cee097b75fe4d1b29f0debd8af938ba6bf729d53
max
  Tue Aug 11 08:18:42 2026 -0700
hgBlat: new client-rendered BLAT search form and sortable results page, refs #37893

An opt-in modern alternative to the classic hyperlink output, gated by the
blatNewForm / blatNewPage hg.conf flags. hgBlat.c emits the hit data and form
config as inline JSON (hgBlatData / hgBlatFormData) into empty containers, and
hgBlat.js builds the UI: the search form, a sortable/filterable DataTable with
identity and query-coverage bars, a docked per-hit detail panel, a FASTA query
viewer, and share-link and rename-track modals.

- hgBlat.css: all styling for both pages, loaded via webIncludeResourceFile
(not injected from JS); layout uses CSS classes rather than inline styles.
- utils.js: setupGenomeSelector, the combobox genome picker the form uses.
- hgc.c: blatOldTracks / blatKeepResults - the "Keep results" checkbox lets a
user accumulate BLAT result tracks instead of each search replacing the last.
- hgConfCatalog: register the blatNewForm / blatNewFormBanner gates.
- blatExample.fa: the example query the form loads on demand.

Markup is built in JS (escaped values via htmlEncode, everything else set through
DOM properties); no HTML strings in the C or a template engine.

diff --git src/hg/js/hgBlat.js src/hg/js/hgBlat.js
index 45e3b2c0126..d3f66718551 100644
--- src/hg/js/hgBlat.js
+++ src/hg/js/hgBlat.js
@@ -1,693 +1,899 @@
 // 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, htmlEncode */
 
 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 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 = `
-    /* Plain white page background, matching the track-settings model (gb.css).  The framework body
-     * is cream (#FFF9D2) and the hgInside content table carries a BGCOLOR=#FFFEE8 attribute; override
-     * both to white so the results sit on one uniform white background. */
-    body.cgi { background:#fff; }
-    table.hgInside { background:#fff; }
-    /* Main page header, styled like gb.css .gbTrackTitleBanner (hgGtexTrackSettings model): black
-     * title on the house gold.  The framework's #sectTtl already holds "<assembly> BLAT Results". */
-    .subheadingBar { background:#eaca92; padding:9px 16px; margin:0; border:0; box-sizing:border-box; }
-    .subheadingBar #sectTtl { color:#000; font-weight:700; font-size:18px;
-        display:flex; align-items:center; justify-content:space-between; flex-wrap:wrap; gap:12px; }
-    #blatResults { --accent:#003a72; --accentHover:#8b1a1a; --navy:#0a2b6b; --ink:#1e2833;
-        --muted:#5b6572; --faint:#93a0ad; --line:#d0d0d0; --lineSoft:#ececec; --card:#ffffff;
-        --panel:#ffffff; --section:#4c759c; --headrow:#ededed; --headrowLine:#cccccc;
-        --sel:#cfe0f5; --hover:#f0f0f0; --stripe:#f7f7f7;
-        --title:#eaca92; --titleLine:#d9bd82; --titleSub:#5a4a24;
-        --btn:#ffffff; --btnLine:#999999; --btnText:#003a72; --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:0; overflow:hidden;
-        box-shadow:0 1px 2px rgba(20,40,70,.10); margin:12px 0 24px; }
-    /* Page actions sit in the gold main header (#sectTtl); no separate toolbar. */
-    .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(--muted); 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; }
-    /* Buttons live both inside the card (#blatResults) and in the gold header (#sectTtl); scope to
-     * both ids so the framework's link styles (which would add an underline) can't beat them. */
-    #blatResults .blatPill, #sectTtl .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:0; padding:5px 12px; cursor:pointer;
-        text-decoration:none; display:inline-block; line-height:1.5; }
-    #blatResults .blatPill:hover, #sectTtl .blatPill:hover,
-    #blatResults .blatStripActions input[type=submit]:hover,
-    #blatResults .blatStripActions input[type=button]:hover { background:var(--btnHover); text-decoration:none; }
-    #blatResults .blatPill.primary, #sectTtl .blatPill.primary { background:var(--btnDark); color:#fff; border-color:var(--btnDark); }
-    #blatResults .blatPill.primary:hover, #sectTtl .blatPill.primary:hover { background:var(--btnDarkHover); }
-    /* In the gold header (#sectTtl) the framework's link styles would otherwise beat .blatPill, so
-     * re-assert the button look with id-level specificity. */
-    #sectTtl .blatPill { color:#003a72; background:#fff; border:1px solid #999; text-decoration:none; }
-    #sectTtl .blatPill:hover { background:#eef2f7; text-decoration:none; }
-    #sectTtl .blatPill.primary { background:#0a2b6b; color:#fff; border-color:#0a2b6b; }
-    #sectTtl .blatPill.primary:hover { background:#0a2350; }
-    .blatShareIcon { vertical-align:-2px; margin-right:6px; }
-    .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:0; background:#fff; }
-    .blatBanner { background:#fbf3e2; border:1px solid var(--titleLine); padding:10px 14px;
-        margin:12px 0 0; font-size:14px; color:var(--ink); }
-    .blatBanner a { color:var(--accent); }
-    .blatBanner a:hover { color:var(--accentHover); }
-    .blatSeqBar { flex:1 1 100%; display:flex; gap:8px; align-items:center; flex-wrap:wrap; }
-    .blatSeqText { flex:1 1 100%; min-height:150px; margin-top:10px; padding:8px; white-space:pre;
-        font-family:'Roboto Mono','Courier New',monospace; font-size:13px; color:var(--ink);
-        border:1px solid var(--btnLine); background:#fff; overflow:auto; }
-    #blatTable { font-size:13px; width:100%; border-collapse:collapse; }
-    /* Let the long text columns wrap so the table shrinks to fit smaller screens, while the fixed
-     * bar columns keep a min-width so they never compress into an overlap; when even that won't fit,
-     * #blatTable_wrapper scrolls horizontally. */
-    #blatTable td.blatPos, #blatTable td.queryCol { white-space:normal; word-break:break-word; }
-    #blatTable td.scoreCol { min-width:118px; }
-    #blatTable td.covCol { min-width:120px; }
-    #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; }
-    #blatTable td.actionsCol .blatActSep { color:var(--line); margin:0 10px; }
-    /* "New tab" shown as the usual box-with-arrow icon (via a CSS background so it isn't repeated in
-     * every row's markup), sitting right after the position link with just a space between them. */
-    #blatTable a.blatNewTab { display:inline-block; width:11px; height:11px;
-        margin-left:4px; vertical-align:-1px; background-repeat:no-repeat; background-position:center;
-        background-size:contain; background-image:url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'%3E%3Cpath fill='%23003a72' d='M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z'/%3E%3C/svg%3E"); }
-    #blatTable a.blatNewTab:hover { opacity:.65; }
-    #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:280px; white-space:nowrap; overflow:hidden; text-overflow:ellipsis; }
-    .chrNote { color:var(--faint); text-decoration:none; margin-left:4px; }
-    .chrNote:hover { color:var(--accent); }
-    .blatScoreWrap { display:flex; align-items:center; gap:9px; justify-content:flex-end; }
-    .blatScoreVal { font-size:13px; font-weight:700; text-align:right; font-variant-numeric:tabular-nums; }
-    .blatScoreBar { flex:0 0 54px; height:8px; background:var(--headrow); border:1px solid var(--headrowLine); overflow:hidden; }
-    .blatScoreBar > i { display:block; height:100%; background:var(--accent); }
-    .blatIdPct { font-size:13px; font-weight:700; font-variant-numeric:tabular-nums; }
-    .blatCov { position:relative; display:block; width:150px; max-width:100%; height:10px; background:var(--headrow); 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:0; padding:5px 9px; font-size:14px; }
-    #blatTable_wrapper { padding:6px 0 4px; overflow-x:auto; }
-    .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(--muted); }
-    .blatSelectHint { font-size:14px; color:var(--ink); }
-    .blatSelectHint a { color:var(--accent); }
-    .blatSelectHint a:hover { color:var(--accentHover); }
-    .blatDetail .dhead .loc { font-size:14px; font-weight:700; color:var(--ink); }
-    .blatDetailCard { display:flex; gap:26px; flex-wrap:wrap; padding:14px 16px; background:var(--card);
-        border:1px solid var(--line); border-radius:0; }
-    .blatTiles { display:grid; grid-template-columns:repeat(4,auto); gap:14px 26px; }
-    .blatTile .k { font-size:13px; color:var(--muted); cursor:help; }
-    .blatTile .v { font-size:14px; font-weight:700; color:var(--ink); }
-    .blatDetailActions { display:flex; gap:8px; margin-top:14px; flex-wrap:wrap; }
-    /* Rename modal.  On this page the old C-emitted inline rename form (#renameFormItem / #renameForm)
-     * is replaced by the JS button + modal below, so keep the C markup hidden even though hgBlat.c
-     * flips its display to block after buildBigPsl (our !important beats that inline style). */
-    #renameFormItem, #renameForm { display:none !important; }
-    .blatModalBg { position:fixed; top:0; right:0; bottom:0; left:0; z-index:1000;
-        background:rgba(0,0,0,.4); display:flex; align-items:center; justify-content:center; }
-    .blatModal { background:#fff; border:1px solid var(--line); border-radius:0;
-        box-shadow:0 4px 18px rgba(0,0,0,.28); padding:18px 20px; min-width:340px; max-width:92vw; }
-    .blatModalTitle { font-size:16px; font-weight:700; color:var(--ink); margin-bottom:12px; }
-    .blatModalText { font-size:13px; color:var(--ink); line-height:1.5; max-width:430px; margin-bottom:14px; }
-    .blatModalText a { color:var(--accent); }
-    .blatModalText a:hover { color:var(--accentHover); }
-    .blatModalLabel { display:block; font-size:12px; font-weight:700; color:var(--muted);
-        margin:10px 0 3px; }
-    .blatModalInput { width:100%; box-sizing:border-box; border:1px solid var(--btnLine);
-        border-radius:0; padding:6px 8px; font-size:14px; font-family:inherit; background:#fff; }
-    .blatModalBtns { display:flex; gap:8px; justify-content:flex-end; margin-top:18px; }
-    `;
-    var st = document.createElement('style');
-    st.id = 'blatStyle';
-    st.textContent = css;
-    document.head.appendChild(st);
-}
-
 // ---- cell renderers ------------------------------------------------------
 
