c7fcdde6db52ba01fbabfa695b49205bf7261a33
max
  Tue Aug 4 07:40:32 2026 -0700
hgBlat/hgc: QA fixes for the new BLAT table view and alignment page

Address Gerardo's QA findings on the new BLAT UI:
- Table view: label each hit with its own query (new Query column +
"Queries" count in the summary) when the search has multiple queries,
reading cfg.multiQuery / hit.qName from the payload.
- Table view: strip the "hub_NNN_" prefix from the Assembly field so hub
assemblies no longer show a doubled prefix.
- Alignment page: strip the same prefix from the organism in the page title
for non-GenArk assembly hubs (blatAsmLabel fallback path).
- Table view: do not pre-select hit #1; show a prompt until the user clicks
a row, since top hits are often tied.
- Table view: add a divider between the Browser / New tab / Alignment links.
- Alignment page: sidebar link now reads "Side by Side Alignment" to match
the section heading.
- Alignment page: comma-format coordinates and base counts in the summary,
matching the table view and the rest of the browser.

refs #37893

diff --git src/hg/js/hgBlat.js src/hg/js/hgBlat.js
index 19eebb0ed1a..6a0d49d2320 100644
--- src/hg/js/hgBlat.js
+++ src/hg/js/hgBlat.js
@@ -1,455 +1,474 @@
 // hgBlat.js - client-side rendering of the hgBlat "Table" output mode.
 //
 // hgBlat.c emits an inline object  var hgBlatData = { config, hits }  and an empty
 // <div id="blatResults">.  This script builds the whole results UI from that data:
 //   - a card with a summary strip (query / length / assembly / hit count + actions)
 //   - a sortable, filterable DataTable whose cells are rendered here (identity bar,
 //     query-coverage bar, linked loci, action links, comma-formatted position)
 //   - a docked "selected hit" detail panel updated on row click
 // Header tooltips reuse the Genome Browser's own mechanism (title + convertTitleTagsToMouseovers).
 
 /* jshint esnext: true */
 /* global $, hgBlatData, convertTitleTagsToMouseovers */
 
 var blatSelectedRank = null;   // rank of the row shown in the detail panel
 
 function blatFmt(n) {
     // 12345 -> "12,345"
     return Number(n).toLocaleString('en-US');
 }
 
 function blatEsc(s) {
     // HTML-escape a value for safe insertion as text
     return $('<div>').text(s === null || s === undefined ? '' : String(s)).html();
 }
 
 function blatIdColor(id) {
     // UCSC identity semantic colors
     if (id >= 98) { return '#1f7a34'; }
     if (id >= 95) { return '#4d7c0f'; }
     if (id >= 90) { return '#b45309'; }
     return '#b1301f';
 }
 
