diff --git a/ChangeLog b/ChangeLog
index a83bb3cf..c204105e 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -14,6 +14,9 @@
 
 ## Interface and handling
 
+- reorganize GUI parameters, add conditional seed/accessibility controls and
+  grouped CSV defaults, expand FASTA limits and refine result headers (PR #299)
+
 - retain computed GUI runs as named, foldable sessions with JSON input restoration,
   independent outputs, per-session ZIP export and deletion (PR #297 review)
 
@@ -282,6 +285,27 @@ energies, restricted partition sums, and trackers.
 ################################################################################  
 ################################################################################
 
+261024 Alexander Mitrofanov
+ * gui/{app,options,columns}.js, gui/{index.html,styles.css}
+   * organize tabs/rows as Sequences, Seed, Output, Model & Energy, Query,
+     Target and CLI-only; align wrapped labels and place Compute first
+   + add a three-way seed selector, synchronized accessibility flags and
+     mode-dependent input availability; place SHAPE beside accessibility
+   * group compact CSV choices with descriptions and group selection actions;
+     default to 10 predictions and expanded task-specific energy columns,
+     explicitly preserving browser defaults in native-compatible JSON
+ * gui/{protocol,uploads,parameter-file}.js, gui/examples/
+   * accept 50 FASTA records per strand of 2-5,000 nt each, with longest
+     selected query x longest selected target <= 1,000,000; allow 1 MB FASTA
+   + warn about ignored FASTA header descriptions while using first-token IDs
+ * gui/{sessions,results}.js
+   * select results from the header/name, order Show/Hide before the name and
+     ZIP/delete actions, compact table headings and distinguish selected rows
+ * gui/tests/, scripts/wasm/test-browser.py, README.md, gui/docs/
+   + cover limits, native JSON replay/defaults, dependent controls, grouped CSV
+     choices, desktop/mobile alignment and result header selection
+   * address https://github.com/BackofenLab/IntaRNA/pull/299#issuecomment-6375752155
+
 261023 Alexander Mitrofanov
  * gui/{app,sessions,results,visualization}.js, gui/{index.html,styles.css}
    + retain successful runs in browser memory with unique IDs, editable names,
diff --git a/README.md b/README.md
index e5b5f6b0..ce94edbd 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,8 @@
 seeding of interaction sites**
 
 Predict short RNA pairs or evaluate supplied structures locally with the [browser interface](https://backofenlab.github.io/IntaRNA/gui/).
-Computed runs stay in separate, foldable sessions in the current tab. Name and select sessions to restore their inputs and compare results; editing or resetting parameters keeps earlier runs.
+The browser accepts up to 50 records per strand, 2–5,000 nucleotides each, with longest selected query × longest selected target at most 1,000,000. Prediction defaults to 10 interactions per pair and includes opening and seed energies; evaluation selects all energy columns.
+Computed runs stay in separate, foldable sessions under Results in the current tab. Name and select sessions to restore their inputs and compare results; editing or resetting parameters keeps earlier runs.
 Select an interaction to view it in vaRRI, or download a session’s ZIP with inputs, compiled versions, reproducible parameters and all outputs. Sessions are temporary and are cleared when the page is reloaded.
 See the [WebAssembly build instructions](gui/docs/step1-wasm-compilation.md) and
 [interface/deployment notes](gui/docs/step4-results-and-deployment.md).
diff --git a/gui/app.js b/gui/app.js
index d265b466..446a7f60 100644
--- a/gui/app.js
+++ b/gui/app.js
@@ -1,6 +1,6 @@
 import { parseFasta, prepareRequest, CSV_COLUMNS } from './protocol.js';
-import { GROUPS, FIELDS, EXTRA_OUTPUTS } from './options.js';
-import { CSV_CATALOG } from './columns.js';
+import { GROUPS, FIELDS, EXTRA_OUTPUTS, UI_DEFAULTS } from './options.js';
+import { CSV_CATALOG, CSV_GROUPS, defaultColumns } from './columns.js';
 import { PredictionRunner } from './runner.js';
 import { downloadText } from './results.js';
 import { SessionsView } from './sessions.js';
@@ -44,7 +44,7 @@ function group(key, label) {
   const body = element('div', '', 'group-body'); panel.append(body);
   byId('parameter-groups').append(panel); addTab(key, label); return body;
 }
-addTab('sequence-input', 'Sequence input');
+addTab('sequence-input', 'Sequences');
 byId('parameter-tabs').addEventListener('keydown', (event) => {
   if (!['ArrowLeft', 'ArrowRight', 'Home', 'End'].includes(event.key)) return;
   const tabs = [...byId('parameter-tabs').children].filter((tab) => !tab.hidden);
@@ -52,34 +52,67 @@ byId('parameter-tabs').addEventListener('keydown', (event) => {
   const next = event.key === 'Home' ? 0 : event.key === 'End' ? tabs.length - 1 : (current + (event.key === 'ArrowRight' ? 1 : -1) + tabs.length) % tabs.length;
   event.preventDefault(); activateGroup(tabs[next].getAttribute('aria-controls'), true);
 });
+// Render each requested row explicitly; labels share a grid row so wrapped
+// labels do not push neighboring controls out of alignment.
+function renderField(field, id = field.key) {
+  const wrapper = element('div', '', `field${field.type === 'checkbox' ? ' check' : ''}`);
+  const label = element('label', field.label); label.htmlFor = id; label.title = `--${field.key}`;
+  const input = element(field.type === 'select' ? 'select' : field.type === 'textarea' ? 'textarea' : 'input'); input.id = id;
+  if (input.tagName === 'INPUT') input.type = field.type;
+  if (field.type === 'select') for (const [value, name] of Object.entries(field.choices)) { const option = element('option', name); option.value = value; input.append(option); }
+  if (field.type === 'number') { input.min = field.min; input.max = field.max; input.step = field.step ?? 1; }
+  if (field.type === 'checkbox') { input.checked = field.value; wrapper.append(input, label); }
+  else { input.value = field.value; wrapper.append(label, input); }
+  if (field.hint) { const hint = element('p', field.hint, 'field-hint'); hint.id = `${id}-help`; input.setAttribute('aria-describedby', hint.id); wrapper.append(hint); }
+  if (field.type === 'textarea') {
+    input.spellcheck = false;
+    const upload = element('input'); upload.type = 'file'; upload.accept = '.txt,.csv,.shape,.dat'; upload.setAttribute('aria-label', `Load ${field.label} from a local text file`);
+    upload.dataset.for = field.key;
+    upload.addEventListener('change', async () => {
+      const file = upload.files[0]; upload.value = ''; if (!file) return;
+      const revision = ++inputRevision;
+      try {
+        if (file.size > 1000000) throw new Error('Choose a text file of at most 1 MB.');
+        const content = await file.text();
+        if (inputRevision !== revision || input.disabled) return;
+        input.value = content; input.dispatchEvent(new Event('input', { bubbles: true }));
+      } catch (error) { if (inputRevision === revision) showInputError(error); }
+    }); wrapper.append(upload);
+  }
+  if (field.key === 'noSeed') wrapper.hidden = true;
+  return wrapper;
+}
+function fieldRow(body, fields, suffix = '') {
+  const grid = element('div', '', `field-grid columns-${fields.length}`);
+  for (const field of fields) grid.append(renderField(field, field.key + suffix));
+  body.append(grid); return grid;
+}
 for (const definition of GROUPS) {
-  const body = group(definition.key, definition.label), grid = element('div', '', 'field-grid'); body.append(grid);
-  for (const field of definition.fields) {
-    const wrapper = element('div', '', `field${field.type === 'checkbox' ? ' check' : ''}`);
-    const label = element('label', field.label); label.htmlFor = field.key; label.title = `--${field.key}`;
-    const input = element(field.type === 'select' ? 'select' : field.type === 'textarea' ? 'textarea' : 'input'); input.id = field.key;
-    if (input.tagName === 'INPUT') input.type = field.type;
-    if (field.type === 'select') for (const [value, name] of Object.entries(field.choices)) { const option = element('option', name); option.value = value; input.append(option); }
-    if (field.type === 'number') { input.min = field.min; input.max = field.max; input.step = field.step ?? 1; }
-    if (field.type === 'checkbox') { input.checked = field.value; wrapper.append(input, label); }
-    else { input.value = field.value; wrapper.append(label, input); }
-    if (field.hint) { const hint = element('p', field.hint, 'field-hint'); hint.id = `${field.key}-help`; input.setAttribute('aria-describedby', hint.id); wrapper.append(hint); }
-    if (field.type === 'textarea') {
-      input.spellcheck = false;
-      const upload = element('input'); upload.type = 'file'; upload.accept = '.txt,.csv,.shape,.dat'; upload.setAttribute('aria-label', `Load ${field.label} from a local text file`);
-      upload.dataset.for = field.key;
-      upload.addEventListener('change', async () => {
-        const file = upload.files[0]; upload.value = ''; if (!file) return;
-        const revision = ++inputRevision;
-        try {
-          if (file.size > 1000000) throw new Error('Choose a text file of at most 1 MB.');
-          const content = await file.text();
-          if (inputRevision !== revision) return;
-          input.value = content; input.dispatchEvent(new Event('input', { bubbles: true }));
-        } catch (error) { if (inputRevision === revision) showInputError(error); }
-      }); wrapper.append(upload);
+  const body = group(definition.key, definition.label);
+  if (definition.key === 'seed-options') {
+    const wrapper = element('div', '', 'field seed-mode');
+    const label = element('label', 'Seed constraint'); label.htmlFor = 'seed-mode';
+    const select = element('select'); select.id = 'seed-mode';
+    for (const [value, name] of [['none', 'Disable seed constraint'], ['explicit', 'Explicit seed'], ['identify', 'Identify seeds']]) {
+      const option = element('option', name); option.value = value; select.append(option);
     }
-    grid.append(wrapper);
+    select.value = 'identify'; wrapper.append(label, select); body.append(wrapper);
+  }
+  if (definition.rows) {
+    for (const row of definition.rows) fieldRow(body, row);
+  } else fieldRow(body, definition.fields);
+  if (definition.strand) {
+    const p = definition.strand;
+    const shared = FIELDS.filter((field) => ['accNoLP', 'accNoGUend'].includes(field.key));
+    fieldRow(body, shared, p === 't' ? '-target' : '');
+    body.append(element('p', 'These two accessibility settings apply to both strands.', 'input-help'));
+    const columns = element('div', '', 'accessibility-columns'); body.append(columns);
+    const accessibility = element('div'), shape = element('div'); columns.append(accessibility, shape);
+    const field = (key) => FIELDS.find((entry) => entry.key === p + key);
+    fieldRow(accessibility, [field('AccConstr')]);
+    fieldRow(accessibility, [field('AccFile')]);
+    fieldRow(shape, [field('Shape')]);
+    fieldRow(shape, [field('ShapeMethod'), field('ShapeConversion')]);
   }
 }
 function checkbox(container, key, labelText, description) {
@@ -89,20 +122,38 @@ function checkbox(container, key, labelText, description) {
 }
 const outputBody = byId('output-options').querySelector('.group-body');
 outputBody.append(element('h3', 'CSV output columns', 'subheading'));
-outputBody.append(element('p', 'seq1 is the target; seq2 is the query. Select columns for both the table and CSV download. You can hide table columns after computation without changing the CSV.', 'input-help'));
+outputBody.append(element('p', 'seq1 is the target; seq2 is the query. Hover over a column name for details. Select columns for the table and CSV download; table visibility can be changed after computation.', 'input-help'));
 const selectionTools = element('div', '', 'selection-tools'); outputBody.append(selectionTools);
-const csvPicker = element('div', '', 'checkbox-grid'); outputBody.append(csvPicker);
-for (const column of [...CSV_COLUMNS.split(',').map((key) => CSV_CATALOG.find((column) => column.key === key)), ...CSV_CATALOG.filter((column) => !CSV_COLUMNS.split(',').includes(column.key))]) csvInputs.push(checkbox(csvPicker, column.key, `${column.key} — ${column.description}`, column.description));
-for (const [name, selection] of [['Select all', CSV_CATALOG.map((c) => c.key)], ['CLI defaults', CSV_COLUMNS.split(',')], ['Clear selection', []]]) {
+const selectColumns = (selection) => {
+  csvOrder = [...selection]; for (const input of csvInputs) input.checked = selection.includes(input.value); inputsChanged();
+};
+for (const [name, selection] of [['Select all', () => CSV_CATALOG.map((c) => c.key)], ['Task defaults', () => defaultColumns(getTask())], ['Clear selection', () => []]]) {
   const button = element('button', name); button.type = 'button';
-  button.addEventListener('click', () => { csvOrder = [...selection]; for (const input of csvInputs) input.checked = selection.includes(input.value); inputsChanged(); }); selectionTools.append(button);
+  button.addEventListener('click', () => selectColumns(selection())); selectionTools.append(button);
+}
+for (const group of CSV_GROUPS) {
+  const section = element('fieldset', '', 'csv-group'), legend = element('legend', group.label);
+  section.dataset.csvGroup = group.label;
+  for (const [name, checked] of [['Select all', true], ['Deselect all', false]]) {
+    const button = element('button', name, 'text-button'); button.type = 'button';
+    button.setAttribute('aria-label', `${name} ${group.label} columns`);
+    button.addEventListener('click', () => {
+      for (const input of csvInputs.filter((input) => group.keys.includes(input.value))) input.checked = checked;
+      inputsChanged();
+    }); legend.append(button);
+  }
+  const picker = element('div', '', 'checkbox-grid csv-columns'); section.append(legend, picker); outputBody.append(section);
+  for (const key of group.keys) {
+    const column = CSV_CATALOG.find((column) => column.key === key);
+    csvInputs.push(checkbox(picker, key, key, column.description));
+  }
 }
 outputBody.append(element('h3', 'Additional output files', 'subheading'));
 outputBody.append(element('p', 'Reports are computed with the same settings. ASCII, detailed and ensemble reports each run a fresh engine instance and can take extra time.', 'input-help'));
 const outputPicker = element('div', '', 'checkbox-grid'); outputBody.append(outputPicker);
 for (const output of EXTRA_OUTPUTS) outputInputs.push(checkbox(outputPicker, output.key, output.label));
-const generalBody = group('general-options', 'General');
-generalBody.append(element('p', 'Tasks run locally in one worker. Abort or Escape stops computation immediately. Process-level settings (threads, log paths, parameter-file paths and terminal help) are available in the CLI.'));
+const generalBody = group('general-options', 'CLI-only');
+generalBody.append(element('p', 'Process-level settings (threads, log paths, parameter-file paths and terminal help) are available in the CLI.'));
 const docs = element('a', 'Full CLI parameter documentation'); docs.href = 'https://github.com/BackofenLab/IntaRNA#readme'; generalBody.append(docs);
 