 function blatPositionCell(hit) {
     // For alt/fix/random/chrUn sequences show an info icon linking to the FAQ ("What is chr_alt &
     // chr_fix?"), with the short explanation as its tooltip.  (Sits after the position link, not
     // nested inside it.)
     var note = hit.chromNote ?
         ` <a class="chrNote" target="_blank" href="../FAQ/FAQblat.html#blat1c" ` +
         `title="${htmlEncode(hit.chromNote)} Click to learn more in the BLAT FAQ.">&#9432;</a>` : '';
     // The position links to the Genome Browser at this match; the new-tab icon right after it opens
     // the same in a new tab (whitespace between them, no divider).
     // URLs are htmlEncode'd before going into href="": they can carry the user's query name, so an
     // unescaped double-quote would otherwise break out of the attribute (XSS).
     return `<a class="blatPos" title="Open the Genome Browser at this location" ` +
         `href="${htmlEncode(hit.browserUrl)}">${htmlEncode(hit.chrom)}:` +
         `${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}</a>` +
         ` <a class="blatNewTab" target="_blank" href="${htmlEncode(hit.newTabUrl)}" ` +
         `title="Open match in a new tab" aria-label="Open match in a new tab"></a>${note}`;
 }
 
 function blatActionsCell(hit) {
     // The "Open" column now holds just the base-by-base alignment link (Browser moved to the Position
     // column).  detailsUrl is htcUserAli on a fresh search, htcBlatAlign on a shared-link reopen; guard
     // in case a future caller omits it.
     if (!hit.detailsUrl) { return ''; }
     // htmlEncode the URL: detailsUrl embeds the user's query name, so an unescaped quote could break
     // out of the href attribute (XSS).
     return `<a title="Show the base-by-base alignment of your sequence to the genome" ` +
         `href="${htmlEncode(hit.detailsUrl)}">Alignment</a>`;
 }
 
 function blatLocusCell(hit) {
     // Locus is plain text (not a link): the gene names are shown for context only.  The cell grows with
     // its content up to a max-width, then a very long locus (many overlapping genes) is clipped with a
     // CSS ellipsis; the full string is always available on mouseover (title).
     if (!hit.locusText) { return ''; }
     return `<div class="blatLocus" title="${htmlEncode(hit.locusText)}">${htmlEncode(hit.locusText)}</div>`;
 }
 