 function blatInjectStyle() {
     if (document.getElementById('blatStyle')) { return; }
     // UCSC house style (per the project's UCSC UI Style Guide): steel-blue section header, tan/white
     // content, navy links with maroon hover, #dbe4ee table header, zebra rows, navy selection bar.
     var css = `
     table.hgInside { background:#eef1f4; }
     #blatResults { --accent:#0a3a7a; --accentHover:#8b1a1a; --navy:#0a2b6b; --ink:#1e2833;
         --muted:#5b6572; --faint:#93a0ad; --line:#c4cdd6; --lineSoft:#e4e9ef; --card:#ffffff;
         --panel:#f4f7fb; --section:#4c7093; --headrow:#dbe4ee; --headrowLine:#a9bcd1;
         --sel:#cfe0f5; --hover:#eef3fb; --stripe:#f4f7fb;
         --btn:#ffffff; --btnLine:#999999; --btnText:#0a2b6b; --btnHover:#eef2f7;
         --btnDark:#0a2b6b; --btnDarkHover:#0a2350;
         font-family:'Helvetica Neue',Helvetica,Arial,sans-serif; color:var(--ink); font-size:14px; }
     .blatCard { background:var(--card); border:1px solid var(--line); border-radius:3px; overflow:hidden;
         box-shadow:0 1px 2px rgba(20,40,70,.10); margin:12px 0 24px; }
     .blatHead { display:flex; align-items:center; justify-content:space-between; gap:12px; flex-wrap:wrap;
         padding:9px 18px; background:var(--section); }
     .blatHead .t { font-weight:700; font-size:16px; color:#ffffff; }
     .blatHead .t .sub { color:#d7e2ee; font-weight:400; }
     .blatHeadActions { display:flex; gap:8px; align-items:center; flex-wrap:wrap; }
     .blatStrip { display:flex; align-items:center; gap:24px; flex-wrap:wrap;
         padding:11px 18px; border-bottom:1px solid var(--line); background:var(--panel); }
     .blatStat { display:flex; flex-direction:column; gap:1px; }
     .blatStat .k { font-size:12px; color:var(--faint); font-weight:700; }
     .blatStat .v { font-size:14px; font-weight:700; color:var(--ink); }
     .blatDiv { width:1px; height:28px; background:var(--line); }
     .blatStripActions { margin-left:auto; display:flex; gap:8px; align-items:center; flex-wrap:wrap; }
     #blatResults .blatPill, #blatResults .blatStripActions input[type=submit],
     #blatResults .blatStripActions input[type=button] {
         font-family:inherit; font-size:13px; font-weight:700; color:var(--btnText); background:var(--btn);
         border:1px solid var(--btnLine); border-radius:3px; padding:5px 12px; cursor:pointer;
         text-decoration:none; display:inline-block; line-height:1.5; }
     #blatResults .blatPill:hover, #blatResults .blatStripActions input[type=submit]:hover,
     #blatResults .blatStripActions input[type=button]:hover { background:var(--btnHover); text-decoration:none; }
     #blatResults .blatPill.primary { background:var(--btnDark); color:#fff; border-color:var(--btnDark); }
     #blatResults .blatPill.primary:hover { background:var(--btnDarkHover); }
     .blatShareBox { display:flex; align-items:center; gap:10px; flex-wrap:wrap;
         padding:11px 18px; border-bottom:1px solid var(--line); background:var(--panel); }
     .blatShareMsg { font-size:14px; color:var(--muted); }
     .blatShareInput { flex:1; min-width:260px; font-size:13px; padding:5px 8px;
         border:1px solid var(--btnLine); border-radius:3px; background:#fff; }
     #blatTable { font-size:13px; width:100%; border-collapse:collapse; }
     #blatTable thead th { background:var(--headrow); border-bottom:1px solid var(--headrowLine);
         font-size:12px; color:var(--navy); font-weight:700; padding:8px 12px; white-space:nowrap; }
     #blatTable tbody td { padding:8px 12px; border-bottom:1px solid var(--lineSoft); white-space:nowrap;
         vertical-align:middle; }
     #blatTable tbody tr { cursor:pointer; }
     #blatTable tbody tr:nth-child(even) { background:var(--stripe); }
     #blatTable tbody tr:hover { background:var(--hover); }
     #blatTable tbody tr.blatSel { background:var(--sel); box-shadow:inset 3px 0 0 var(--navy); }
     #blatTable td.num, #blatTable th.num { text-align:right; font-variant-numeric:tabular-nums; }
     #blatTable td.rankCol { color:var(--faint); }
     #blatTable td.strandCol { text-align:center; color:var(--muted); }
-    #blatTable td.actionsCol a { color:var(--accent); font-weight:700; margin-right:12px; }
+    #blatTable td.actionsCol a { color:var(--accent); font-weight:700; }
+    #blatTable td.actionsCol .blatActSep { color:var(--line); margin:0 10px; }
     #blatTable a { color:var(--accent); text-decoration:none; }
     #blatTable a:hover { color:var(--accentHover); text-decoration:underline; }
     .blatRowHint { padding:11px 18px 2px; font-size:13px; color:var(--muted); }
     .blatLocus { max-width:230px; overflow:hidden; text-overflow:ellipsis; white-space:nowrap; }
     .chrNote { color:var(--faint); cursor:help; margin-left:4px; }
     .blatIdWrap { display:flex; align-items:center; gap:9px; justify-content:flex-end; }
     .blatIdBar { flex:0 0 54px; height:8px; background:#dce4ee; border:1px solid var(--headrowLine); overflow:hidden; }
     .blatIdBar > i { display:block; height:100%; }
     .blatIdPct { font-size:13px; font-weight:700; width:48px; text-align:right; font-variant-numeric:tabular-nums; }
     .blatCov { position:relative; display:block; width:150px; height:10px; background:#dce4ee; border:1px solid var(--headrowLine); }
     .blatCov > i { position:absolute; top:0; bottom:0; background:var(--accent); }
     #blatTable_filter { float:left; margin:0 0 10px; }
     #blatTable_filter input { width:300px; max-width:55vw; border:1px solid var(--btnLine);
         border-radius:3px; padding:5px 9px; font-size:14px; }
     #blatTable_wrapper { padding:6px 18px 4px; }
     .blatDetail { border-bottom:1px solid var(--line); background:var(--panel); padding:14px 18px 16px; }
     .blatDetail .dhead { display:flex; align-items:baseline; gap:10px; margin-bottom:12px; flex-wrap:wrap; }
     .blatDetail .dhead .lab { font-size:13px; color:var(--faint); }
     .blatDetail .dhead .loc { font-size:15px; font-weight:700; color:var(--accent); }
     .blatDetailCard { display:flex; gap:26px; flex-wrap:wrap; padding:14px 16px; background:var(--card);
         border:1px solid var(--line); border-radius:3px; }
     .blatTiles { display:grid; grid-template-columns:repeat(4,auto); gap:14px 26px; }
     .blatTile .k { font-size:13px; color:var(--faint); cursor:help; }
     .blatTile .v { font-size:17px; font-weight:700; color:var(--ink); }
     .blatDetailActions { display:flex; gap:8px; margin-top:14px; flex-wrap:wrap; }
     `;
     var st = document.createElement('style');
     st.id = 'blatStyle';
     st.textContent = css;
     document.head.appendChild(st);
 }
 