 function inputsChanged(message = 'Inputs changed. Compute to update the interactions.') {
@@ -111,9 +162,11 @@ function inputsChanged(message = 'Inputs changed. Compute to update the interact
   byId('diagnostics').hidden = true; byId('diagnostic-text').textContent = ''; status.textContent = message;
 }
 function updateLength(name) {
+  const warning = byId(`${name}-warning`); warning.hidden = true; warning.textContent = '';
   if (!byId(name).value.trim()) { byId(`${name}-length`).textContent = 'No sequence entered'; return; }
   try {
     const parsed = parseFasta(byId(name).value, name === 'query' ? 'Query' : 'Target', getTask() === 'prediction');
+    warning.textContent = parsed.warnings.join(' '); warning.hidden = !parsed.warnings.length;
     byId(`${name}-length`).textContent = `${parsed.records.length} record${parsed.records.length === 1 ? '' : 's'}, ${parsed.records.reduce((sum, r) => sum + r.sequence.length, 0).toLocaleString()} nucleotides`;
   } catch { byId(`${name}-length`).textContent = 'Check sequence format and length'; }
 }
@@ -130,9 +183,22 @@ function updateAvailability() {
     }
     for (const field of definition.fields) {
       const input = byId(field.key);
-      input.disabled = evaluation && !!field.prediction || !evaluation && definition.key === 'helix-options' && byId('model').value !== 'B' || field.key === 'kineticScore' && byId('mode').value !== 'K';
+      input.disabled = evaluation && !!field.prediction || field.key.startsWith('helix') && byId('model').value !== 'B' || field.key === 'kineticScore' && byId('mode').value !== 'K';
     }
   }
+  byId('noSeed').checked = byId('seed-mode').value === 'none';
+  for (const field of FIELDS.filter((field) => field.key.startsWith('seed'))) {
+    byId(field.key).disabled = evaluation || (field.key === 'seedTQ' ? byId('seed-mode').value !== 'explicit' : byId('seed-mode').value !== 'identify');
+  }
+  for (const p of ['q', 't']) {
+    const mode = byId(`${p}Acc`).value;
+    for (const key of ['AccW', 'AccL', 'PfScale', 'AccConstr', 'AccFile', 'Shape', 'ShapeMethod', 'ShapeConversion']) {
+      byId(p + key).disabled = mode === 'N' || ['AccW', 'AccL'].includes(key) && mode !== 'C' || key === 'AccFile' && !['P', 'E'].includes(mode);
+    }
+    for (const key of ['accNoLP', 'accNoGUend']) byId(key + (p === 't' ? '-target' : '')).disabled = mode === 'N';
+  }
+  // Upload controls follow the text area they populate, including async reads.
+  for (const upload of form.querySelectorAll('input[data-for]')) upload.disabled = byId(upload.dataset.for).disabled;
   for (const input of outputInputs) { input.disabled = evaluation && EXTRA_OUTPUTS.find((entry) => entry.key === input.value).prediction; if (input.disabled) input.checked = false; }
   updateLength('query'); updateLength('target');
 }
@@ -143,17 +209,26 @@ function resetParameters({ clearInputs = false } = {}) {
     for (const input of form.querySelectorAll('input[type=file]')) input.value = '';
     byId('examples-menu').open = false; activateGroup('sequence-input');
   }
-  csvOrder = CSV_COLUMNS.split(',');
-  for (const field of FIELDS) { const input = byId(field.key); if (field.type === 'checkbox') input.checked = field.value; else input.value = field.value; }
-  for (const input of csvInputs) input.checked = CSV_COLUMNS.split(',').includes(input.value);
+  csvOrder = defaultColumns(getTask());
+  byId('seed-mode').value = 'identify';
+  for (const field of FIELDS) { const input = byId(field.key); if (field.type === 'checkbox') input.checked = UI_DEFAULTS[field.key]; else input.value = UI_DEFAULTS[field.key]; }
+  syncAccessibilityFlags();
+  for (const input of csvInputs) input.checked = csvOrder.includes(input.value);
   for (const input of outputInputs) input.checked = false;
   byId('qIdxPos0').value = 1; byId('tIdxPos0').value = 1; byId('rri').value = '';
-  updateAvailability(); errorBox.hidden = true; inputsChanged(clearInputs ? 'Inputs cleared. Enter sequences or choose an example.' : 'Parameters reset to CLI defaults. Compute to update the interactions.');
+  updateAvailability(); errorBox.hidden = true; inputsChanged(clearInputs ? 'Inputs cleared. Enter sequences or choose an example.' : 'Parameters reset to task defaults. Compute to update the interactions.');
 }
 byId('task').addEventListener('change', resetParameters);
 byId('reset').addEventListener('click', () => resetParameters({ clearInputs: true }));
+function syncAccessibilityFlags(source) {
+  for (const key of ['accNoLP', 'accNoGUend']) {
+    if (source?.id === key + '-target') byId(key).checked = source.checked;
+    byId(key + '-target').checked = byId(key).checked;
+  }
+}
 form.addEventListener('input', (event) => {
   if (event.target.type === 'file') return;
+  syncAccessibilityFlags(event.target);
   updateAvailability(); errorBox.hidden = true; inputsChanged();
 });
 function showInputError(error) {
@@ -169,6 +244,8 @@ function applyParameters(request, message = 'Parameters loaded. Compute to analy
     if (field.type === 'checkbox') byId(field.key).checked = value;
     else byId(field.key).value = value;
   }
+  byId('seed-mode').value = request.parameters.noSeed ? 'none' : request.parameters.seedTQ ? 'explicit' : 'identify';
+  syncAccessibilityFlags();
   csvOrder = [...request.csvColumns];
   for (const input of csvInputs) input.checked = request.csvColumns.includes(input.value);
   for (const input of outputInputs) input.checked = request.outputs.includes(input.value);
@@ -253,13 +330,24 @@ byId('examples-menu').addEventListener('keydown', (event) => {
 byId('abort').addEventListener('click', () => runner.abort());
 dialog.addEventListener('cancel', (event) => { event.preventDefault(); runner.abort(); });
 window.addEventListener('pagehide', () => runner.abort());
+function currentParameters() {
+  // Keep inactive edits in the form for toggling back, but exclude them from
+  // validation, saved JSON and native computation. Shared flags stay active
+  // whenever either strand uses accessibility.
+  return Object.fromEntries(FIELDS.map((field) => {
+    const input = byId(field.key);
+    const inactive = ['accNoLP', 'accNoGUend'].includes(field.key)
+      ? input.disabled && byId(field.key + '-target').disabled : input.disabled;
+    return [field.key, inactive ? field.value : field.type === 'checkbox' ? input.checked : input.value];
+  }));
+}
 function currentRequest() {
   const selected = csvInputs.filter((input) => input.checked).map((input) => input.value);
   const columns = [...csvOrder.filter((key) => selected.includes(key)), ...selected.filter((key) => !csvOrder.includes(key))];
   return {
     task: getTask(), query: byId('query').value, target: byId('target').value,
     qIdxPos0: byId('qIdxPos0').value, tIdxPos0: byId('tIdxPos0').value, rri: byId('rri').value,
-    parameters: Object.fromEntries(FIELDS.map((field) => [field.key, field.type === 'checkbox' ? byId(field.key).checked : byId(field.key).value])),
+    parameters: currentParameters(),
     csvColumns: columns, outputs: outputInputs.filter((input) => input.checked && !input.disabled).map((input) => input.value),
   };
 }
@@ -268,7 +356,9 @@ form.addEventListener('submit', async (event) => {
   const request = currentRequest();
   errorBox.hidden = true;
   let prepared;
-  try { prepared = prepareRequest(request); } catch (error) { errorBox.textContent = error.message; errorBox.hidden = false; return; }
+  try {
+    if (getTask() === 'prediction' && byId('seed-mode').value === 'explicit' && !request.parameters.seedTQ.trim()) throw new Error('Explicit seed: enter target&query dot-bar encodings.');
+    prepared = prepareRequest(request); } catch (error) { errorBox.textContent = error.message; errorBox.hidden = false; return; }
   inputsChanged('Computing interactions…'); byId('loading-status').textContent = 'Loading the prediction engine…';
   byId('inputs').disabled = true; byId('results').setAttribute('aria-busy', 'true'); dialog.showModal();
   try {
diff --git a/gui/columns.js b/gui/columns.js
index 6b42b93a..9c096021 100644
--- a/gui/columns.js
+++ b/gui/columns.js
@@ -313,3 +313,23 @@ export const CSV_CATALOG = [
     "numeric": true
   }
 ];
+
+// Every native column appears once. Ensemble energies and their components are
+// grouped with probabilities so users can see the cost/meaning of those outputs.
+export const CSV_GROUPS = [
+  { label: 'Energy', keys: ['E', 'ED1', 'ED2', 'E_init', 'E_loops', 'E_dangleL', 'E_dangleR', 'E_endL', 'E_endR', 'E_hybrid', 'E_norm', 'E_hybridNorm', 'E_add', 'seedE', 'seedED1', 'seedED2'] },
+  { label: 'Output', keys: ['subseqDP', 'subseqDB', 'hybridDP', 'hybridDB', 'hybridDPfull', 'hybridDBfull', 'bpList'] },
+  { label: 'Sequence', keys: ['id1', 'id2', 'seq1', 'seq2', 'subseq1', 'subseq2'] },
+  { label: 'Interaction', keys: ['start1', 'end1', 'start2', 'end2', 'seedStart1', 'seedEnd1', 'seedStart2', 'seedEnd2'] },
+  { label: 'Partition Function', keys: ['Pu1', 'Pu2', 'seedPu1', 'seedPu2', 'w', 'Etotal', 'Eall', 'Eall1', 'Eall2', 'Zall', 'Zall1', 'Zall2', 'EallTotal', 'P_E', 'RT'] },
+];
+
+export function defaultColumns(task) {
+  const context = ['id1', 'start1', 'end1', 'id2', 'start2', 'end2', 'subseqDP', 'hybridDP', 'E'];
+  // Seed energies remain available in evaluation, where native output is NAN.
+  // List them explicitly: seedEnd1/2 are coordinates, not energy columns.
+  const extra = task === 'evaluation'
+    ? [...CSV_CATALOG.filter(({ key }) => key.startsWith('E')).map(({ key }) => key), 'seedE', 'seedED1', 'seedED2']
+    : ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2'];
+  return [...new Set([...context, ...extra])];
+}
diff --git a/gui/docs/json-workflow.md b/gui/docs/json-workflow.md
index 342d1f24..df5f7dfb 100644
--- a/gui/docs/json-workflow.md
+++ b/gui/docs/json-workflow.md
@@ -1,6 +1,7 @@
 # JSON settings and reproducible runs
 