 function blatScoreCell(hit, maxScore) {
     // Score with a little bar chart after it, scaled to the highest score in this result set.
     var pct = maxScore > 0 ? (hit.score / maxScore * 100) : 0;
     return `<span class="blatScoreWrap"><span class="blatScoreVal">${blatFmt(hit.score)}</span>` +
         `<span class="blatScoreBar"><i style="width:${pct.toFixed(1)}%"></i></span></span>`;
 }
 
 function blatIdentityCell(hit) {
     // Just the percentage now (the bar chart moved to the Score column), kept in its semantic color.
     var c = blatIdColor(hit.identity);
     return `<span class="blatIdPct" style="color:${c}">${hit.identity.toFixed(1)}%</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 matches the genome at ${blatFmt(hit.qStart)}-${blatFmt(hit.qEnd)}bp out 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, 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 assembly = stat('Assembly', htmlEncode(cfg.organism) + ' / ' + htmlEncode(cfg.db)) + div +
         stat('Matches', 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', htmlEncode(cfg.queryName)) + div +
             stat('Length', blatFmt(cfg.querySize) + ' bp') + div + assembly;
     }
     var actions = '';
     // "View all in browser" is the primary action, so it comes first.
     if (cfg.viewAllUrl) {
         actions += `<a class="blatPill" title="Open the Genome Browser with all these BLAT hits shown together as one custom track" href="${htmlEncode(cfg.viewAllUrl)}">View all in browser</a>`;
     }
     // "Show Query Sequence" opens the query FASTA in a panel (with Download / Copy). Only on a fresh
     // search, where the uploaded sequence is available (cfg.querySeqs emitted by hgBlat.c).
     if (cfg.querySeqs && cfg.querySeqs.length) {
         actions += '<button type="button" class="blatPill" id="blatSeqBtn" ' +
             'title="Show the sequence you searched with, in FASTA format">Show Query Sequence</button>';
     }
     // "Share a link" just reveals the page's stable URL (cfg.shareUrl, a trash-backed reopen link).
     // cfg.canShare covers old session-based links (?u=&s=), where the current URL is already shareable.
     if (cfg.shareUrl || cfg.canShare) {
         // A small share-nodes icon precedes the label so users learn to associate it with sharing.
         var shareIcon = '<svg class="blatShareIcon" viewBox="0 0 24 24" width="13" height="13" ' +
             'fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" ' +
             'stroke-linejoin="round" aria-hidden="true"><circle cx="18" cy="5" r="3"></circle>' +
             '<circle cx="6" cy="12" r="3"></circle><circle cx="18" cy="19" r="3"></circle>' +
             '<line x1="8.6" y1="10.5" x2="15.4" y2="6.5"></line>' +
             '<line x1="8.6" y1="13.5" x2="15.4" y2="17.5"></line></svg>';
         actions += '<button type="button" class="blatPill" id="blatShareBtn" ' +
             'title="Show a link that reopens these results (works for a limited time)">' +
             shareIcon + 'Share a link</button>';
     }
     // "Rename BLAT Track" opens a modal to rename the results custom track. This is a JS-native
     // button (renders immediately with the strip) that replaces the old C-emitted inline form, which
     // only appeared after the buildBigPsl AJAX finished and reflowed the page when clicked.
     if (cfg.canRename) {
         actions += '<button type="button" class="blatPill" id="blatRenameBtn" ' +
             'title="Rename this BLAT results custom track and its description">Rename BLAT Track</button>';
     }
     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:${color}"` : '';
     var tip = BLAT_TILE_TIPS[label] || '';
     return `<div class="blatTile"><div class="k" title="${htmlEncode(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') +
         blatTileSkeleton('Mismatch', 'dvMismatch') +
         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="blatDetailCard"><div class="blatDetailCol">` +
         `<div class="blatTiles">${tiles}</div>` +
         `<div class="blatDetailActions">` +
         `<a class="blatPill" id="dvBrowser" title="Open this hit in the Genome Browser" href="#">Open in browser</a>` +
         `<a class="blatPill" id="dvNewTab" target="_blank" title="Open this hit in the Genome Browser in a new tab" 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 id="dvAlignBox" class="blatAlignBox">` +
         `<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" ` +
+        `<div id="dvAlign" class="blatAlignText"></div>` +
+        `<a class="blatPill" id="dvViewAlign" ` +
         `title="See the base-by-base alignment of your query against this hit" 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 ? htmlEncode(hit.locusText) + ' · ' : '';
-    var q = hgBlatData.config.multiQuery ? htmlEncode(hit.qName) + ' · ' : '';
-    blatSet('dvLoc', 'html',
-        `#${hit.rank} · ${q}${locus}${htmlEncode(hit.chrom)}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`);
+    // Location line is plain text, so set it via textContent (blatSet 'text') - no HTML, nothing to
+    // escape.  q and locus stay raw here for that reason.
+    var locus = hit.locusText ? hit.locusText + ' · ' : '';
+    var q = hgBlatData.config.multiQuery ? hit.qName + ' · ' : '';
+    blatSet('dvLoc', 'text',
+        `#${hit.rank} · ${q}${locus}${hit.chrom}:${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',
     'Open in Genome Browser': 'Genomic location of the match (1-based). Click the position to ' +
         'open the Genome Browser there, or the icon to open it in a new tab.',
     'Show': 'Show the base-by-base alignment of your sequence to the genome',
     '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() {
     // No session, no AJAX: the results page already has a stable, shareable URL (hgBlat.c emits it as
     // cfg.shareUrl and blatBuild() pins it into the address bar with history.replaceState), so this
     // just shows/copies window.location.  The link reopens straight from the trash .pslx/.fa, so it
     // works until those trash files are cleaned - hence the retention note.
     var box = document.getElementById('blatShareBox');
     if (!box) { return; }
     if (box.style.display === 'flex') { box.style.display = 'none'; return; }   // toggle off
     var url = window.location.href;
     box.style.display = 'flex';
     box.innerHTML =
-        '<span class="blatShareMsg" style="flex:1 1 100%">Shareable link — anyone with it can reopen ' +
+        '<span class="blatShareMsg blatShareFull">Shareable link — anyone with it can reopen ' +
         'these results. The results are stored temporarily, so the link works for at least 48 hours ' +
         'after they were last viewed.</span>' +
         '<input id="blatShareInput" class="blatShareInput" type="text" readonly>' +
         '<button type="button" class="blatPill" id="blatShareCopy" title="Copy the link to the clipboard">Copy</button>';
     var inp = document.getElementById('blatShareInput');
     inp.value = url;
     inp.focus();
     inp.select();
     $('#blatShareCopy').on('click', function() {
         inp.select();
         if (navigator.clipboard) { navigator.clipboard.writeText(url); }
         else { document.execCommand('copy'); }
         this.textContent = 'Copied';
     });
 }
 