 // ---- cell renderers ------------------------------------------------------
 
 function blatPositionCell(hit) {
     var note = hit.chromNote ?
         ` <span class="chrNote" title="${blatEsc(hit.chromNote)}">&#9432;</span>` : '';
     return `<a class="blatPos" href="${hit.browserUrl}">${blatEsc(hit.chrom)}:` +
         `${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}</a>${note}`;
 }
 
 function blatActionsCell(hit) {
     // detailsUrl is the base-by-base alignment page (htcUserAli on a fresh search, htcBlatAlign on a
     // shared-link reopen); it is always present now, but guard in case a future caller omits it.
-    var align = hit.detailsUrl ? `<a href="${hit.detailsUrl}">Alignment</a>` : '';
-    return `<a href="${hit.browserUrl}">Browser</a>` +
-        `<a target="_blank" href="${hit.newTabUrl}">New&nbsp;tab</a>` + align;
+    var parts = [`<a href="${hit.browserUrl}">Browser</a>`,
+        `<a target="_blank" href="${hit.newTabUrl}">New&nbsp;tab</a>`];
+    if (hit.detailsUrl) { parts.push(`<a href="${hit.detailsUrl}">Alignment</a>`); }
+    // a thin divider between the links makes the grouping clearer
+    return parts.join('<span class="blatActSep">|</span>');
 }
 
 function blatLocusCell(hit, cfg) {
     if (!hit.locusText) { return ''; }
     var inner;
     if (hit.locusType && hit.locusGenes && hit.locusGenes.length) {
         var links = hit.locusGenes.map(function(g) {
             return `<a href="${cfg.geneUrlBase}${encodeURIComponent(g)}">${blatEsc(g)}</a>`;
         }).join('-');
         inner = `${blatEsc(hit.locusType)} ${links}`;
     } else {
         inner = blatEsc(hit.locusText);
     }
     return `<div class="blatLocus" title="${blatEsc(hit.locusText)}">${inner}</div>`;
 }
 
 function blatIdentityCell(hit) {
     var c = blatIdColor(hit.identity);
     return `<span class="blatIdWrap"><span class="blatIdBar">` +
         `<i style="width:${hit.identity}%;background:${c}"></i></span>` +
         `<span class="blatIdPct" style="color:${c}">${hit.identity.toFixed(1)}%</span></span>`;
 }
 
 function blatCoverageCell(hit) {
     var left = (hit.qStart - 1) / hit.qSize * 100;
     var width = (hit.qEnd - hit.qStart + 1) / hit.qSize * 100;
     var tip = `query ${blatFmt(hit.qStart)}–${blatFmt(hit.qEnd)} of ${blatFmt(hit.qSize)} bp`;
     return `<span class="blatCov" title="${tip}"><i style="left:${left.toFixed(1)}%;` +
         `width:${width.toFixed(1)}%"></i></span>`;
 }
 