-Load and Store sit to the right of Reset parameters. Store downloads
+The action bar starts with Compute/Evaluate, followed by Input Parameters:
+Examples, Store, Load and Reset. Store downloads
 `parameter.json` containing non-default settings and embedded input text in the
 [native JSON format](../../doc/json-parameters.md). `_comment` records compiled
 tool/library versions and executable reproduction commands. It is JSON metadata,
@@ -35,11 +36,11 @@ CSV output, additional files and diagnostics. Editing parameters, Load, examples
 Reset, invalid inputs, failed computations and cancellation preserve prior
 sessions. Failed or aborted computations do not create a session.
 
-The newest session opens automatically. Use **Show results** (or **Restore
-inputs** after editing), or select its output area, to restore that session’s
+The newest session opens automatically under **Results**. Use **Show**, select
+its header/name, or select its output area to restore that session’s
 computed inputs and fold the other sessions. The task, sequence text, signed
 indices, SHAPE/accessibility text, CSV selection/order and additional output
-selection are restored together. **Hide results** folds the output. Each session
+selection are restored together. **Hide** folds the output. Each session
 keeps its own filter, sorting and visible columns; folded vaRRI frames are unloaded
 and restored when their session is reopened.
 
@@ -60,8 +61,14 @@ JSON explicitly records that version information is unavailable.
 ## Reset and examples
 
 Reset clears the editable sequences, interactions and uploaded files and restores
-prediction defaults. Previously computed sessions remain available. Empty FASTA
-fields show the short demonstration sequences as placeholders only. The Example disclosure menu sits to the left of Reset.
+prediction defaults (10 interactions per pair, expanded energy/seed columns).
+Evaluation defaults select all energy columns. These GUI defaults are written
+explicitly in JSON when they differ from the CLI; importing existing JSON still
+uses native defaults for omitted parameters. Inactive controls keep their edits
+in the form for switching modes, but their values are omitted from executed and
+stored settings. Previously computed sessions remain available. Empty FASTA
+fields show the short demonstration sequences as placeholders only. The Examples
+disclosure menu follows the Input Parameters label.
 
 Maintainers edit `gui/examples/index.json` (an array of local JSON filenames).
 Each listed file contains `name`, `description`, and `configuration`, where the
@@ -73,9 +80,13 @@ examples show an error in the menu; they never overwrite the form.
 ## Local FASTA files
 
 Each strand has an Upload button and accepts a text-file drop into its textarea.
-Files are read locally (at most 60 KB), validated with the same FASTA checks as
+Files are read locally (at most 1 MB), validated with the same FASTA checks as
 manual entry, and replace only that strand after successful validation. Prediction
-accepts multi-FASTA; evaluation requires one record. Invalid files leave the
+accepts up to 50 FASTA records per strand, each 2–5,000 nt; evaluation requires
+one record. The longest selected query × longest selected target must be at most
+1,000,000. Names end at the first whitespace; ignored header descriptions produce
+a warning below the corresponding field. Both FASTA fields scroll horizontally
+and vertically. Invalid files leave the
 previous input intact. A later edit, reset, import or computation discards any
 pending file read, so delayed reads cannot replace newer input.
 
@@ -117,3 +128,22 @@ pending file read, so delayed reads cannot replace newer input.
   `tests/data` directory for the existing CLI harness.
 - Static staging (including the new session module and engine digest checks),
   shell syntax and `git diff --check` passed.
+
+## PR #299 review validation (2026-10-24)
+
+- `npm test --prefix gui`: all 20 tests passed, including FASTA limits, header
+  warnings, complete column grouping and explicit browser-default JSON replay.
+- `scripts/wasm/test-browser.py` passed with real WASM in Chromium and Firefox.
+  It covers the reordered panels, aligned controls, shared accessibility flags,
+  seed/accessibility/helix modes, inactive values, explicit-seed Load/Store,
+  group selection, FASTA scrolling/warnings and result header/name selection,
+  plus the existing prediction/evaluation, ZIP, abort and session checks.
+- Desktop and 390 px mobile screenshots were inspected. All seven panels have
+  no document overflow; table contents retain their own horizontal scrolling.
+- `node scripts/wasm/smoke-protocol.mjs <staged-engine>` passed native-reference
+  checks and byte-identical JSON archive replay. The unchanged engine uses the
+  parent branch's Emscripten 4.0.23 / ViennaRNA 2.7.2 assets and original metadata.
+- A fresh GCC 14 release build passed `make tests -j2`: all nine API/CLI groups.
+  Existing CLI fixtures were linked into the out-of-tree `tests/data` directory.
+- Static staging with engine digest validation, JavaScript/Python syntax checks,
+  shell syntax and `git diff --check` passed.
diff --git a/gui/docs/step3-frontend-ui.md b/gui/docs/step3-frontend-ui.md
index 5cc524bd..e0436b75 100644
--- a/gui/docs/step3-frontend-ui.md
+++ b/gui/docs/step3-frontend-ui.md
@@ -21,25 +21,26 @@ the group website. Footer and table notes use the available width, wrapping only
 when the viewport requires it.
 
 ```text
-Group logo       IntaRNA / RNA–RNA interaction analysis        University logo
+Group logo       IntaRNA package / RNA–RNA interaction analysis        University logo
 RNA–RNA interactions                             Computations stay on your device
-Task: Prediction / Evaluation                                Load example
-[ Sequence input | Query | Target | Seed | Helix | SHAPE | Energy | Output | General ]
+Task: Prediction / Evaluation
+[ Sequences | Seed | Output | Model & Energy | Query | Target | CLI-only ]
 [ Active panel: e.g. query + target, start indices, evaluation structures      ]
-Reset parameters                                                Compute
-Interactions / search / show-hide columns / CSV + ZIP download
+Compute     Input Parameters: Examples / Store / Load / Reset
+Results / Show-Hide / name / ZIP download / delete
+Interactions / search / show-hide columns / CSV download
 Selected interaction / embedded vaRRI
 Additional output files / diagnostics / compiled versions
 ```
 
-Every CLI group has a tab with one visible panel. Sequence input is selected
+Every CLI group has a tab with one visible panel. Sequences is selected
 initially. Tabs expose `aria-selected`, `aria-controls` and roving focus; Left/Right
 move between available tabs, and Home/End select the first/last. Tab names wrap
 on narrow screens. Prediction-only tabs and controls are disabled/hidden during
-evaluation; if the selected tab becomes unavailable, Sequence input is selected.
-Changing task resets parameters to their CLI defaults while preserving sequence text; Load example also restores the
-complementary pair. The native default output count is one; browser users can
-request 0–100 interactions per pair. Zero enables accessibility-only output.
+evaluation; if the selected tab becomes unavailable, Sequences is selected.
+Changing task resets parameters to their task defaults while preserving sequence text; Load example also restores the
+complementary pair. The browser defaults to 10 interactions per pair (the native default remains
+one), and accepts 0–100. Zero enables accessibility-only output.
 
 ## Inputs, defaults and validation
 
@@ -53,15 +54,29 @@ CSV uses a fixed semicolon delimiter.
 Process settings (threads, file/log paths, parameter files, help/version commands)
 are replaced by the worker lifecycle, local data inputs, downloads and displayed
 compiled versions. The base-pair maximization energy model is intentionally
-excluded. The helix-block interaction model B is supported.
+excluded. The helix-block interaction model B is supported, with helix controls at the end
+of Model & Energy, enabled only for model B. Seed constraint offers Disable,
+Explicit seed and Identify seeds, enabling only the relevant controls. Query and
+Target include their own accessibility/SHAPE columns and synchronized copies of
+the two shared accessibility flags. Ignore disables accessibility controls;
+import modes disable window/span and enable the data input. Disabled settings
+remain editable when re-enabled but do not enter the request. Explicit row grids
+align inputs even when their labels wrap.
 
-Prediction accepts plain sequence or up to 20 FASTA records per strand.
+CSV columns are grouped as Energy, Output, Sequence, Interaction and Partition
+Function, with per-group selection actions and name-only labels with description
+tooltips. Prediction adds ED1, ED2, seedE, seedStart1 and seedStart2 to the native
+CSV columns; evaluation selects all energy outputs. JSON records these browser
+defaults explicitly so native replay retains the same output.
+
+Prediction accepts plain sequence or up to 50 FASTA records per strand.
 Evaluation requires one query and target and 1–100 predefined structures.
 Wrapped/lowercase sequence text and DNA T normalize to uppercase RNA U. A/C/G/U/N
-are accepted. Each record is 2–2,000 nt; seed predictions additionally require
+are accepted. Each record is 2–5,000 nt; seed predictions additionally require
 at least `seedBP` nucleotides. FASTA IDs end at the first whitespace, matching the CLI. Duplicate IDs (including collisions after
-native CSV semicolon replacement) are rejected. The total selected all-vs-all
-query length × target length, or sum of pairwise products, is capped at 1,000,000.
+native CSV semicolon replacement) are rejected. Ignored header descriptions are reported below the input. The longest selected
+query length × longest selected target length is capped at 1,000,000, including
+pairwise mode; the cap is not summed over records.
 The per-strand start index applies to all records and defaults to one. Negative
 indices skip zero, matching `RnaSequence`; output coordinates remain inclusive.
 