 // ---- Rename BLAT track (modal) -------------------------------------------
 // The results custom track is built (and renamed) by hgBlat.c's inline code, which exposes a small
 // window.blatRenameCt(name, description) helper (it POSTs to hgc's buildBigPsl and rebuilds the
 // track).  We reuse that helper (no new endpoint), just swapping its old inline toggle-form UI for a
 // proper modal dialog.  The current name/description come from cfg (hgBlat.c), not a global, so this
 // does not depend on any generic page-global.
 
 function blatRenameModalHtml(cfg) {
     // hgSession link is relative (same /cgi-bin/), carrying db + hgsid so the session page opens in
     // this assembly and cart.
     var sessionUrl = `hgSession?db=${encodeURIComponent(cfg.db)}&hgsid=${encodeURIComponent(cfg.hgsid)}`;
     return '<div id="blatModalBg" class="blatModalBg" style="display:none">' +
         '<div class="blatModal" role="dialog" aria-modal="true" aria-labelledby="blatModalTitle">' +
         '<div class="blatModalTitle" id="blatModalTitle">Rename BLAT Track</div>' +
         '<div class="blatModalText">Every BLAT result is stored in its own track in the Genome ' +
         'Browser. You can rename the track here. Results will disappear after 2–3 days, unless ' +
         `they are saved into a <a href="${sessionUrl}">Session link</a>.</div>` +
         '<label class="blatModalLabel" for="blatRenameName">Track name</label>' +
         '<input id="blatRenameName" class="blatModalInput" type="text" maxlength="80">' +
         '<label class="blatModalLabel" for="blatRenameDesc">Description</label>' +
         '<input id="blatRenameDesc" class="blatModalInput" type="text" maxlength="120">' +
         '<div class="blatModalBtns">' +
         '<button type="button" class="blatPill" id="blatRenameCancel">Cancel</button>' +
         '<button type="button" class="blatPill primary" id="blatRenameOk">OK</button>' +
         '</div></div></div>';
 }
 
 function blatCloseRename() {
     var bg = document.getElementById('blatModalBg');
     if (bg) { bg.style.display = 'none'; }
 }
 
 function blatOpenRename() {
     var bg = document.getElementById('blatModalBg');
     if (!bg) { return; }
     // Pre-fill with the track's current name/description (emitted by hgBlat.c in cfg).
     var cfg = hgBlatData.config;
     document.getElementById('blatRenameName').value = cfg.trackName || '';
     document.getElementById('blatRenameDesc').value = cfg.trackDescription || '';
     bg.style.display = 'flex';
     document.getElementById('blatRenameName').focus();
     document.getElementById('blatRenameName').select();
 }
 
 function blatWireRename() {
     $('#blatRenameBtn').on('click', blatOpenRename);
     $('#blatRenameCancel').on('click', blatCloseRename);
     // Click on the dark backdrop (but not the dialog itself) closes.
     $('#blatModalBg').on('click', function(ev) {
         if (ev.target === this) { blatCloseRename(); }
     });
     $(document).on('keydown.blatRename', function(ev) {
         var bg = document.getElementById('blatModalBg');
         if (bg && bg.style.display !== 'none' && ev.key === 'Escape') { blatCloseRename(); }
     });
     $('#blatRenameOk').on('click', function() {
         var name = document.getElementById('blatRenameName').value.trim();
         var desc = document.getElementById('blatRenameDesc').value.trim();
         if (!name) { document.getElementById('blatRenameName').focus(); return; }
         // Reuse hgBlat.c's window.blatRenameCt(name, description): rebuilds the custom track under the
         // new name via the existing hgc buildBigPsl call.  Keep cfg in sync so a re-open of the modal
         // shows the new values.
         if (typeof window.blatRenameCt === 'function') {
             hgBlatData.config.trackName = name;
             hgBlatData.config.trackDescription = desc;
             window.blatRenameCt(name, desc);
         }
         blatCloseRename();
     });
 }
 
 // ---- FASTA viewer (generic) ----------------------------------------------
 
 function blatToFasta(seqs) {
     // seqs: [{name, seq}, ...] -> FASTA text, sequence wrapped at 60 chars per line.
     return seqs.map(function(s) {
         var body = String(s.seq || '').toUpperCase().replace(/(.{60})/g, '$1\n').replace(/\n$/, '');
         return '>' + s.name + '\n' + body;
     }).join('\n');
 }
 
 function blatShowFasta(box, seqs, fileName) {
     // Render seqs as FASTA inside `box`, with Copy-to-clipboard and Download buttons. Generic — takes
     // any [{name, seq}] list so it can be reused for other sequences later.
     var fasta = blatToFasta(seqs);
     box.style.display = 'flex';
     box.innerHTML =
         '<div class="blatSeqBar">' +
         '<span class="blatShareMsg">Query sequence (FASTA):</span>' +
         '<button type="button" class="blatPill" id="blatSeqCopy" title="Copy the FASTA to the clipboard">Copy to Clipboard</button>' +
         '<button type="button" class="blatPill" id="blatSeqDownload" title="Download the FASTA as a .fa file">Download</button>' +
         '<button type="button" class="blatPill" id="blatSeqClose" title="Hide the query sequence">Close</button>' +
         '</div><textarea id="blatSeqText" class="blatSeqText" readonly></textarea>';
     var ta = document.getElementById('blatSeqText');
     ta.value = fasta;
     document.getElementById('blatSeqCopy').addEventListener('click', function() {
         ta.select();
         if (navigator.clipboard) { navigator.clipboard.writeText(fasta); }
         else { document.execCommand('copy'); }
         this.textContent = 'Copied';
     });
     document.getElementById('blatSeqDownload').addEventListener('click', function() {
         var a = document.createElement('a');
         a.href = URL.createObjectURL(new Blob([fasta], { type: 'text/plain' }));
         a.download = fileName || 'query.fa';
         document.body.appendChild(a);
         a.click();
         document.body.removeChild(a);
         setTimeout(function() { URL.revokeObjectURL(a.href); }, 0);
     });
     document.getElementById('blatSeqClose').addEventListener('click', function() {
         box.style.display = 'none';
     });
 }
 
 function blatShowQuerySeq() {
     var box = document.getElementById('blatSeqBox');
     if (box.style.display === 'flex') { box.style.display = 'none'; return; }   // toggle off
     blatShowFasta(box, hgBlatData.config.querySeqs, 'blatQuery.fa');
 }
 
