:#9BDAF1;"></div>
|
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</div>
|
||
</div>
|
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<div style="display:inherit;">
|
||
<div class="legend-subcont">
|
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<div class="legend-rect" style="background-color:#989898"></div>
|
||
<p class="legend-text">Forward orientation</p>
|
||
</div>
|
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<div class="legend-subcont">
|
||
<div class="legend-rect" style="background-color:#54278F"></div>
|
||
<p class="legend-text">Reverse orientation</p>
|
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</div>
|
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</div>
|
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<div class="legend-subcont">
|
||
<div class="legend-rect" style="background-color:#D6D7D9"></div>
|
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<p style="margin: 0;">Unaligned anchor assembly region</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<table class="mcgv-aln" style="border-top: 4px solid #D6D7D9;border-bottom: 4px solid #D6D7D9;margin-bottom:0;font-family:'Roboto';">
|
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<thead id="mcgv-anchor"></thead></table>
|
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<div class="selector"><div></div></div>
|
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|
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style="margin: -39px 11px 0 -40px;min-width:fit-content;font-size:16px;position:fixed;">Unaligned region</span>
|
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|
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|
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</div>
|
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<table class="usa-table usa-table--borderless mcgv-aln" style="width:100%;font-size:16px;margin-top:-2px;font-family:'Roboto';overflow:hidden;">
|
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|
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|
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<div class="infobox ncbi-popup popup-arrow" id="chrInfo">
|
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|
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|
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aria-label="Close this window" style="background-color:inherit;margin:0;">✖
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|
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<a class="usa-link" target="_blank" title="Follow link">View in GDV</a><br><br>
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<a class="usa-link" target="blank"></a><br>
|
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<span style="white-space: nowrap;">...</span>
|
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</div>
|
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|
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<!--Modal dialog for filtering alignments-->
|
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<div class="usa-modal" id="filter-modal" aria-labelledby="filter-heading" aria-describedby="filter-description"
|
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style="min-width: min-content;">
|
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<div class="usa-modal__content" style="width: 505px; min-width: fit-content;">
|
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<div class="usa-modal__main" style="font-family:Roboto;">
|
||
<h3 class="usa-modal__heading" id="filter-heading">Filter assemblies</h3>
|
||
<p id="filter-subtitle" style="margin-bottom: 0;">
|
||
Assemblies in this alignment are displayed relative to <span id="anchor-assm"></span>, which cannot be hidden.
|
||
A minimum of two assemblies must be shown.
|
||
</p>
|
||
<div class="open-close-wrapper" onclick="MCGV.onFilterOpenCloseClicks(event)">
|
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<a id="show-all-icon" href="#">
|
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<span>
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<use xlink:href="/mcgv/static/django_uswds/uswds/img/sprite.svg#unfold_more"></use>
|
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<a id="close-all-icon" href="#">
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<span>
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<svg class="usa-icon open-close-icon" aria-hidden="true" focusable="false" role="img">
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<use xlink:href="/mcgv/static/django_uswds/uswds/img/sprite.svg#unfold_less"></use>
|
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</svg>
|
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</span>
|
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</a>
|
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<a id="toggle-tree" href="#" class="usa-link open-close-text">Open all</a>
|
||
</div>
|
||
<fieldset class="usa-fieldset" style="height:40vh;overflow-y:auto">
|
||
<ul class="usa-list filter-tree" id="assm-tree"></ul>
|
||
</fieldset>
|
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<div class="usa-modal__footer">
|
||
<ul class="usa-button-group">
|
||
<li class="usa-button-group__item">
|
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<button type="button" class="usa-button filter-apply" onclick="MCGV.filterTracks(event)" data-close-modal>Apply</button>
|
||
</li>
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<li class="usa-button-group__item">
|
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<button type="button" class="usa-button usa-button--unstyled padding-105 text-center filter-cancel" data-close-modal>Cancel</button>
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</li>
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<button type="button" class="usa-button usa-modal__close" aria-label="Close this window" data-close-modal>
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<svg class="usa-icon" aria-hidden="true" focusable="false" role="img">
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<use xlink:href="/mcgv/static/django_uswds/uswds/img/sprite.svg#close"></use>
|
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</svg>
|
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</button>
|
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</div>
|
||
</div>
|
||
<!-- End of Modal dialog -->
|
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</section>
|
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</main>
|
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|
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|
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<!-- ========== BEGIN FOOTER ========== -->
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<path class="cls-12"
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