diff --git a/gui/examples/evaluation.json b/gui/examples/evaluation.json
index b8994f18..84cab246 100644
--- a/gui/examples/evaluation.json
+++ b/gui/examples/evaluation.json
@@ -5,9 +5,14 @@
     "schema": "IntaRNA-parameters-v1",
     "parameters": {
       "personality": "IntaRNAeval",
-      "query": {"text": ">query\nGGGAGGAGGG\n"},
-      "target": {"text": ">target\nCCCUCCUCCC\n"},
-      "rri": "1||||||||||&1||||||||||"
+      "query": {
+        "text": ">query\nGGGAGGAGGG\n"
+      },
+      "target": {
+        "text": ">target\nCCCUCCUCCC\n"
+      },
+      "rri": "1||||||||||&1||||||||||",
+      "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,Etotal,ED1,ED2,E_init,E_loops,E_dangleL,E_dangleR,E_endL,E_endR,E_hybrid,E_norm,E_hybridNorm,E_add,Eall,Eall1,Eall2,EallTotal,seedE,seedED1,seedED2"
     }
   }
 }
diff --git a/gui/examples/prediction.json b/gui/examples/prediction.json
index 2b834042..bd76029a 100644
--- a/gui/examples/prediction.json
+++ b/gui/examples/prediction.json
@@ -4,8 +4,14 @@
   "configuration": {
     "schema": "IntaRNA-parameters-v1",
     "parameters": {
-      "query": {"text": ">query\nGGGAGGAGGG\n"},
-      "target": {"text": ">target\nCCCUCCUCCC\n"}
+      "query": {
+        "text": ">query\nGGGAGGAGGG\n"
+      },
+      "target": {
+        "text": ">target\nCCCUCCUCCC\n"
+      },
+      "outNumber": 10,
+      "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,ED1,ED2,seedE,seedStart1,seedStart2"
     }
   }
 }
diff --git a/gui/index.html b/gui/index.html
index 679c15b0..a77b74e7 100644
--- a/gui/index.html
+++ b/gui/index.html
@@ -14,7 +14,7 @@
   <a class="skip-link" href="#workspace">Skip to sequence inputs</a>
   <header class="site-header">
     <a href="https://www.bioinf.uni-freiburg.de" aria-label="Bioinformatics Group Freiburg"><img class="group-logo" src="assets/bioinf-fr-logo-blau.png" alt="Bioinformatics Group Freiburg"></a>
-    <a class="brand" href="./"><img src="mark.svg" width="44" height="44" alt=""><span>IntaRNA<small>RNA–RNA interaction analysis</small></span></a>
+    <a class="brand" href="./"><img src="mark.svg" width="44" height="44" alt=""><span>IntaRNA package<small>RNA–RNA interaction analysis</small></span></a>
     <a class="university-link" href="https://www.bioinf.uni-freiburg.de" aria-label="Bioinformatics - University of Freiburg"><span>Bioinformatics -<br>University of Freiburg</span><img class="uni-logo" src="assets/logo-uni-freiburg.png" alt="University of Freiburg"></a>
   </header>
   <main id="workspace">
@@ -38,33 +38,33 @@
             <div class="group-body">
               <div class="sequence-grid">
                 <section class="strand"><div class="strand-heading"><label for="query">Query RNA</label><span>5′ to 3′</span><div class="upload-controls"><button id="query-upload-button" type="button" class="secondary small-button" aria-label="Upload query FASTA">Upload</button><small>or drop in the field</small><input id="query-upload" type="file" accept=".fa,.fasta,.fna,.fas,.txt,text/plain" hidden></div></div>
-                  <textarea id="query" spellcheck="false" autocapitalize="off" autocomplete="off" aria-describedby="sequence-help query-length" placeholder=">query&#10;GGGAGGAGGG"></textarea>
-                  <div class="sequence-meta"><span id="query-length">No sequence entered</span><label for="qIdxPos0">Start index <input id="qIdxPos0" type="number" min="-2000000000" max="2000000000" step="1" value="1"></label></div>
+                  <textarea id="query" wrap="off" spellcheck="false" autocapitalize="off" autocomplete="off" aria-describedby="sequence-help query-length query-warning" placeholder=">query&#10;GGGAGGAGGG"></textarea>
+                  <div class="sequence-meta"><label for="qIdxPos0">Start index <input id="qIdxPos0" type="number" min="-2000000000" max="2000000000" step="1" value="1"></label><span id="query-length">No sequence entered</span></div><p id="query-warning" class="input-warning" role="status" hidden></p>
                 </section>
                 <section class="strand"><div class="strand-heading"><label for="target">Target RNA</label><span>5′ to 3′</span><div class="upload-controls"><button id="target-upload-button" type="button" class="secondary small-button" aria-label="Upload target FASTA">Upload</button><small>or drop in the field</small><input id="target-upload" type="file" accept=".fa,.fasta,.fna,.fas,.txt,text/plain" hidden></div></div>
-                  <textarea id="target" spellcheck="false" autocapitalize="off" autocomplete="off" aria-describedby="sequence-help target-length" placeholder=">target&#10;CCCUCCUCCC"></textarea>
-                  <div class="sequence-meta"><span id="target-length">No sequence entered</span><label for="tIdxPos0">Start index <input id="tIdxPos0" type="number" min="-2000000000" max="2000000000" step="1" value="1"></label></div>
+                  <textarea id="target" wrap="off" spellcheck="false" autocapitalize="off" autocomplete="off" aria-describedby="sequence-help target-length target-warning" placeholder=">target&#10;CCCUCCUCCC"></textarea>
+                  <div class="sequence-meta"><label for="tIdxPos0">Start index <input id="tIdxPos0" type="number" min="-2000000000" max="2000000000" step="1" value="1"></label><span id="target-length">No sequence entered</span></div><p id="target-warning" class="input-warning" role="status" hidden></p>
                 </section>
               </div>
-              <p id="sequence-help" class="input-help">Plain sequence or multi-FASTA (prediction only), A/C/G/U/T/N. Up to 20 records per field and 2–2,000 nt per record; total query × target length across selected pairs ≤ 1,000,000. Seed predictions also require at least as many nucleotides as seed base pairs. Signed start indices apply to every record on that strand; negative indexing skips zero.</p>
+              <p id="sequence-help" class="input-help">Plain sequence or multi-FASTA (prediction only), A/C/G/U/T/N. Up to 50 records per field and 2–5,000 nt per record; longest selected query × longest selected target ≤ 1,000,000. FASTA names stop at the first whitespace. Seed predictions also require at least as many nucleotides as seed base pairs. Signed start indices apply to every record on that strand; negative indexing skips zero.</p>
               <div id="evaluation-input" hidden><label for="rri">Interactions to evaluate (target &amp; query)</label><textarea id="rri" spellcheck="false" aria-describedby="rri-help" placeholder="1||||||||||&amp;1||||||||||"></textarea><p id="rri-help" class="input-help">Each strand uses its start coordinate and dots/bars in 5′ to 3′ order; pair bars antiparallel. Example: 1|||&amp;1|||. Separate structures with a colon. Evaluation retains energy/accessibility settings and ignores prediction filters.</p></div>
             </div>
           </section>
         </div>
-        <div class="compute-bar"><details id="examples-menu" class="examples-menu"><summary>Example</summary><div id="example-options"><p class="input-help">Loading examples…</p></div></details><button id="reset" type="button" class="secondary">Reset parameters</button><button id="load-parameters" type="button" class="secondary" title="Load settings and embedded inputs from JSON">Load</button><button id="store-parameters" type="button" class="secondary" title="Download current settings and embedded inputs as JSON">Store</button><input id="parameter-upload" type="file" accept=".json,application/json" hidden><button id="compute" type="submit" class="primary">Compute interactions</button></div>
+        <div class="compute-bar"><button id="compute" type="submit" class="primary">Compute interactions</button><span class="parameter-actions-label">Input Parameters:</span><details id="examples-menu" class="examples-menu"><summary>Examples</summary><div id="example-options"><p class="input-help">Loading examples…</p></div></details><button id="store-parameters" type="button" class="secondary" title="Download current settings and embedded inputs as JSON">Store</button><button id="load-parameters" type="button" class="secondary" title="Load settings and embedded inputs from JSON">Load</button><button id="reset" type="button" class="secondary">Reset</button><input id="parameter-upload" type="file" accept=".json,application/json" hidden></div>
       </fieldset>
       <p id="input-error" class="error" role="alert" hidden></p>
     </form>
     <section id="results" class="results" aria-labelledby="results-title" aria-busy="false">
-      <div class="results-heading"><h2 id="results-title">Sessions</h2><p id="result-status" role="status" aria-live="polite">Enter your sequences or choose an example, then compute.</p></div>
+      <div class="results-heading"><h2 id="results-title">Results</h2><p id="result-status" role="status" aria-live="polite">Enter your sequences or choose an example, then compute.</p></div>
       <p class="input-help">Completed runs stay in this tab until deleted or the page is reloaded. Select a session to restore its inputs; download its ZIP to keep a copy.</p>
       <div id="sessions"></div>
       <details id="diagnostics" hidden><summary>Computation diagnostics</summary><pre id="diagnostic-text"></pre></details>
       <template id="session-template">
         <article class="session">
           <div class="session-header">
+            <button data-role="toggle" class="secondary" type="button" aria-expanded="false">Show</button>
             <label class="session-name">Session name <input data-role="name" type="text" maxlength="120" autocomplete="off"></label>
-            <button data-role="toggle" class="secondary" type="button" aria-expanded="false">Show results</button>
             <button data-role="download-zip" class="secondary" type="button" title="Download this session’s parameter.json, CSV and all additional outputs.">Download ZIP</button>
             <button data-role="delete" class="secondary delete-session" type="button" title="Delete session"><svg viewBox="0 0 24 24" width="20" height="20" aria-hidden="true"><path d="M4 7h16M9 7V4h6v3M6 7l1 13h10l1-13M10 10v7m4-7v7" fill="none" stroke="currentColor" stroke-width="1.8" stroke-linecap="round" stroke-linejoin="round"/></svg><span class="sr-only">Delete session</span></button>
           </div>
diff --git a/gui/options.js b/gui/options.js
index efd310b0..4e95bccf 100644
--- a/gui/options.js
+++ b/gui/options.js
@@ -20,62 +20,83 @@ const strand = (prefix, label) => [
   number(`${prefix}RegionLenMax`, 'Automatic region length limit', 0, 0, 99999, { ...prediction, hint: '0 disables automatic region detection.' }),
   number(`${prefix}PfScale`, `${label} partition-function scale`, 1.07, 1, 99999, { step: 'any' }),
 ];
-export const GROUPS = [
-  { key: 'query-options', label: 'Query', fields: strand('q', 'Query') },
-  { key: 'target-options', label: 'Target', fields: strand('t', 'Target') },
-  { key: 'seed-options', label: 'Seed', prediction: true, fields: [
-    flag('noSeed', 'Do not require a seed', prediction),
-    text('seedTQ', 'Explicit seeds', { ...prediction, hint: 'Target&query dot-bar encodings, e.g. 1|||&1|||; separate seeds with commas.' }),
-    number('seedBP', 'Seed base pairs', 7, 2, 20, prediction),
-    number('seedMaxUP', 'Maximum unpaired seed bases (both strands)', 0, 0, 20, prediction),
-    number('seedQMaxUP', 'Maximum unpaired query seed bases', -1, -1, 20, { ...prediction, hint: '-1 uses the combined limit.' }),
-    number('seedTMaxUP', 'Maximum unpaired target seed bases', -1, -1, 20, prediction),
-    number('seedMaxE', 'Maximum seed energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
-    number('seedMaxEhybrid', 'Maximum seed hybridization energy (kcal/mol)', 999, -999, 999, { ...prediction, step: 'any' }),
-    number('seedMinPu', 'Minimum seed unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
-    text('seedQRange', 'Query seed regions', prediction), text('seedTRange', 'Target seed regions', prediction),
-    flag('seedNoGU', 'Exclude GU pairs in seeds', prediction), flag('seedNoGUend', 'Exclude GU pairs at seed ends', prediction),
-  ] },
-  { key: 'helix-options', label: 'Helix (model B)', prediction: true, fields: [
-    number('helixMinBP', 'Minimum helix base pairs', 2, 2, 4, prediction),
-    number('helixMaxBP', 'Maximum helix base pairs', 10, 2, 20, prediction),
-    number('helixMaxIL', 'Maximum helix interior-loop size', 0, 0, 2, prediction),
-    number('helixMinPu', 'Minimum helix unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
-    number('helixMaxE', 'Maximum helix energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
-    flag('helixFullE', 'Use full helix energy for the energy limit', prediction),
-  ] },
-  { key: 'shape-options', label: 'SHAPE', fields: ['q', 't'].flatMap((p) => [
+const fields = new Map([
+  ...strand('q', 'Query'), ...strand('t', 'Target'),
+  flag('accNoLP', 'Exclude lonely pairs in accessibility'),
+  flag('accNoGUend', 'Exclude GU helix ends in accessibility'),
+  flag('noSeed', 'Do not require a seed', prediction),
+  text('seedTQ', 'Explicit seeds', { ...prediction, hint: 'Target&query dot-bar encodings, e.g. 1|||&1|||; separate seeds with commas.' }),
+  number('seedBP', 'Seed base pairs', 7, 2, 20, prediction),
+  number('seedMaxUP', 'Maximum unpaired seed bases (both strands)', 0, 0, 20, prediction),
+  number('seedQMaxUP', 'Maximum unpaired query seed bases', -1, -1, 20, { ...prediction, hint: '-1 uses the combined limit.' }),
+  number('seedTMaxUP', 'Maximum unpaired target seed bases', -1, -1, 20, prediction),
+  number('seedMaxE', 'Maximum seed energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
+  number('seedMaxEhybrid', 'Maximum seed hybridization energy (kcal/mol)', 999, -999, 999, { ...prediction, step: 'any' }),
+  number('seedMinPu', 'Minimum seed unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
+  text('seedQRange', 'Query seed regions', prediction), text('seedTRange', 'Target seed regions', prediction),
+  flag('seedNoGU', 'Exclude GU pairs in seeds', prediction), flag('seedNoGUend', 'Exclude GU pairs at seed ends', prediction),
+  number('helixMinBP', 'Minimum helix base pairs', 2, 2, 4, prediction),
+  number('helixMaxBP', 'Maximum helix base pairs', 10, 2, 20, prediction),
+  number('helixMaxIL', 'Maximum helix interior-loop size', 0, 0, 2, prediction),
+  number('helixMinPu', 'Minimum helix unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
+  number('helixMaxE', 'Maximum helix energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
+  flag('helixFullE', 'Use full helix energy for the energy limit', prediction),
+  select('model', 'Interaction model', 'X', { X: 'Seed extension (MFE)', S: 'Single site (MFE)', P: 'Ensemble energy', B: 'Helix blocks (MFE)' }, prediction),
+  select('mode', 'Prediction algorithm', 'H', { H: 'Heuristic', M: 'Exact', S: 'Seed only', K: 'Greedy seed extension' }, prediction),
+  select('kineticScore', 'Greedy extension score', 'A', { A: 'Energy change', B: 'Change / (1 + s1 + s2)', C: 'Change / (1 + 2 max(s1,s2))' }, prediction),
+  select('energyVRNA', 'ViennaRNA parameter set', 'Turner04', { Turner04: 'Turner 2004', Turner99: 'Turner 1999', Andronescu07: 'Andronescu 2007' }),
+  number('temperature', 'Temperature (°C)', 37, 0, 100, { step: 'any' }),
+  number('energyAdd', 'Additional energy (kcal/mol)', 0, -999, 999, { step: 'any' }),
+  flag('energyNoDangles', 'Exclude dangling-end energy'),
+  number('windowWidth', 'Prediction window width', 0, 0, 99999, { ...prediction, hint: '0 disables prediction windows; otherwise at least 10 nt.' }),
+  number('windowOverlap', 'Prediction window overlap', 150, 0, 99999, prediction),
+  number('outNumber', 'Maximum interactions per sequence pair', 1, 0, 100, { ...prediction, hint: 'Browser limit: 100; 0 computes accessibility only.' }),
+  select('outOverlap', 'Allow overlapping interactions', 'B', { B: 'Both strands', N: 'Neither strand', T: 'Target only', Q: 'Query only' }, prediction),
+  number('outMaxE', 'Maximum interaction energy (exclusive, kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
+  number('outDeltaE', 'Maximum difference from MFE (kcal/mol)', 100, 0, 100, { ...prediction, step: 'any' }),
+  number('outMinPu', 'Minimum unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
+  flag('outBestSeedOnly', 'Report only the best seed', prediction),
+  flag('outNoLP', 'Exclude lonely interaction pairs', prediction), flag('outNoGUend', 'Exclude GU interaction helix ends', prediction),
+  flag('outPerRegion', 'Report each region combination separately', prediction), flag('outPairwise', 'Match FASTA records pairwise', prediction),
+  select('outCsvSort', 'CSV download sort column', '', { '': 'Native computation order', ...Object.fromEntries(CSV_CATALOG.map((column) => [column.key, column.label])) }),
+  text('outSpotProbSpots', 'Interaction probability spots', { ...prediction, hint: 'Optional target&query coordinate pairs, e.g. 3&7,5&9. Empty selects all spots.' }),
+  ...['q', 't'].flatMap((p) => [
     text(`${p}Shape`, `${p === 'q' ? 'Query' : 'Target'} SHAPE data`, { type: 'textarea', hint: 'One sequence only. Paste position and reactivity, one pair per line; positions start at 1.' }),
     { ...text(`${p}ShapeMethod`, 'SHAPE method'), value: 'D', hint: 'D, Dm1.8b-0.6, Z, Zb0.89 or W.' },
     { ...text(`${p}ShapeConversion`, 'SHAPE conversion'), value: 'Os1.6i-2.29', hint: 'M, C0.25, S, Ls0.68i0.2 or Os1.6i-2.29.' },
+  ]),
+].map((field) => [field.key, field]));
+
+// Explicit rows separate visual order from native parameter defaults.
+const rows = (keys) => keys.map((row) => row.map((key) => fields.get(key)));
+const strandRows = (p) => rows([
+  [`${p}Set`, `${p}Region`, `${p}IntLenMax`, `${p}IntLoopMax`, `${p}RegionLenMax`],
+  [`${p}Acc`, `${p}AccW`, `${p}AccL`, `${p}PfScale`],
+]);
+const strandGroup = (p, label) => ({
+  key: `${label.toLowerCase()}-options`, label, strand: p,
+  rows: strandRows(p),
+  fields: [...strandRows(p).flat(), ...rows([
+    ...(p === 'q' ? [['accNoLP', 'accNoGUend']] : []),
+    [`${p}AccConstr`, `${p}AccFile`, `${p}Shape`, `${p}ShapeMethod`, `${p}ShapeConversion`],
+  ]).flat()],
+});
+export const GROUPS = [
+  { key: 'seed-options', label: 'Seed', prediction: true, rows: rows([
+    ['noSeed'], ['seedTQ'], ['seedBP', 'seedMaxUP', 'seedQMaxUP', 'seedTMaxUP'],
+    ['seedMaxE', 'seedMinPu', 'seedMaxEhybrid'], ['seedQRange', 'seedTRange'], ['seedNoGU', 'seedNoGUend'],
   ]) },
-  { key: 'interaction-options', label: 'Interaction and energy', fields: [
-    select('model', 'Interaction model', 'X', { X: 'Seed extension (MFE)', S: 'Single site (MFE)', P: 'Ensemble energy', B: 'Helix blocks (MFE)' }, prediction),
-    select('mode', 'Prediction algorithm', 'H', { H: 'Heuristic', M: 'Exact', S: 'Seed only', K: 'Greedy seed extension' }, prediction),
-    select('kineticScore', 'Greedy extension score', 'A', { A: 'Energy change', B: 'Change / (1 + s1 + s2)', C: 'Change / (1 + 2 max(s1,s2))' }, prediction),
-    select('energyVRNA', 'ViennaRNA parameter set', 'Turner04', { Turner04: 'Turner 2004', Turner99: 'Turner 1999', Andronescu07: 'Andronescu 2007' }),
-    number('temperature', 'Temperature (°C)', 37, 0, 100, { step: 'any' }),
-    number('energyAdd', 'Additional energy (kcal/mol)', 0, -999, 999, { step: 'any' }),
-    flag('energyNoDangles', 'Exclude dangling-end energy'), flag('accNoLP', 'Exclude lonely pairs in accessibility'),
-    flag('accNoGUend', 'Exclude GU helix ends in accessibility'),
-    number('windowWidth', 'Prediction window width', 0, 0, 99999, { ...prediction, hint: '0 disables prediction windows; otherwise at least 10 nt.' }),
-    number('windowOverlap', 'Prediction window overlap', 150, 0, 99999, prediction),
-  ] },
-  { key: 'output-options', label: 'Output', fields: [
-    number('outNumber', 'Maximum interactions per sequence pair', 1, 0, 100, { ...prediction, hint: 'Browser limit: 100; 0 computes accessibility only.' }),
-    select('outOverlap', 'Allow overlapping interactions', 'B', { B: 'Both strands', N: 'Neither strand', T: 'Target only', Q: 'Query only' }, prediction),
-    number('outMaxE', 'Maximum interaction energy (exclusive, kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }),
-    number('outDeltaE', 'Maximum difference from MFE (kcal/mol)', 100, 0, 100, { ...prediction, step: 'any' }),
-    number('outMinPu', 'Minimum unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }),
-    flag('outBestSeedOnly', 'Report only the best seed', prediction),
-    flag('outNoLP', 'Exclude lonely interaction pairs', prediction), flag('outNoGUend', 'Exclude GU interaction helix ends', prediction),
-    flag('outPerRegion', 'Report each region combination separately', prediction), flag('outPairwise', 'Match FASTA records pairwise', prediction),
-    select('outCsvSort', 'CSV download sort column', '', { '': 'Native computation order', ...Object.fromEntries(CSV_CATALOG.map((column) => [column.key, column.label])) }),
-    text('outSpotProbSpots', 'Interaction probability spots', { ...prediction, hint: 'Optional target&query coordinate pairs, e.g. 3&7,5&9. Empty selects all spots.' }),
-  ] },
-];
+  { key: 'output-options', label: 'Output', fields: [...fields.values()].filter((field) => field.key.startsWith('out')) },
+  { key: 'interaction-options', label: 'Model & Energy', rows: rows([
+    ['model', 'mode'], ['energyVRNA', 'temperature', 'energyAdd'], ['energyNoDangles'],
+    ['windowWidth', 'windowOverlap'], ['kineticScore'],
+    ['helixMinBP', 'helixMaxBP', 'helixMaxIL', 'helixMinPu', 'helixMaxE'], ['helixFullE'],
+  ]) },
+  strandGroup('q', 'Query'), strandGroup('t', 'Target'),
+].map((group) => ({ ...group, fields: group.fields ?? group.rows.flat() }));
 export const FIELDS = GROUPS.flatMap((group) => group.fields);
 export const PARAMETER_DEFAULTS = Object.freeze(Object.fromEntries(FIELDS.map((field) => [field.key, field.value])));
+export const UI_DEFAULTS = Object.freeze({ ...PARAMETER_DEFAULTS, outNumber: 10 });
 export const EXTRA_OUTPUTS = [
   ['qMinE', 'Query minimum energies', true], ['tMinE', 'Target minimum energies', true],
   ['qAcc', 'Query opening energies'], ['tAcc', 'Target opening energies'],
diff --git a/gui/parameter-file.js b/gui/parameter-file.js
index a076ee1e..7e52f341 100644
--- a/gui/parameter-file.js
+++ b/gui/parameter-file.js
@@ -1,4 +1,4 @@
-import { JSON_SCHEMA, CSV_COLUMNS, normalizeParameters } from './protocol.js';
+import { JSON_SCHEMA, CSV_COLUMNS, LIMITS, normalizeParameters } from './protocol.js';
 import { FIELDS, PARAMETER_DEFAULTS, EXTRA_OUTPUTS } from './options.js';
 import { CSV_CATALOG } from './columns.js';
 