 // ---- summary strip + detail panel ---------------------------------------
 
-function blatSummaryStrip(cfg) {
+function blatSummaryStrip(cfg, queryCount) {
     var stat = (k, v) => `<div class="blatStat"><span class="k">${k}</span>` +
         `<span class="v">${v}</span></div>`;
     var div = '<span class="blatDiv"></span>';
-    var stats = stat('Query', blatEsc(cfg.queryName)) + div +
-        stat('Length', blatFmt(cfg.querySize) + ' bp') + div +
-        stat('Assembly', blatEsc(cfg.organism) + ' / ' + blatEsc(cfg.db)) + div +
+    var assembly = stat('Assembly', blatEsc(cfg.organism) + ' / ' + blatEsc(cfg.db)) + div +
         stat('Hits', blatFmt(cfg.hitCount));
+    var stats;
+    if (cfg.multiQuery) {
+        // With more than one query sequence a single query name/length would be wrong, so show the
+        // number of distinct queries; each hit's own query is in the table's Query column.
+        stats = stat('Queries', blatFmt(queryCount)) + div + assembly;
+    } else {
+        stats = stat('Query', blatEsc(cfg.queryName)) + div +
+            stat('Length', blatFmt(cfg.querySize) + ' bp') + div + assembly;
+    }
     var actions = '';
     // "Share a link" saves a durable anonymous session that reopens these results; it only works
     // when a stable custom track was made from them (cfg.canShare, i.e. autoBigPsl is on).
     if (cfg.canShare) {
         actions += '<button type="button" class="blatPill" id="blatShareBtn">Share a link</button>';
     }
     if (cfg.viewAllUrl) {
         actions += `<a class="blatPill" href="${cfg.viewAllUrl}">View all in browser</a>`;
     }
     // custom-track Rename/Delete buttons (emitted by hgBlat.c) get relocated here after render
     return `<div class="blatStrip">${stats}<span class="blatStripActions">${actions}</span></div>`;
 }
 
 var BLAT_TILE_TIPS = {
     'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.',
     'Identity': 'Percent identity of the aligned bases.',
     'Matches': 'Query bases that match the genome.',
     'Mismatch': 'Bases that differ between query and genome.',
     'Gaps': 'Number of gaps (insertions or deletions) in the alignment.',
     'Blocks': 'Number of ungapped aligned blocks.',
     'Strand': 'Genome strand the query matched (+ or -).',
     'Q span': 'Range of the query sequence that aligned (1-based).'
 };
 
 function blatTileSkeleton(label, id, color) {
     var style = color ? ` style="color:${color}"` : '';
     var tip = BLAT_TILE_TIPS[label] || '';
     return `<div class="blatTile"><div class="k" title="${blatEsc(tip)}">${label}</div>` +
         `<div class="v" id="${id}"${style}></div></div>`;
 }
 
 function blatDetailSkeleton() {
     // Built once; blatRenderDetail() only updates values, so the tile-label tooltips
     // are wired a single time by convertTitleTagsToMouseovers.
     var tiles =
         blatTileSkeleton('Score', 'dvScore') +
         blatTileSkeleton('Identity', 'dvIdentity') +
         blatTileSkeleton('Matches', 'dvMatches', '#15803d') +
         blatTileSkeleton('Mismatch', 'dvMismatch', '#b45309') +
         blatTileSkeleton('Gaps', 'dvGaps') +
         blatTileSkeleton('Blocks', 'dvBlocks') +
         blatTileSkeleton('Strand', 'dvStrand') +
         blatTileSkeleton('Q span', 'dvQspan');
     document.getElementById('blatDetail').innerHTML =
         `<div class="dhead"><span class="lab">Selected hit</span>` +
         `<span class="loc" id="dvLoc"></span></div>` +
         `<div class="blatDetailCard"><div style="display:flex;flex-direction:column;gap:16px;min-width:250px">` +
         `<div class="blatTiles">${tiles}</div>` +
         `<div class="blatDetailActions">` +
         `<a class="blatPill" id="dvBrowser" href="#">Open in browser</a>` +
         `<a class="blatPill" id="dvNewTab" target="_blank" href="#">Open in new tab</a></div></div>` +
         `<div id="dvAlignBox" style="flex:1;min-width:320px;border-left:1px solid var(--line);padding-left:24px;` +
         `display:flex;flex-direction:column;justify-content:center">` +
         `<div class="blatTile"><div class="k">Alignment</div></div>` +
         `<div id="dvAlign" style="font-size:14px;color:var(--muted);line-height:1.55;` +
         `margin:8px 0 14px;max-width:360px"></div>` +
         `<a class="blatPill" id="dvViewAlign" style="align-self:flex-start" href="#">` +
         `View alignment</a></div></div>`;
     if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); }
 }
 