 // ---- build ---------------------------------------------------------------
 
 function blatBuild() {
     var cfg = hgBlatData.config;
     var hits = hgBlatData.hits;
-    blatInjectStyle();
 
     // Pin a stable, shareable URL into the address bar (no server redirect) so refresh, bookmark and
     // "Share a link" all use the trash-backed reopen link instead of the transient POST/search URL.
     if (cfg.shareUrl) {
         try { history.replaceState(null, '', cfg.shareUrl); } catch (e) { /* older browsers: ignore */ }
     }
 
     var back = cfg.backUrl ?
         `<a class="blatPill" title="Return to the Genome Browser at your previous location (${htmlEncode(cfg.backPos)})" ` +
         `href="${htmlEncode(cfg.backUrl)}">Back to Genome Browser</a>` : '';
     // The page actions live in the gold main-header bar (framework #sectTtl), next to the title -
     // so there is no separate toolbar (.blatHead is gone).  Injected into #sectTtl below.
     var headActions =
         `${back}<a class="blatPill primary" title="Start a new BLAT search" href="${htmlEncode(cfg.newSearchUrl)}">New BLAT search</a>`;
 
     // Top banner: note this is the new page, link back to the classic page (fresh searches only,
     // where the trash files still exist), and invite feedback.  The old page also clears the
     // blatNewPage preference so later searches use the classic page until the user opts back in.
     var origPage = cfg.canOldPage ?
         ` You can go back to <a title="Show these results on the classic BLAT results page" ` +
         `href="hgBlat?blatNewPage=0&blatReopen=1&hgsid=${encodeURIComponent(cfg.hgsid)}">the original page</a> anytime.` : '';
     var bannerHtml =
         `<div class="blatBanner">We are testing a new BLAT output page.${origPage} ` +
         `If you have feedback on this new page, do not hesitate to let us know via ` +
         `<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</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>Open in Genome Browser</th>');
     th.push('<th>Show</th>');
     th.push('<th>Query coverage</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 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 =
         bannerHtml +
         `<div class="blatCard">${blatSummaryStrip(cfg, queryCount)}` +
         `<div id="blatShareBox" class="blatShareBox" style="display:none"></div>` +
         `<div id="blatSeqBox" class="blatShareBox" style="display:none"></div>` +
         `<div id="blatDetail" class="blatDetail"></div>` +
-        `<table id="blatTable" class="display" style="width:100%"><thead><tr>${th.join('')}</tr></thead></table></div>` +
+        `<table id="blatTable" class="display"><thead><tr>${th.join('')}</tr></thead></table></div>` +
         (cfg.canRename ? blatRenameModalHtml(cfg) : '');
 
     // Put the page actions in the gold main-header bar, to the right of the title (framework #sectTtl).
     var sectTtl = document.getElementById('sectTtl');
     if (sectTtl) {
         var acts = document.createElement('span');
         acts.className = 'blatHeadActions';
         acts.innerHTML = headActions;
         sectTtl.appendChild(acts);
     }
 
     $('#blatShareBtn').on('click', blatShareLink);
     $('#blatSeqBtn').on('click', blatShowQuerySeq);
     blatWireRename();
 
     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) : '') });
     columns.push({ data: null, className: 'covCol', orderable: false,
         render: (d, type, row) => (type === 'display' ? blatCoverageCell(row) :
             (row.qEnd - row.qStart + 1)) });
     if (cfg.hasLocus) {
         columns.push({ data: 'locusText',
             render: (d, type, row) => (type === 'display' ? blatLocusCell(row) : (d || '')) });
     }
     // Score carries a bar scaled to the highest score in this result set (raw score kept for sorting).
     var maxScore = hits.reduce((m, h) => Math.max(m, h.score || 0), 0);
     columns.push({ data: 'score', className: 'num scoreCol',
         render: (d, type, row) => (type === 'display' ? blatScoreCell(row, maxScore) : d) });
     columns.push({ data: 'identity', className: 'num identCol',
         render: (d, type, row) => (type === 'display' ? blatIdentityCell(row) : d) });
     columns.push({ data: 'strand', className: 'strandCol' });
     columns.push({ data: 'span', className: 'num',
         render: (d, type, row) => (type === 'display' ? blatFmt(d) : d) });
 
     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); }
     });
 
     // 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="blatSelectHint">Click a hit below to see its alignment details. ` +
         `If you are missing matches that you think should be there, ` +
         `<a target="_blank" href="../FAQ/FAQblat.html#blat1b">read our BLAT FAQ</a> or ` +
         `<a href="mailto:genome@soe.ucsc.edu">contact us</a>.</div>`;
     blatApplyTooltips();
 }
 