@@ -25,8 +25,8 @@ export function exportParameters(request, provenance) {
   const normalized = normalizeParameters(request);
   const { columns, outputs } = selections(request);
   const parameters = {
-    query: { text: text(typeof request.query === 'string' ? request.query : request.query.fasta, 'Query', 60000) },
-    target: { text: text(typeof request.target === 'string' ? request.target : request.target.fasta, 'Target', 60000) },
+    query: { text: text(typeof request.query === 'string' ? request.query : request.query.fasta, 'Query', LIMITS.maxFastaBytes) },
+    target: { text: text(typeof request.target === 'string' ? request.target : request.target.fasta, 'Target', LIMITS.maxFastaBytes) },
   };
   if (request.task === 'evaluation') parameters.personality = 'IntaRNAeval';
   for (const [key, value] of Object.entries(normalized)) {
@@ -73,7 +73,7 @@ export function importParameters(source) {
       // Plain nucleotide strings are native inline sequences; file paths need
       // explicit embedding because the browser cannot open local paths.
       if (typeof content !== 'string' || (content === value && (embeddedKeys.includes(key) || !/^[ACGUTNacgutn]*$/.test(value)))) throw new Error(`${key}: embed the input using {"text":"file contents"}.`);
-      if (key === 'query' || key === 'target') request[key] = text(content, key, 60000);
+      if (key === 'query' || key === 'target') request[key] = text(content, key, LIMITS.maxFastaBytes);
       else request.parameters[key] = text(content, key);
     } else if (key === 'personality') {
       if (!['IntaRNA', 'IntaRNAeval'].includes(value)) throw new Error('The browser supports IntaRNA prediction and IntaRNAeval evaluation.');
diff --git a/gui/protocol.js b/gui/protocol.js
index 92f078f8..d452de28 100644
--- a/gui/protocol.js
+++ b/gui/protocol.js
@@ -1,41 +1,41 @@
 import { FIELDS, PARAMETER_DEFAULTS, EXTRA_OUTPUTS, ENSEMBLE_COLUMNS } from './options.js';
 import { CSV_CATALOG } from './columns.js';
 