 function blatSet(id, prop, val) {
     var e = document.getElementById(id);
     if (!e) { return; }
     if (prop === 'text') { e.textContent = val; }
     else if (prop === 'html') { e.innerHTML = val; }
     else if (prop === 'href') { e.setAttribute('href', val); }
     else if (prop === 'color') { e.style.color = val; }
 }
 
 function blatRenderDetail(hit) {
     if (!hit || !document.getElementById('blatDetail')) { return; }
     if (!document.getElementById('dvScore')) { blatDetailSkeleton(); }
     var idc = blatIdColor(hit.identity);
     var locus = hit.locusText ? blatEsc(hit.locusText) + ' · ' : '';
+    var q = hgBlatData.config.multiQuery ? blatEsc(hit.qName) + ' · ' : '';
     blatSet('dvLoc', 'html',
-        `#${hit.rank} · ${locus}${blatEsc(hit.chrom)}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`);
+        `#${hit.rank} · ${q}${locus}${blatEsc(hit.chrom)}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`);
     blatSet('dvScore', 'text', blatFmt(hit.score));
     blatSet('dvIdentity', 'text', hit.identity.toFixed(1) + '%');
     blatSet('dvIdentity', 'color', idc);
     blatSet('dvMatches', 'text', blatFmt(hit.matches));
     blatSet('dvMismatch', 'text', blatFmt(hit.misMatch));
     blatSet('dvGaps', 'text', blatFmt(hit.gaps));
     blatSet('dvBlocks', 'text', blatFmt(hit.blocks));
     blatSet('dvStrand', 'text', hit.strand);
     blatSet('dvQspan', 'text', blatFmt(hit.qStart) + '–' + blatFmt(hit.qEnd));
     blatSet('dvBrowser', 'href', hit.browserUrl);
     blatSet('dvNewTab', 'href', hit.newTabUrl);
     // Show the Alignment box whenever a base-by-base alignment page is available (htcUserAli on a
     // fresh search, htcBlatAlign on a shared-link reopen); hide it only if detailsUrl is missing.
     var alignBox = document.getElementById('dvAlignBox');
     if (alignBox) { alignBox.style.display = hit.detailsUrl ? '' : 'none'; }
     if (hit.detailsUrl) {
         blatSet('dvViewAlign', 'href', hit.detailsUrl);
         blatSet('dvAlign', 'text',
             'See the base-by-base alignment of your query against ' + hit.chrom +
             ': matches, mismatches and gaps across the whole span.');
     }
 }
 
 function blatSelect(dt, rank) {
     blatSelectedRank = rank;
     $('#blatTable tbody tr').each(function() {
         var d = dt.row(this).data();
         $(this).toggleClass('blatSel', !!d && d.rank === rank);
     });
     var hit = hgBlatData.hits.find(h => h.rank === rank);
     blatRenderDetail(hit);
 }
 