+// ==== search form (the input page) ========================================
+// hgBlat.c emits  var hgBlatFormData = {...}  together with a real <form name="mainForm"> that
+// contains an empty <div id="blatFormBox"> and the C-generated genome search bar.  We build the
+// controls as real form fields *inside that form*, so the browser serializes them natively -
+// including the file input - and Submit / I'm feeling lucky / Clear stay plain submit buttons
+// handled by the existing C code.  There is no shadow form and no copying of values on submit.
+// Styling comes from hgBlat.css (loaded by webIncludeResourceFile in hgBlat.c), shared with the results page.
+
+// The Genome Browser's standard info icon, copied from printInfoIconSvg() in hg/lib/hui.c so the
+// form's icons are pixel-identical to the C-rendered ones elsewhere in the browser.
+var BLAT_INFO_SVG =
+    "<svg style='height:1.1em; vertical-align:top' viewBox='0 0 24 24' fill='none' " +
+    "xmlns='http://www.w3.org/2000/svg'>" +
+    "<circle cx='12' cy='12' r='10' stroke='#1C274C' stroke-width='1.5'/>" +
+    "<path d='M12 17V11' stroke='#1C274C' stroke-width='1.5' stroke-linecap='round'/>" +
+    "<circle cx='1' cy='1' r='1' transform='matrix(1 0 0 -1 11 9)' fill='#1C274C'/></svg>";
+
+// The assembly-search syntax help.  setupGenomeSelector hides the info icon that
+// printGenomeSearchBar (hg/lib/web.c) normally puts next to the box, so the new form loses that
+// explanation of +word/-word/word*/"phrase"; we re-attach it to an icon after the label instead.
+// Kept word-for-word in sync with searchHelpText in web.c so both pickers explain the box the same
+// way.  This is HTML (a bullet list), rendered as such by the mouseover, so it is NOT htmlEncode'd -
+// like the C printInfoIcon, it relies on the string containing no double quotes to sit in a title=.
+var BLAT_GENOME_SEARCH_HELP =
+    "All genome searches are case-insensitive.  Single-word searches default to prefix " +
+    "matching if an exact match is not found. " +
+    "<ul id='searchTipList' class='noBullets'>" +
+    "<li> Force inclusion: Use a + sign before <b>+word</b> to ensure it appears in result.</li>" +
+    "<li> Exclude words: Use a - sign before <b>-word</b> to exclude it from the search result.</li>" +
+    "<li> Wildcard search: Add an * (asterisk) at end of <b>word*</b> to search for all terms starting with that prefix.</li>" +
+    "<li> Phrase search: Enclose 'words in quotes' to search for the exact phrase.</li>" +
+    "</ul>";
+
+// Cross-session memory of the "Keep results" checkbox.  A plain '1'/'0' string under one key;
+// wrapped in try/catch because localStorage throws in private-mode / disabled-storage browsers, in
+// which case we simply fall back to the cart-supplied default and skip persistence.
+var BLAT_KEEP_RESULTS_KEY = 'blatKeepResults';
+
+function blatGetKeepResultsPref() {
+    // Returns true/false for a stored preference, or null if the user has never set one here.
+    try {
+        var v = localStorage.getItem(BLAT_KEEP_RESULTS_KEY);
+        return v === null ? null : (v === '1');
+    } catch (e) { return null; }
+}
+
+function blatSetKeepResultsPref(on) {
+    try { localStorage.setItem(BLAT_KEEP_RESULTS_KEY, on ? '1' : '0'); } catch (e) { /* ignore */ }
+}
+
+function blatOpts(list, cur) {
+    return list.map(function(v) {
+        return `<option value="${htmlEncode(v)}"${v === cur ? ' selected' : ''}>${htmlEncode(v)}</option>`;
+    }).join('');
+}
+
+function blatFormCount() {
+    // Live character count under the textarea.  Only these two nodes are touched on input - the
+    // textarea itself is never re-rendered, so the caret stays where the user put it.
+    var ta = document.getElementById('blatUserSeq');
+    var out = document.getElementById('blatCountText');
+    if (!ta || !out) { return; }
+    var n = ta.value.replace(/[^A-Za-z*]/g, '').length;
+    out.textContent = blatFmt(n) + ' of 25,000 characters';
+    $('#blatLimitLink').toggleClass('over', n > 25000);
+}
+
+function blatFormTab(showUpload) {
+    $('#blatTabPaste').toggleClass('on', !showUpload);
+    $('#blatTabUpload').toggleClass('on', showUpload);
+    $('#blatPanePaste').toggle(!showUpload);
+    $('#blatPaneUpload').toggle(showUpload);
+}
+
+function blatFormLimitsModal() {
+    var row = (k, v) => `<div class="blatLimitRow"><span>${k}</span><strong>${v}</strong></div>`;
+    return '<div id="blatLimitsBg" class="blatModalBg" style="display:none">' +
+        '<div class="blatModal" role="dialog" aria-modal="true" aria-labelledby="blatLimitsTitle">' +
+        '<div class="blatModalTitle" id="blatLimitsTitle">Input limits</div>' +
+        row('DNA per sequence', '25,000 bases') +
+        row('Protein / translated', '10,000 letters') +
+        row('Sequences per run', '25') +
+        row('Total per submission', '50,000 bases') +
+        '<div class="blatModalText blatModalNote">Queries above these limits are rejected ' +
+        'before alignment. For larger jobs, run BLAT from the ' +
+        '<a target="_blank" href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">' +
+        'command line</a> on your own server.</div>' +
+        '<div class="blatModalBtns"><button type="button" class="blatPill" id="blatLimitsClose">Close</button></div>' +
+        '</div></div>';
+}
+
+function blatFormSetDb(db) {
+    // Called by hgBlat.c's setupGenomeSearchBar onSelect.  Picking a genome does not reload the
+    // page, so everything on it that depends on db is updated here instead: the hidden field that
+    // the search is submitted with, and the sidebar links that carry a db= parameter.  The current
+    // assembly label is updated by setupGenomeSearchBar itself.
+    document.mainForm.db.value = db;
+    $('#blatFormBox a[data-urltpl]').each(function() {
+        this.href = this.getAttribute('data-urltpl').replace('$DB$', encodeURIComponent(db));
+    });
+}
+
+function blatFormSidebar(cfg) {
+    // Same links the classic page offered.  hgBlat.c supplies them as templates holding $DB$ (see
+    // blatFormSetDb); the template is kept in data-urltpl so the link can be retargeted later.
+    var tools = '';
+    var tplLink = (tpl, label) => {
+        var href = tpl.replace('$DB$', encodeURIComponent(hgBlatFormData.db));
+        return `<a data-urltpl="${htmlEncode(tpl)}" href="${htmlEncode(href)}">${label}</a>`;
+    };
+    if (cfg.pcrUrlTpl) {
+        tools += `<div>${tplLink(cfg.pcrUrlTpl, 'In-Silico PCR')} — better than BLAT for ` +
+            'locating PCR primers.</div>';
+    }
+    if (cfg.oligoMatchUrlTpl) {
+        tools += `<div>${tplLink(cfg.oligoMatchUrlTpl, 'Short Sequence Match')} — for ` +
+            'sequences under 20 bp, within the region shown in the Genome Browser.</div>';
+    }
+    tools += '<div><a target="_blank" href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">' +
+        'findMotifs</a> — command-line search across a whole genome.</div>';
+    return '<div>' +