-// Bound total work as well as per-strand length, including all-vs-all FASTA jobs.
-export const LIMITS = Object.freeze({ minLength: 2, maxLength: 2000, maxRecords: 20, maxPairs: 1000000 });
+// Bound the largest pair's matrix while allowing batches of shorter sequences.
+export const LIMITS = Object.freeze({ minLength: 2, maxLength: 5000, maxRecords: 50, maxPairs: 1000000, maxFastaBytes: 1000000 });
 export const CSV_COLUMNS = 'id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E';
 export const CONTEXT_COLUMNS = ['id1', 'start1', 'end1', 'id2', 'start2', 'end2', 'E'];
 export const DEFAULTS = Object.freeze({ query: '>query\nGGGAGGAGGG', target: '>target\nCCCUCCUCCC', task: 'prediction' });
 export const EVALUATION_EXAMPLE = '1||||||||||&1||||||||||';
 
 export function parseFasta(text, label, multiple = true) {
-  if (typeof text !== 'string' || text.length > 60000 || !text.trim()) throw new Error(`${label}: enter a sequence or FASTA records.`);
+  if (typeof text !== 'string' || text.length > LIMITS.maxFastaBytes || !text.trim()) throw new Error(`${label}: enter a sequence or FASTA records (at most 1 MB).`);
   const lines = text.trim().split(/\r?\n/).map((line) => line.trim()).filter(Boolean);
-  const records = [];
+  const records = [], warnings = [];
   let current;
   for (const line of lines) {
     if (line.startsWith('>')) {
-      current = { id: line.slice(1).trim(), sequence: '' };
+      const header = line.slice(1).trim();
+      current = { id: header.split(/\s+/)[0], sequence: '' };
       if (!current.id || current.id.length > 200 || /[\x00-\x1f\x7f]/.test(current.id)) throw new Error(`${label}: the FASTA header needs a name (at most 200 characters).`);
-      // The native FASTA parser takes the identifier before the first space.
-      current.id = current.id.split(/\s+/)[0];
+      if (/\s+\S/.test(header)) warnings.push(`${label}: ignoring FASTA description after the name “${current.id}”.`);
       records.push(current);
     } else {
       if (!current) { current = { id: label.toLowerCase(), sequence: '' }; records.push(current); }
       current.sequence += line.replace(/\s/g, '').toUpperCase().replaceAll('T', 'U');
     }
   }
-  if ((!multiple && records.length !== 1) || records.length > LIMITS.maxRecords) throw new Error(`${label}: ${multiple ? 'use at most 20 FASTA records' : 'evaluation requires exactly one FASTA record'}.`);
+  if ((!multiple && records.length !== 1) || records.length > LIMITS.maxRecords) throw new Error(`${label}: ${multiple ? 'use at most 50 FASTA records' : 'evaluation requires exactly one FASTA record'}.`);
   const ids = new Set();
   for (const record of records) {
     if (!record.sequence || /[^ACGUN]/.test(record.sequence)) throw new Error(`${label}: use only A, C, G, U, T or N in every sequence.`);
-    if (record.sequence.length < LIMITS.minLength || record.sequence.length > LIMITS.maxLength) throw new Error(`${label}: use 2–2,000 nucleotides per record.`);
+    if (record.sequence.length < LIMITS.minLength || record.sequence.length > LIMITS.maxLength) throw new Error(`${label}: use 2–5,000 nucleotides per record.`);
     // Native CSV replaces semicolons with underscores. Keep pair grouping unique.
     const id = record.id.replaceAll(';', '_');
     if (ids.has(id)) throw new Error(`${label}: FASTA identifiers must be unique (also after replacing semicolons with underscores).`);
     ids.add(id);
   }
-  return { records, fasta: records.map(({ id, sequence }) => `>${id}\n${sequence}\n`).join('') };
+  return { records, warnings, fasta: records.map(({ id, sequence }) => `>${id}\n${sequence}\n`).join('') };
 }
 export function parseSequence(text, label) {
   const parsed = parseFasta(text, label, false);
@@ -148,8 +148,8 @@ export function prepareRequest(request) {
   const parameters = normalizeParameters(request);
   const qRecords = selectedRecords(query, parameters.qSet, 'qSet'), tRecords = selectedRecords(target, parameters.tSet, 'tSet');
   if (parameters.outPairwise && qRecords.length !== tRecords.length) throw new Error('Pairwise output requires the same number of selected query and target records.');
-  const work = parameters.outPairwise ? qRecords.reduce((sum, q, i) => sum + q.sequence.length * tRecords[i].sequence.length, 0) : qRecords.reduce((sum, q) => sum + q.sequence.length, 0) * tRecords.reduce((sum, t) => sum + t.sequence.length, 0);
-  if (work > LIMITS.maxPairs) throw new Error('The total query × target length across selected sequence pairs must be at most 1,000,000.');
+  const work = Math.max(...qRecords.map((q) => q.sequence.length)) * Math.max(...tRecords.map((t) => t.sequence.length));
+  if (work > LIMITS.maxPairs) throw new Error('The longest selected query × longest selected target must be at most 1,000,000.');
 
   // Validate sequence-dependent settings before loading the engine.
   for (const [p, records] of [['q', qRecords], ['t', tRecords]]) {
diff --git a/gui/results.js b/gui/results.js
index 8f4385f0..92a06f70 100644
--- a/gui/results.js
+++ b/gui/results.js
@@ -103,11 +103,15 @@ export class ResultsView {
     const rows = selectRows(this.rows, this.search.value, this.key, this.direction);
     const columns = this.columns.filter((column) => this.visible.has(column.key));
     this.header.replaceChildren();
-    const viewHeading = document.createElement('th'); viewHeading.scope = 'col'; viewHeading.textContent = 'vaRRI';
+    const viewHeading = document.createElement('th'); viewHeading.scope = 'col'; viewHeading.setAttribute('aria-label', 'Interaction visualization');
     this.header.append(viewHeading);
     for (const column of columns) {
       const cell = document.createElement('th'), button = document.createElement('button');
-      cell.scope = 'col'; button.type = 'button'; button.textContent = column.label;
+      cell.scope = 'col'; button.type = 'button';
+      const split = column.numeric ? column.label.indexOf(' ') : -1;
+      if (split > 0) button.append(document.createTextNode(column.label.slice(0, split)), document.createElement('br'), document.createTextNode(column.label.slice(split + 1)));
+      else button.textContent = column.label;
+      button.title = column.description ?? column.label;
       const active = column.key === this.key, direction = this.direction === 1 ? 'ascending' : 'descending';
       cell.setAttribute('aria-sort', active ? direction : 'none');
       button.setAttribute('aria-label', `Sort by ${column.label}${active ? `, currently ${direction}` : ''}`);
diff --git a/gui/sessions.js b/gui/sessions.js
index a4b6d3d0..71b712d0 100644
--- a/gui/sessions.js
+++ b/gui/sessions.js
@@ -14,14 +14,14 @@ export class SessionsView {
     this.selected = null;
     for (const session of this.entries.values()) {
       session.root.dataset.selected = 'false';
-      session.toggle.textContent = session.panel.hidden ? 'Show results' : 'Restore inputs';
+      session.toggle.textContent = 'Show';
     }
   }
 
   setExpanded(session, expanded) {
     session.panel.hidden = !expanded;
     session.toggle.setAttribute('aria-expanded', String(expanded));
-    session.toggle.textContent = expanded ? 'Hide results' : 'Show results';
+    session.toggle.textContent = expanded ? 'Hide' : 'Show';
     // Unload third-party viewers while folded. The table selection is retained
     // and can be visualized again without recomputing the prediction.
     if (!expanded) session.view.visualization.clear();
@@ -65,6 +65,17 @@ export class SessionsView {
     name.addEventListener('change', () => { rename(); name.value = session.name; });
     name.addEventListener('keydown', (event) => { if (event.key === 'Enter') name.blur(); });
     rename();
+    // The name and header background also select a run. Action buttons retain
+    // their own behavior, so exporting/deleting cannot overwrite edited inputs.
+    const header = root.querySelector('.session-header');
+    header.tabIndex = 0; header.setAttribute('role', 'group');
+    header.setAttribute('aria-label', 'Select result and restore its inputs');
+    for (const event of ['click', 'focusin']) header.addEventListener(event, (event) => {
+      if (!event.target.closest('button') && (this.selected !== id || session.panel.hidden)) this.select(session);
+    });
+    header.addEventListener('keydown', (event) => {
+      if (event.target === header && ['Enter', ' '].includes(event.key)) { event.preventDefault(); this.select(session); }
+    });
     // Clicking or keyboard-focusing an output area selects its computed inputs.
     for (const event of ['click', 'focusin']) session.panel.addEventListener(event, () => {
       if (this.selected !== id) this.select(session);
diff --git a/gui/styles.css b/gui/styles.css
index f6e4e451..360ba4c4 100644
--- a/gui/styles.css
+++ b/gui/styles.css
@@ -4,6 +4,8 @@
   --brand-blue:#145a96;
   --brand-blue-dark:#0f4676;
   --brand-blue-soft:#eaf2f8;
+  --table-header:#d9e8f6;
+  --table-selection:#c6e5f4;
   --brand-accent:#f4bb44;
   --surface:#fff;
   --surface-muted:#f3f7fb;
@@ -282,8 +284,26 @@ fieldset {
   grid-template-columns:repeat(auto-fill,minmax(220px,1fr));
   gap:20px 24px;
   align-items:start;
+  margin-bottom:20px;
 }
 
+/* Explicit rows preserve the requested grouping; subgrid aligns inputs below
+   labels of different heights without fixing a font-dependent label height. */
+.field-grid.columns-1 { grid-template-columns:minmax(0,1fr); }
+.field-grid.columns-2 { grid-template-columns:repeat(2,minmax(0,1fr)); }
+.field-grid.columns-3 { grid-template-columns:repeat(3,minmax(0,1fr)); }
+.field-grid.columns-4 { grid-template-columns:repeat(4,minmax(0,1fr)); }
+.field-grid.columns-5 { grid-template-columns:repeat(5,minmax(0,1fr)); }
+.field-grid > .field:not(.check) { display:grid; grid-row:span 4; grid-template-rows:subgrid; row-gap:5px; }
+.field-grid > .field:not(.check) > :nth-child(2) { align-self:start; }
+.accessibility-columns { display:grid; grid-template-columns:repeat(2,minmax(0,1fr)); gap:24px; margin-top:20px; }
+.accessibility-columns > div { min-width:0; }
+.seed-mode { max-width:24rem; margin-bottom:20px; }
+.field-grid:has(#noSeed) { display:none; }
+#query,#target { white-space:pre; overflow:auto; }
+#sequence-help,#general-options p { max-width:none; }
+.input-warning { font-size:.85rem; color:#79510b; max-width:none; overflow-wrap:anywhere; }
+
 .strand-heading,.sequence-meta {
   display:flex;
   align-items:center;
@@ -354,10 +374,6 @@ fieldset {
   background:transparent;
 }
 