 // ---- header tooltips (reuse the browser's title -> mouseover system) -----
 
 var BLAT_HEADER_TIPS = {
     '#': 'Rank by the chosen sort order',
+    'Query': 'The query sequence this hit came from',
     'Position': 'Genomic location of the match (1-based). Click to open the Genome Browser.',
     'Actions': 'Open the match in the browser, see the alignment details, or open in a new tab',
     'Locus': 'Nearest gene(s), and whether the hit falls in an exon, intron, or intergenic region',
     'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.',
     'Identity': 'Percent identity of the aligned bases',
     'Strand': 'Genome strand the query matched (+ or -)',
     'Query coverage': 'Which part of the query aligned (blue) across its full length',
     'Span': 'Length of the match on the genome (bp). Larger than the query length means ' +
         'the alignment crosses introns or deletions.'
 };
 
 function blatApplyTooltips() {
     $('#blatTable thead th').each(function() {
         var tip = BLAT_HEADER_TIPS[$(this).text().trim()];
         if (tip) { $(this).attr('title', tip); }
     });
     if (typeof convertTitleTagsToMouseovers === 'function') {
         convertTitleTagsToMouseovers();
     }
 }
 
 // ---- share a link --------------------------------------------------------
 
 function blatShareLink() {
     // Save the current cart as an anonymous shared session (hgSession API), then build a link back
     // to this page that restores it.  The restored cart carries the durable bigPsl custom track
     // made from these results, which hgBlat rebuilds this table from (no BLAT re-run) on open.
     var cfg = hgBlatData.config;
     var box = document.getElementById('blatShareBox');
     box.style.display = 'flex';
     box.innerHTML = '<span class="blatShareMsg">Creating shareable link…</span>';
     // Save the cart as an anonymous shared session; same endpoint/params as topLinks.js "Share a link".
     $.ajax({
         type: 'POST',
         url: '../cgi-bin/hgSession',
         data: { hgsid: cfg.hgsid, 'hgS_doSaveSessionJson': 1, 'hgS_shareAnon': 1 },
         dataType: 'json',
         success: function(data) {
             if (!data || !data.name) {
                 box.innerHTML = '<span class="blatShareMsg">Could not create link: ' +
                     blatEsc(data && data.error ? data.error : 'unknown error') + '</span>';
                 return;
             }
             // anonymous sessions are saved under the reserved user "l"; hgBlat maps the short
             // u=/s= params to the session load and rebuilds this table from the durable bigPsl
             // custom track (no BLAT re-run)
             var link = window.location.origin + window.location.pathname +
                 '?u=l&s=' + encodeURIComponent(data.name);
             box.innerHTML =
                 '<span class="blatShareMsg">Shareable link (opens these results for anyone):</span>' +
                 '<input id="blatShareInput" class="blatShareInput" type="text" readonly>' +
                 '<button type="button" class="blatPill" id="blatShareCopy">Copy</button>';
             var inp = document.getElementById('blatShareInput');
             inp.value = link;
             inp.focus();
             inp.select();
             $('#blatShareCopy').on('click', function() {
                 inp.select();
                 if (navigator.clipboard) { navigator.clipboard.writeText(link); }
                 else { document.execCommand('copy'); }
                 document.getElementById('blatShareCopy').textContent = 'Copied';
             });
         },
         error: function() {
             box.innerHTML = '<span class="blatShareMsg">Could not reach the server. Please try again.</span>';
         }
     });
 }
 
 // ---- build ---------------------------------------------------------------
 
 function blatBuild() {
     var cfg = hgBlatData.config;
     var hits = hgBlatData.hits;
     blatInjectStyle();
 
     var back = cfg.backUrl ?
         `<a class="blatPill" title="${blatEsc(cfg.backPos)}" href="${cfg.backUrl}">Back to browser</a>` : '';
     // "Old BLAT result page" re-renders the classic list from this session's fresh trash files and
     // clears the blatNewPage preference (blatNewPage=0), so future searches use the classic page
     // until the user opts back in.  Only offered on a fresh search (cfg.canOldPage), not a reopen.
     var oldPage = cfg.canOldPage ?
         `<a class="blatPill" title="Switch back to the classic BLAT results page" ` +
         `href="hgBlat?blatNewPage=0&blatReopen=1&hgsid=${encodeURIComponent(cfg.hgsid)}">Old BLAT result page</a>` : '';
     var headHtml =
         `<div class="blatHead"><span class="t">BLAT <span class="sub">results</span></span>` +
         `<span class="blatHeadActions">${oldPage}${back}` +
         `<a class="blatPill primary" href="${cfg.newSearchUrl}">New BLAT search</a></span></div>`;
 