+        (tools ? `<div class="blatCard"><h3>Similar tools</h3>${tools}</div>` : '') +
+        '<div class="blatCard"><h3>Help</h3>' +
+        '<div><a href="../FAQ/FAQblat.html">BLAT FAQ</a></div>' +
+        '<div><a href="../goldenPath/help/hgTracksHelp.html#BLATAlign">BLAT documentation</a></div>' +
+        // No "Search all genomes FAQ" here: that link now lives in the "Search many genomes"
+        // tooltip, next to the checkbox it actually explains.
+        '<div><a href="../FAQ/FAQblat.html#blat14">Programmatic / batch BLAT</a></div>' +
+        '</div>' +
+        '<div class="blatCard"><h3>About BLAT</h3>' +
+        '<div>DNA BLAT quickly finds sequences of 95% and greater similarity that are at least 25 bases ' +
+        'long; it finds perfect matches down to 20 bases, and may miss shorter or more divergent ' +
+        'alignments. Protein BLAT finds sequences of 80% and greater similarity at least 20 amino acids ' +
+        'long.</div>' +
+        '<div>Kent WJ. <a target="_blank" href="https://genome.cshlp.org/content/12/4/656.abstract">' +
+        'BLAT — the BLAST-like alignment tool</a>. Genome Res. 2002 Apr;12(4):656-64.</div>' +
+        '</div></div>';
+}
+
+function blatFormBuild() {
+    var cfg = hgBlatFormData;
+
+    var banner = '';
+    if (cfg.classicUrl) {
+        banner = '<div class="blatBanner">We are testing a new BLAT search page. You can go back to ' +
+            `<a href="${htmlEncode(cfg.classicUrl)}">the original page</a> anytime. If you have feedback ` +
+            'on this new page, do not hesitate to let us know via ' +
+            '<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</div>';
+    }
+
+    // Checkbox plus the browser's standard info icon.  Same SVG and same title +
+    // convertTitleTagsToMouseovers mechanism as printInfoIcon()/printInfoIconSvg() in hg/lib/hui.c,
+    // so these read identically to the info icons on every other Genome Browser page.
+    var check = (name, on, label, tip) =>
+        `<span class="blatCheck"><label><input type="checkbox" name="${name}" ` +
+        `id="blat_${name}"${on ? ' checked' : ''}>${label}</label>` +
+        `<span class="blatInfo" title="${htmlEncode(tip)}">${BLAT_INFO_SVG}</span></span>`;
+
+    // "Keep results" starting state.  The cart (cfg.keepResults) only remembers the choice within a
+    // session; localStorage carries it across sessions so a user who wants their BLAT results to
+    // accumulate does not have to re-tick the box on every visit.  localStorage wins when set (it is
+    // the more durable record of the user's own preference); the cart is the fallback for a browser
+    // that has never stored one.  Only consulted where the box is actually shown (blatOldTracks=
+    // delete); elsewhere the choice has no effect, so there is nothing worth persisting.
+    var keepResultsInit = cfg.keepResults;
+    if (cfg.showKeepResults) {
+        var storedKeep = blatGetKeepResultsPref();
+        if (storedKeep !== null) { keepResultsInit = storedKeep; }
+    }
+
+    document.getElementById('blatFormBox').innerHTML =
+        banner +
+        '<div class="blatFormGrid"><div>' +
+
+        '<div class="blatSection">Search &ndash; type keywords to find the target assembly</div>' +
+        '<div class="blatRow">' +
+            '<div class="blatField blatGenomeSlot"><span>Genome or assembly ' +
+                `<span class="blatInfo" title="${BLAT_GENOME_SEARCH_HELP}">${BLAT_INFO_SVG}</span>` +
+                '</span>' +
+                '<div id="blatGenomeSlot"></div></div>' +
+            `<label class="blatField"><span>Query type</span><select name="type">${blatOpts(cfg.types, cfg.type)}</select></label>` +
+            // Sort and output are submitted but not offered: sorting by anything other than score
+            // is rarely useful, and this page always wants the hyperlink (results table) output.
+            // Kept as hidden fields so the request hgBlat receives is unchanged.
+            `<input type="hidden" name="sort" value="${htmlEncode(cfg.sort)}">` +
+            `<input type="hidden" name="output" value="${htmlEncode(cfg.output)}">` +
+        '</div>' +
+
+        '<div class="blatChecks">' +
+            // The mouseover popup keeps itself open while the pointer is inside it (see the
+            // mouseoverContainer mouseenter handler in utils.js), and renders its text as HTML, so
+            // a link in the tip is genuinely clickable.  htmlEncode keeps the title attribute
+            // well-formed; the browser decodes it back to markup before it is injected.
+            check('allGenomes', cfg.allGenomes, 'Search many genomes',
+                'Runs the same query against every default assembly and attached hub that has a ' +
+                'dedicated BLAT server. Dynamic BLAT servers are skipped and listed as such in the ' +
+                "output. See our <a target='_blank' href='../FAQ/FAQblat.html#blat9'>BLAT All FAQ</a> " +
+                'for more information.') +
+            check('allResults', cfg.allResults, 'No min. score',
+                'Turns off minimum-match filtering so every alignment is returned. A human DNA search ' +
+                'normally requires 20 matching bases, based on the genome size, to filter out ' +
+                'lower-quality results; useful for short queries and the tiny genomes of ' +
+                'microorganisms.') +
+            check('autoRearr', cfg.autoRearr, 'Show rearrangements',
+                'Shows duplications of the query sequence using multiple lines with connecting lines ' +
+                'between fragments, and displays inversions better (the "snakes" display). Can also ' +
+                'be switched on or off from the BLAT track configuration page.') +
+            // Only offered where hg.conf blatOldTracks=delete, i.e. where there is something to opt
+            // out of.  Unlike the three above (which keep the classic form's plain-checkbox
+            // behaviour), this one is submitted through an explicit hidden field: a checkbox sends
+            // nothing when unticked, so cartUsualBoolean would never see it go back to false and
+            // "Keep results" could not be switched off again once used.
+            (cfg.showKeepResults ?
+                '<span class="blatCheck">' +
+                `<input type="hidden" name="blatKeepResults" id="blatKeepResultsVal" value="${keepResultsInit ? 1 : 0}">` +
+                `<label><input type="checkbox" id="blat_keepResults"${keepResultsInit ? ' checked' : ''}>` +
+                'Keep results</label>' +
+                `<span class="blatInfo" title="${htmlEncode(
+                    'A new BLAT search always overrides your previous BLAT results: each search ' +
+                    'replaces the result track of the one before it in the Genome Browser. Check ' +
+                    'this box to keep earlier results instead, so every search adds its own track ' +
+                    'and results accumulate. Your choice is remembered for next time.')}">` +