-.field:has(textarea) {
-  grid-column:1/-1;
-}
-
 .field:has(:disabled) {
   opacity:.65;
 }
@@ -396,6 +412,11 @@ fieldset {
   padding:.3rem .6rem;
 }
 
+.csv-group { margin-top:16px; }
+.csv-group legend { font-weight:600; }
+.text-button { background:none; border:0; padding:.15rem .5rem; color:var(--brand-blue); font-size:.8rem; text-decoration:underline; font-weight:400; }
+.csv-columns { grid-template-columns:repeat(auto-fill,minmax(125px,1fr)); gap:6px 16px; padding:6px 0; }
+
 .results {
   background:var(--surface);
   border:1px solid var(--border);
@@ -450,14 +471,15 @@ table {
 }
 
 th {
-  background:var(--brand-blue-soft);
+  background:var(--table-header);
   text-align:left;
+  padding:0 5px;
 }
 
 th button {
   background:transparent;
   border:0;
-  padding:12px;
+  padding:10px 0;
   color:var(--brand-blue-dark);
   width:100%;
   text-align:left;
@@ -473,7 +495,7 @@ th[aria-sort=descending] button::after {
 
 td {
   border-top:1px solid #e0e8f0;
-  padding:10px 12px;
+  padding:10px 5px;
 }
 
 tr:nth-child(even) {
@@ -491,7 +513,7 @@ td.number {
 }
 
 .view-interaction {
-  padding:.25rem .6rem;
+  padding:.25rem .35rem;
   color:var(--brand-blue-dark);
   background:var(--surface);
 }
@@ -500,9 +522,10 @@ tbody tr {
   cursor:pointer;
 }
 
-tbody tr:hover,tbody tr.selected {
+tbody tr:hover {
   background:var(--brand-blue-soft);
 }
+tbody tr.selected { background:var(--table-selection); }
 
 .view-interaction[aria-pressed=true] {
   background:var(--brand-blue);
@@ -674,6 +697,7 @@ dialog::backdrop {
   .field-grid {
     grid-template-columns:repeat(auto-fill,minmax(min(100%,220px),1fr));
   }
+  .field-grid[class*=columns-],.accessibility-columns { grid-template-columns:1fr; }
   .results {
     padding:14px;
   }
@@ -721,8 +745,9 @@ textarea.drag-over { outline:3px solid var(--brand-accent); background:var(--bra
 .task-choice:has(:checked) small { color:white; }
 .task-choice:has(:focus-visible) { outline:3px solid var(--brand-accent); outline-offset:3px; }
 .compute-bar { justify-content:flex-start; gap:8px; }
-#compute { margin-left:auto; }
-@media(max-width:480px) { #compute { flex-basis:100%; margin-left:0; } }
+#compute { margin-right:24px; }
+.parameter-actions-label { font-size:.9rem; }
+@media(max-width:480px) { #compute { flex-basis:100%; margin-right:0; } .parameter-actions-label { flex-basis:100%; } }
 
 /* Every completed run owns its controls and output, even while folded. */
 .session { margin-top:18px; border:1px solid var(--border); border-radius:6px; min-width:0; }
diff --git a/gui/tests/protocol.test.mjs b/gui/tests/protocol.test.mjs
index 42517703..07a60071 100644
--- a/gui/tests/protocol.test.mjs
+++ b/gui/tests/protocol.test.mjs
@@ -3,7 +3,7 @@ import assert from 'node:assert/strict';
 import { readFileSync } from 'node:fs';
 import { DEFAULTS, EVALUATION_EXAMPLE, parseSequence, parseFasta, prepareRequest, makeArguments, CSV_COLUMNS, sequenceOffset } from '../protocol.js';
 import { FIELDS } from '../options.js';
-import { CSV_CATALOG } from '../columns.js';
+import { CSV_CATALOG, CSV_GROUPS, defaultColumns } from '../columns.js';
 const request = (parameters = {}, extra = {}) => ({ ...DEFAULTS, parameters, ...extra });
 
 test('FASTA normalization, identifiers, bounded multi-record work and subsets', () => {
@@ -12,11 +12,11 @@ test('FASTA normalization, identifiers, bounded multi-record work and subsets',
   const fasta = '>a\nGGGAGGAGGG\n>b\nGGGAGGAGGG';
   assert.equal(prepareRequest(request({}, { query: fasta })).query.records.length, 2);
   assert.throws(() => prepareRequest(request({}, { task: 'evaluation', query: fasta, rri: EVALUATION_EXAMPLE })), /exactly one/);
-  assert.throws(() => prepareRequest(request({}, { query: '>a\n'+'A'.repeat(2000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) })), /1,000,000/);
-  assert.doesNotThrow(() => prepareRequest(request({ qSet: '2-2' }, { query: '>a\n'+'A'.repeat(2000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) })));
+  assert.throws(() => prepareRequest(request({}, { query: '>a\n'+'A'.repeat(5000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) })), /1,000,000/);
+  assert.doesNotThrow(() => prepareRequest(request({ qSet: '2-2' }, { query: '>a\n'+'A'.repeat(5000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) })));
   assert.throws(() => prepareRequest(request({ outPairwise: true }, { query: fasta })), /same number/);
   assert.throws(() => prepareRequest(request({ qSet: '3-3' })), /within/);
-  assert.throws(() => prepareRequest(request({}, { query: 'A'.repeat(2001) })));
+  assert.throws(() => prepareRequest(request({}, { query: 'A'.repeat(5001) })));
 });
 
 test('CLI defaults, ranges and strict typed controls reject invalid values', () => {
@@ -85,3 +85,35 @@ test('JSON worker boundary embeds all inputs with typed non-default settings', a
   const worker = readFileSync(new URL('../intarna-worker.js', import.meta.url), 'utf8');
   assert.ok(worker.includes("callMain(['--parameterFile=/parameter.json'])"));
 });
+
+
+test('browser batches use longest selected strands and round-trip full FASTA inputs', async () => {
+  const batch = Array.from({ length: 50 }, (_, i) => `>q${i}\n${'A'.repeat(5000)}\n`).join('');
+  assert.equal(parseFasta(batch, 'Query').records.length, 50);
+  assert.throws(() => parseFasta(batch + '>extra\nAA', 'Query'), /50 FASTA/);
+  assert.doesNotThrow(() => prepareRequest(request({}, { query: batch, target: 'C'.repeat(200) })));
+  assert.throws(() => prepareRequest(request({}, { query: batch, target: 'C'.repeat(201) })), /1,000,000/);
+  const crossed = { query: '>q1\n' + 'A'.repeat(5000) + '\n>q2\nAA', target: '>t1\nCC\n>t2\n' + 'C'.repeat(5000) };
+  assert.throws(() => prepareRequest(request({ outPairwise: true, noSeed: true }, crossed)), /1,000,000/);
+  const { serializeParameters, importParameters } = await import('../parameter-file.js');
+  assert.equal(importParameters(serializeParameters(request({}, { query: batch }), 'test')).query, batch);
+  const parsed = parseFasta('>one\tdescription here\nACGU\n>two   \nACGU', 'Query');
+  assert.deepEqual(parsed.records.map((record) => record.id), ['one', 'two']);
+  assert.equal(parsed.warnings.length, 1);
+  assert.match(parsed.warnings[0], /one/);
+  assert.equal(parsed.fasta, '>one\nACGU\n>two\nACGU\n');
+});
+
+test('CSV groups cover native columns once and task defaults serialize explicitly', async () => {
+  assert.deepEqual(CSV_GROUPS.flatMap((group) => group.keys).toSorted(), CSV_CATALOG.map((column) => column.key).toSorted());
+  const energy = [...CSV_GROUPS.find((group) => group.label === 'Energy').keys, 'Etotal', 'Eall', 'Eall1', 'Eall2', 'EallTotal'];
+  for (const key of energy) assert.ok(defaultColumns('evaluation').includes(key), key);
+  for (const key of ['seedStart1', 'seedStart2', 'seedEnd1', 'seedEnd2']) assert.ok(!defaultColumns('evaluation').includes(key), key);
+  for (const key of ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2']) assert.ok(defaultColumns('prediction').includes(key), key);
+  const { exportParameters, importParameters } = await import('../parameter-file.js');
+  const input = request({ outNumber: 10 }, { csvColumns: defaultColumns('prediction') });
+  const saved = exportParameters(input, 'test');
+  assert.equal(saved.parameters.outNumber, 10);
+  assert.equal(saved.parameters.outCsvCols, input.csvColumns.join(','));
+  assert.deepEqual(prepareRequest(importParameters(saved)), prepareRequest(input));
+});
diff --git a/gui/tests/uploads.test.mjs b/gui/tests/uploads.test.mjs
index c4c34a1d..76a13200 100644
--- a/gui/tests/uploads.test.mjs
+++ b/gui/tests/uploads.test.mjs
@@ -9,5 +9,7 @@ test('FASTA uploads accept text/CRLF and validate size, format and task before r
   assert.equal(await readFastaFile(file(multi), 'Query', 'prediction'), multi);
   await assert.rejects(readFastaFile(file(multi), 'Query', 'evaluation'), /exactly one/);
   for (const invalid of ['', '\u0000bin', '>q\n--!', '>q\n']) await assert.rejects(readFastaFile(file(invalid), 'Query', 'prediction'));
-  await assert.rejects(readFastaFile({ size: 60001, text: () => { throw Error('must not read'); } }, 'Query', 'prediction'), /60 KB/);
+  const batch = Array.from({ length: 50 }, (_, i) => `>q${i}\n${'A'.repeat(5000)}\n`).join('');
+  assert.equal(await readFastaFile(file(batch), 'Query', 'prediction'), batch);
+  await assert.rejects(readFastaFile({ size: 1000001, text: () => { throw Error('must not read'); } }, 'Query', 'prediction'), /1 MB/);
 });
diff --git a/gui/uploads.js b/gui/uploads.js
index 10035231..81748047 100644
--- a/gui/uploads.js
+++ b/gui/uploads.js
@@ -1,8 +1,8 @@
-import { parseFasta } from './protocol.js';
+import { parseFasta, LIMITS } from './protocol.js';
 
 /** Read and validate a local text file before replacing a FASTA input. */
 export async function readFastaFile(file, label, task) {
-  if (!file || file.size > 60000) throw new Error(`${label}: choose a FASTA text file of at most 60 KB.`);
+  if (!file || file.size > LIMITS.maxFastaBytes) throw new Error(`${label}: choose a FASTA text file of at most 1 MB.`);
   const text = await file.text();
   parseFasta(text, label, task !== 'evaluation');
   return text;
diff --git a/scripts/wasm/test-browser.py b/scripts/wasm/test-browser.py
index 34b09e23..990e5e58 100644
--- a/scripts/wasm/test-browser.py
+++ b/scripts/wasm/test-browser.py
@@ -76,7 +76,7 @@ def predict():
     expect(page.locator('#version-info')).to_contain_text(f'ViennaRNA {vienna_version}')
     for logo in page.locator('.site-header img').all():
         assert logo.evaluate('node => node.complete && node.naturalWidth > 0')
-    for key in ['query-options', 'target-options', 'seed-options', 'helix-options', 'shape-options', 'interaction-options', 'output-options', 'general-options', 'sequence-input']:
+    for key in ['seed-options', 'output-options', 'interaction-options', 'query-options', 'target-options', 'general-options', 'sequence-input']:
         open_group(key)
 
     expect(page.get_by_role('radio', name='Prediction')).to_be_checked()
@@ -91,13 +91,90 @@ def predict():
     # Tabs support keyboard navigation and wrap without page overflow.
     page.locator('#tab-sequence-input').focus()
     page.keyboard.press('ArrowRight')
-    expect(page.locator('#tab-query-options')).to_be_focused()
-    expect(page.locator('#query-options')).to_be_visible()
+    expect(page.locator('#tab-seed-options')).to_be_focused()
+    expect(page.locator('#seed-options')).to_be_visible()
     page.keyboard.press('End')
     expect(page.locator('#tab-general-options')).to_be_focused()
     page.keyboard.press('Home')
     expect(page.locator('#tab-sequence-input')).to_be_focused()
 