+    var queryCount = new Set(hits.map(h => h.qName)).size;
+
     var th = [];
     th.push('<th class="num">#</th>');
+    if (cfg.multiQuery) { th.push('<th>Query</th>'); }
     th.push('<th>Position</th>');
     th.push('<th>Actions</th>');
     if (cfg.hasLocus) { th.push('<th>Locus</th>'); }
     th.push('<th class="num">Score</th>');
     th.push('<th class="num">Identity</th>');
     th.push('<th>Strand</th>');
     th.push('<th>Query coverage</th>');
     th.push('<th class="num">Span</th>');
 
     // detail dock sits above the table: with long hit lists a bottom dock scrolls out of view
     document.getElementById('blatResults').innerHTML =
-        `<div class="blatCard">${headHtml}${blatSummaryStrip(cfg)}` +
+        `<div class="blatCard">${headHtml}${blatSummaryStrip(cfg, queryCount)}` +
         `<div id="blatShareBox" class="blatShareBox" style="display:none"></div>` +
         `<div id="blatDetail" class="blatDetail"></div>` +
         `<div class="blatRowHint">Click any row to inspect it in the panel above.</div>` +
         `<table id="blatTable" class="display" style="width:100%"><thead><tr>${th.join('')}</tr></thead></table></div>`;
 
     // relocate the C-emitted custom-track buttons into the summary strip
     var actionBar = document.querySelector('.blatStripActions');
     ['renameFormItem', 'deleteCtForm'].forEach(function(id) {
         var el = document.getElementById(id);
         if (el && actionBar) { actionBar.appendChild(el); }
     });
     $('#blatShareBtn').on('click', blatShareLink);
 
     var columns = [];
     columns.push({ data: 'rank', className: 'num rankCol' });
+    if (cfg.multiQuery) { columns.push({ data: 'qName', className: 'queryCol' }); }
     columns.push({ data: null, orderable: false, className: 'blatPos',
         render: (d, type, row) => (type === 'display' ? blatPositionCell(row) : row.chrom + ':' + row.tStart) });
     columns.push({ data: null, orderable: false, className: 'actionsCol',
         render: (d, type, row) => (type === 'display' ? blatActionsCell(row) : '') });
     if (cfg.hasLocus) {
         columns.push({ data: 'locusText',
             render: (d, type, row) => (type === 'display' ? blatLocusCell(row, cfg) : (d || '')) });
     }
     columns.push({ data: 'score', className: 'num' });
     columns.push({ data: 'identity', className: 'num',
         render: (d, type, row) => (type === 'display' ? blatIdentityCell(row) : d) });
     columns.push({ data: 'strand', className: 'strandCol' });
     columns.push({ data: null, className: 'covCol', orderable: false,
         render: (d, type, row) => (type === 'display' ? blatCoverageCell(row) :
             (row.qEnd - row.qStart + 1)) });
     columns.push({ data: 'span', className: 'num' });
 
     var dt = $('#blatTable').DataTable({
         data: hits,
         columns: columns,
         paging: false,
         info: false,
         order: [],
         language: { search: '', searchPlaceholder: 'Filter hits by locus, chrom, position…' }
     });
 
     $('#blatTable tbody').on('click', 'tr', function(ev) {
         if ($(ev.target).closest('a').length) { return; }   // let links work normally
         var d = dt.row(this).data();
         if (d) { blatSelect(dt, d.rank); }
     });
 
     // Keep the selected-row highlight after sort/filter.  Header tooltips are wired once below (the
     // <thead> persists across draws); we deliberately do NOT re-run convertTitleTagsToMouseovers on
     // every draw, as it re-scans the whole document and adds global listeners on each call.
     dt.on('draw', function() {
         if (blatSelectedRank !== null) { blatSelect(dt, blatSelectedRank); }
     });
 
-    if (hits.length) { blatSelect(dt, hits[0].rank); }
+    // No hit is pre-selected: several hits are often tied on score/identity, so picking one for the
+    // user is misleading.  The detail panel shows a prompt until a row is clicked.
+    document.getElementById('blatDetail').innerHTML =
+        `<div class="dhead"><span class="lab">Select a hit below to see its alignment details.</span></div>`;
     blatApplyTooltips();
 }
 
 $(document).ready(function() {
     if (typeof hgBlatData !== 'undefined' && document.getElementById('blatResults')) {
         blatBuild();
     }
 });