+                `${BLAT_INFO_SVG}</span></span>` : '') +
+        '</div>' +
+
+        '<div class="blatSection">Query sequence</div>' +
+        '<div class="blatTabs">' +
+            '<button type="button" class="blatTab on" id="blatTabPaste">Paste sequence</button>' +
+            '<button type="button" class="blatTab" id="blatTabUpload">Upload file</button>' +
+        '</div>' +
+
+        '<div id="blatPanePaste">' +
+            '<div class="blatPaneHint"><span>Separate multiple sequences with a &gt;name line. ' +
+            'Up to 25 sequences.</span>' +
+            `<a href="#" id="blatExample">${htmlEncode(cfg.exampleLabel)}</a></div>` +
+            '<textarea class="blatSeq" name="userSeq" id="blatUserSeq" spellcheck="false" ' +
+            'aria-label="Paste in a query sequence"></textarea>' +
+            '<div class="blatCount"><span id="blatCountText"></span>' +
+            '<a href="#" id="blatLimitLink">Show input limits</a></div>' +
+        '</div>' +
+
+        '<div id="blatPaneUpload" style="display:none">' +
+            '<div class="blatDrop" id="blatDrop">' +
+                '<div class="blatDropTitle">Drop a sequence file here</div>' +
+                '<div class="blatDropSub">Plain text or FASTA, up to 50,000 bases total</div>' +
+                '<input type="file" name="seqFile" id="blatSeqFile">' +
+                '<div class="blatFileName" id="blatFileName"></div>' +
+            '</div>' +
+        '</div>' +
+
+        '<div class="blatActions">' +
+            '<input type="submit" class="blatPill primary" name="Submit" value="Submit" ' +
+            `title="${htmlEncode('Align the sequence and show all matches')}">` +
+            '<input type="submit" class="blatPill" name="Lucky" value="I&#39;m feeling lucky" ' +
+            `title="${htmlEncode('Skip the list of matches and open the best-scoring one straight ' +
+                'away in the Genome Browser. Ignored when "Search many genomes" is ticked.')}">` +
+            '<input type="submit" class="blatPill" name="Clear" value="Clear" ' +
+            `title="${htmlEncode('Empty the query sequence box')}">` +
+        '</div>' +
+
+        '</div>' + blatFormSidebar(cfg) + '</div>' +
+        blatFormLimitsModal();
+
+    // Move the C-generated genome search bar (real autocomplete over every assembly, already wired
+    // by setupGenomeSearchBar) into its slot, rather than reimplementing it with a hardcoded list.
+    var holder = document.getElementById('blatGenomeHolder');
+    if (holder) { document.getElementById('blatGenomeSlot').appendChild(holder); }
+
+
+    // Show the current assembly in the search bar itself instead of in a separate "Current genome:"
+    // line - the bar is wide enough for the whole description.  setupGenomeSearchBar writes the new
+    // one in on each pick, and focusing the bar selects all of it, so it reads as a filled-in search
+    // box rather than as a value the user has to clear by hand.
+    var genomeInput = document.getElementById('genomeSearch');
+    if (genomeInput && cfg.dbLabel) { genomeInput.value = cfg.dbLabel; }
+
+    // Restore the sequence from the cart without going through innerHTML (avoids re-escaping).
+    document.getElementById('blatUserSeq').value = cfg.userSeq || '';
+    blatFormCount();
+
+    $('#blatUserSeq').on('input', blatFormCount);
+    // Mirror the "Keep results" checkbox into its hidden field so an unticked box submits an
+    // explicit 0 rather than nothing at all, and remember the choice in localStorage so it comes
+    // back pre-set on the user's next visit (see keepResultsInit above).
+    $('#blat_keepResults').on('change', function() {
+        document.getElementById('blatKeepResultsVal').value = this.checked ? '1' : '0';
+        blatSetKeepResultsPref(this.checked);
+    });
+    $('#blatTabPaste').on('click', function() { blatFormTab(false); });
+    $('#blatTabUpload').on('click', function() { blatFormTab(true); });
+    // The example sequence is a real ~14 kb query, fetched on demand so it is not carried in every
+    // page load.  The link doubles as its own status indicator while the request is in flight.
+    $('#blatExample').on('click', function(ev) {
+        ev.preventDefault();
+        var link = this;
+        var label = cfg.exampleLabel;
+        link.textContent = 'Loading example…';
+        fetch(cfg.exampleUrl)
+            .then(function(resp) {
+                if (!resp.ok) { throw new Error('HTTP ' + resp.status); }
+                return resp.text();
+            })
+            .then(function(fa) {
+                var ta = document.getElementById('blatUserSeq');
+                ta.value = fa.trim();
+                blatFormCount();
+                ta.focus();
+                ta.setSelectionRange(0, 0);
+                ta.scrollTop = 0;
+                link.textContent = label;
+                blatFormTab(false);   // in case the user was on the upload tab
+            })
+            .catch(function(err) {
+                link.textContent = 'Could not load example';
+                // Leave the message up briefly, then let the user try again.
+                setTimeout(function() { link.textContent = label; }, 4000);
+                console.error('hgBlat: example fetch failed:', err);
+            });
+    });
+    $('#blatLimitLink').on('click', function(ev) {
+        ev.preventDefault();
+        $('#blatLimitsBg').css('display', 'flex');
+    });
+    $('#blatLimitsClose').on('click', function() { $('#blatLimitsBg').hide(); });
+    $('#blatLimitsBg').on('click', function(ev) { if (ev.target === this) { $(this).hide(); } });
+    $(document).on('keydown.blatLimits', function(ev) {
+        if (ev.key === 'Escape') { $('#blatLimitsBg').hide(); }
+    });
+
+    var fileInput = document.getElementById('blatSeqFile');
+    var drop = document.getElementById('blatDrop');
+    $(fileInput).on('change', function() {
+        document.getElementById('blatFileName').textContent =
+            this.files && this.files.length ? this.files[0].name : '';
+    });
+    ['dragenter', 'dragover'].forEach(function(e) {
+        drop.addEventListener(e, function(ev) { ev.preventDefault(); drop.classList.add('hot'); });
+    });
+    ['dragleave', 'drop'].forEach(function(e) {
+        drop.addEventListener(e, function(ev) { ev.preventDefault(); drop.classList.remove('hot'); });
+    });
+    drop.addEventListener('drop', function(ev) {
+        if (ev.dataTransfer.files.length) {
+            fileInput.files = ev.dataTransfer.files;
+            $(fileInput).trigger('change');
+        }
+    });
+
+    if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); }
+}
+
 $(document).ready(function() {
     if (typeof hgBlatData !== 'undefined' && document.getElementById('blatResults')) {
         blatBuild();
     }
+    if (typeof hgBlatFormData !== 'undefined' && document.getElementById('blatFormBox')) {
+        blatFormBuild();
+    }
 });