+    # Review layout, task defaults and modes work with native parameters.
+    assert page.locator('[role=tab]').all_text_contents() == ['Sequences', 'Seed', 'Output', 'Model & Energy', 'Query', 'Target', 'CLI-only']
+    expect(page.locator('.brand')).to_contain_text('IntaRNA package')
+    expect(page.locator('#results-title')).to_have_text('Results')
+    expect(page.locator('#outNumber')).to_have_value('10')
+    assert page.locator('.compute-bar').evaluate('node => node.firstElementChild.id') == 'compute'
+    assert page.locator('.sequence-meta').first.evaluate('node => node.firstElementChild.tagName') == 'LABEL'
+    fill('query', '>named\tignored description\n' + 'G' * 1000 + '\n' * 20 + 'GG')
+    expect(page.locator('#query-warning')).to_contain_text('ignoring FASTA description')
+    expect(page.locator('#query-warning')).to_contain_text('named')
+    assert page.locator('#query').evaluate('node => node.scrollWidth > node.clientWidth && node.scrollHeight > node.clientHeight')
+    fill('query', '>named   \nGGGAGGAGGG')
+    expect(page.locator('#query-warning')).not_to_be_visible()
+
+    for prefix, group in [('q', 'query-options'), ('t', 'target-options')]:
+        open_group(group)
+        # Each explicit row shares label height, including wrapped labels.
+        for keys in [[prefix + suffix for suffix in ['Set', 'Region', 'IntLenMax', 'IntLoopMax', 'RegionLenMax']], [prefix + suffix for suffix in ['Acc', 'AccW', 'AccL', 'PfScale']]]:
+            tops = [page.locator('#' + key).bounding_box()['y'] for key in keys]
+            assert max(tops) - min(tops) < 1, tops
+        expect(page.locator('#' + prefix + 'AccFile')).to_be_disabled()
+        page.locator('#' + prefix + 'Acc').select_option('P')
+        expect(page.locator('#' + prefix + 'AccFile')).to_be_enabled()
+        for suffix in ['AccW', 'AccL']:
+            expect(page.locator('#' + prefix + suffix)).to_be_disabled()
+        page.locator('#' + prefix + 'Acc').select_option('N')
+        for suffix in ['AccW', 'AccL', 'AccConstr', 'AccFile', 'PfScale', 'Shape', 'ShapeMethod', 'ShapeConversion']:
+            expect(page.locator('#' + prefix + suffix)).to_be_disabled()
+        expect(page.locator('input[data-for="' + prefix + 'Shape"]')).to_be_disabled()
+        page.locator('#' + prefix + 'Acc').select_option('C')
+        expect(page.locator('#' + prefix + 'Shape')).to_be_enabled()
+    page.locator('#accNoLP-target').check()
+    expect(page.locator('#accNoLP')).to_be_checked()
+    open_group('query-options')
+    page.locator('#accNoLP').uncheck()
+    expect(page.locator('#accNoLP-target')).not_to_be_checked()
+    open_group('interaction-options')
+    expect(page.locator('#helixMinBP')).to_be_disabled()
+    page.locator('#model').select_option('B')
+    expect(page.locator('#helixMinBP')).to_be_enabled()
+    page.locator('#model').select_option('X')
+    expect(page.locator('#helixMinBP')).to_be_disabled()
+    open_group('seed-options')
+    expect(page.locator('#seedTQ')).to_be_disabled()
+    page.locator('#seed-mode').select_option('none')
+    for key in ['seedBP', 'seedTQ', 'seedQRange', 'seedNoGU']:
+        expect(page.locator('#' + key)).to_be_disabled()
+    page.locator('#seed-mode').select_option('explicit')
+    expect(page.locator('#seedTQ')).to_be_enabled()
+    expect(page.locator('#seedBP')).to_be_disabled()
+    page.locator('#seed-mode').select_option('identify')
+    expect(page.locator('#seedBP')).to_be_enabled()
+    expect(page.locator('#seedTQ')).to_be_disabled()
+    open_group('output-options')
+    groups = page.locator('.csv-group')
+    assert groups.count() == 5
+    for group in groups.all():
+        group.get_by_role('button', name=re.compile('^Select all')).click()
+        assert group.locator('input:not(:checked)').count() == 0
+        group.get_by_role('button', name='Deselect all').click()
+        assert group.locator('input:checked').count() == 0
+    page.get_by_role('button', name='Task defaults', exact=True).click()
+    for key in ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2']:
+        expect(page.locator('.csv-group input[value="' + key + '"]')).to_be_checked()
+    assert all(label.get_attribute('title') and ' — ' not in label.inner_text() for label in groups.locator('label').all())
+    # Inspect all changed panels at desktop and mobile widths.
+    for width in [1440, 390]:
+        page.set_viewport_size({'width': width, 'height': 1100 if width == 1440 else 844})
+        for key in ['sequence-input', 'seed-options', 'output-options', 'interaction-options', 'query-options', 'target-options', 'general-options']:
+            open_group(key)
+            assert page.evaluate('document.documentElement.scrollWidth <= innerWidth'), (width, key)
+            if args.screenshot:
+                path = Path(args.screenshot)
+                page.screenshot(path=str(path.with_name(f'{path.stem}-{key}-{width}.png')), full_page=True)
+    page.set_viewport_size({'width': 1440, 'height': 1100})
+    page.locator('#reset').click()
+
     # Upload and file drop use local text, validate before replacing, and reset.
     with page.expect_file_chooser() as chooser:
         page.locator('#query-upload-button').click()
@@ -135,13 +212,50 @@ def predict():
     expect(page.locator('#rri')).to_have_value('')
     load_example()
 
+    # Disabled stale edits neither block a run nor leak into JSON. Re-enabling
+    # restores local edits; loading/storing uses effective native settings.
+    fill('seedBP', '')
+    page.locator('#seed-mode').select_option('explicit')
+    compute.click()
+    expect(page.locator('#input-error')).to_contain_text('Explicit seed: enter')
+    fill('seedTQ', '1|||&1|||')
+    predict()
+    explicit_settings = json.loads(download_archive()['parameter.json'])
+    assert explicit_settings['parameters']['seedTQ'] == '1|||&1|||'
+    assert 'seedBP' not in explicit_settings['parameters']
+    with page.expect_download() as stored:
+        page.locator('#store-parameters').click()
+    explicit_file = Path(stored.value.path()).read_bytes()
+    page.locator('#reset').click()
+    page.locator('#parameter-upload').set_input_files({'name': 'explicit.json', 'mimeType': 'application/json', 'buffer': explicit_file})
+    expect(page.locator('#seed-mode')).to_have_value('explicit')
+    open_group('seed-options')
+    page.locator('#seedTQ').fill('invalid inactive seed')
+    page.locator('#seed-mode').select_option('none')
+    fill('qShape', 'invalid inactive shape')
+    page.locator('#qAcc').select_option('N')
+    open_group('target-options')
+    page.locator('#accNoGUend-target').check()
+    predict()
+    inactive_settings = json.loads(download_archive()['parameter.json'])['parameters']
+    assert inactive_settings['noSeed'] is True
+    assert inactive_settings['qAcc'] == 'N'
+    assert inactive_settings['accNoGUend'] is True
+    assert 'qShape' not in inactive_settings and 'seedTQ' not in inactive_settings
+    open_group('query-options')
+    page.locator('#qAcc').select_option('C')
+    expect(page.locator('#qShape')).to_have_value('invalid inactive shape')
+    page.locator('#reset').click()
+    load_example()
+
     # Reference prediction, selectable CSV output and independent table visibility.
     fill('outNumber', 10)
     page.locator('#outCsvSort').select_option('E')
     predict()
     expect(rows).to_have_count(10)
     assert rows.first.locator('td').all_text_contents()[1:7] == ['target', '1', '10', 'query', '1', '10']
-    assert rows.first.locator('td').all_text_contents()[-2:] == ['-21.40', '0.00']
+    assert rows.first.locator('td').nth(9).inner_text() == '-21.40'
+    assert rows.first.locator('td').last.inner_text() == '0.00'
     page.get_by_role('button', name='Sort by Energy (kcal/mol)', exact=False).click()
     assert float(rows.first.locator('td').nth(9).inner_text()) == -14.3
     page.get_by_role('button', name='Sort by Energy (kcal/mol)', exact=False).click()
@@ -157,9 +271,12 @@ def predict():
     with page.expect_download() as downloaded:
         active.locator('[data-role=download]').click()
     csv = Path(downloaded.value.path()).read_text()
-    assert csv.splitlines()[0] == 'id1;start1;end1;id2;start2;end2;subseqDP;hybridDP;E'
+    assert csv.splitlines()[0] == 'id1;start1;end1;id2;start2;end2;subseqDP;hybridDP;E;ED1;ED2;seedE;seedStart1;seedStart2'
     assert 'target;1;10;query;1;10;' in csv
     assert 'deltaE' not in csv
+    assert active.locator('thead th').first.inner_text() == ''
+    assert active.locator('thead th button br').count() >= 4
+    assert rows.first.locator('td').first.evaluate('node => getComputedStyle(node).paddingLeft') == '5px'
     assert not visualization_urls  # Third-party content loads only on selection.
     rows.first.get_by_role('button', name='Visualize').click()
     expect(active.locator('[data-role=varri-frame]')).to_be_visible()
@@ -211,6 +328,7 @@ def predict():
 
     # Multi-FASTA prediction, signed inclusive output and additional files.
     load_example()
+    fill('outNumber', 1)
     fill('query', '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG')
     fill('qIdxPos0', -3)
     fill('tIdxPos0', -5)
@@ -400,9 +518,12 @@ def predict():
     assert 'intarna-detailed.txt' in second_archive
 
     # Selecting reloads all computed inputs while retaining each table's filter.
-    first.locator('[data-role=toggle]').press('Space')
+    first.locator('.session-header').focus()
+    first.locator('.session-header').press('Space')
     expect(second.locator('[data-role=panel]')).not_to_be_visible()
     expect(first.locator('[data-role=panel]')).to_be_visible()
+    assert first.locator('.session-header').evaluate('node => node.firstElementChild.dataset.role') == 'toggle'
+    expect(first.locator('[data-role=toggle]')).to_have_text('Hide')
     expect(page.get_by_role('radio', name='Prediction')).to_be_checked()
     expect(page.locator('#qIdxPos0')).to_have_value('-3')
     expect(page.locator('#tIdxPos0')).to_have_value('-5')
@@ -442,6 +563,8 @@ def predict():
     # Names are literal text and cannot introduce markup, duplicate IDs or paths.
     first.get_by_label('Session name', exact=True).fill('<img src=x onerror=alert(1)> / β')
     first.get_by_label('Session name', exact=True).press('Enter')
+    expect(page.locator('#temperature')).to_have_value('24')
+    expect(first.locator('[data-role=panel]')).to_be_visible()
     assert first.locator('img').count() == 0
     with page.expect_download() as renamed:
         first.locator('[data-role=download-zip]').click()
@@ -464,6 +587,7 @@ def predict():
     page.set_viewport_size({'width': 1440, 'height': 1100})
 
     # Delete releases only that output; current inputs and other sessions survive.
+    second.locator('[data-role=toggle]').click()
     first.locator('[data-role=delete]').click()
     expect(sessions).to_have_count(1)
     expect(page.locator('#temperature')).to_have_value('42')