:root {
  --bg: #0b1020;
  --panel: rgba(16, 24, 48, 0.86);
  --panel-2: rgba(22, 31, 61, 0.92);
  --line: rgba(255, 255, 255, 0.12);
  --text: #edf2ff;
  --muted: #b7c0dd;
  --accent: #6ee7f2;
  --accent-2: #9b8cff;
  --green: #5be49b;
  --gold: #ffd166;
  --plus: #6ee7f2;
  --minus: #ff8db3;
  --danger: #ff7d7d;
  --shadow: 0 16px 48px rgba(0, 0, 0, 0.28);
  --radius: 18px;
  --font: Inter, ui-sans-serif, system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif;
}

* { box-sizing: border-box; }
html, body { margin: 0; padding: 0; min-height: 100%; }
body {
  font-family: var(--font);
  color: var(--text);
  background:
    radial-gradient(circle at top left, rgba(110, 231, 242, 0.16), transparent 28%),
    radial-gradient(circle at top right, rgba(155, 140, 255, 0.18), transparent 24%),
    linear-gradient(180deg, #08101d 0%, #0e1529 100%);
}

.hero, .layout, .footer { width: min(1500px, calc(100vw - 32px)); margin: 0 auto; }
.hero {
  display: flex; justify-content: space-between; gap: 24px; align-items: center;
  padding: 28px 0 18px;
}
.eyebrow { color: var(--accent); font-size: 0.85rem; text-transform: uppercase; letter-spacing: 0.12em; }
h1 { margin: 8px 0 12px; font-size: clamp(2rem, 4vw, 3.3rem); line-height: 1; }
.subtitle { max-width: 820px; color: var(--muted); font-size: 1.02rem; line-height: 1.5; margin: 0; }
.hero-actions { display: flex; gap: 12px; flex-wrap: wrap; justify-content: flex-end; }

/* === Added for PAM logo === */
.hero-title {
  display: flex;
  align-items: center;
  gap: 16px;
}

.logo {
  width: 112px;
  height:112px;
  object-fit: contain;
}

.layout {
  display: grid;
  grid-template-columns: 360px minmax(0, 1fr);
  gap: 20px;
  padding-bottom: 20px;
}

.main-stack { display: grid; gap: 20px; }
.two-up { display: grid; grid-template-columns: minmax(0, 1.4fr) minmax(360px, 0.9fr); gap: 20px; }

.panel {
  background: linear-gradient(180deg, var(--panel), var(--panel-2));
  border: 1px solid var(--line);
  border-radius: var(--radius);
  box-shadow: var(--shadow);
  backdrop-filter: blur(10px);
  padding: 18px;
}
.panel h2 { margin: 0 0 14px; font-size: 1.15rem; }
.label { display: block; margin-bottom: 8px; font-size: 0.92rem; color: var(--muted); }
.muted { color: var(--muted); }
code {
  background: rgba(255,255,255,0.08);
  padding: 2px 6px; border-radius: 7px; color: #fff;
}
select, input[type="text"], input[type="search"], .table-filter {
  width: 100%;
  background: rgba(8, 13, 28, 0.9);
  color: var(--text);
  border: 1px solid rgba(255,255,255,0.12);
  border-radius: 12px;
  padding: 11px 12px;
  font-size: 0.96rem;
}
input[type="range"] { width: 100%; }
.control-group { margin-bottom: 16px; }
.checkbox-group { display: grid; gap: 10px; }
.checkbox-group.two-col { grid-template-columns: 1fr 1fr; }
.motifs-box {
  border: 1px solid rgba(255,255,255,0.1);
  border-radius: 14px;
  padding: 12px;
  background: rgba(255,255,255,0.04);
}
.motif-line { display: flex; gap: 10px; align-items: center; margin: 6px 0; }
.button-row { display: flex; gap: 10px; }
.button-row.wrap { flex-wrap: wrap; }
.button {
  border: none; border-radius: 12px; cursor: pointer; font-weight: 700;
  padding: 11px 14px; transition: transform 0.14s ease, opacity 0.14s ease, background 0.14s ease;
  color: #07111f;
}
.button:hover { transform: translateY(-1px); }
.button.primary { background: linear-gradient(135deg, var(--accent), #9ef7ff); }
.button.secondary { background: linear-gradient(135deg, #d5d9ff, #f1f3ff); }
.button.ghost { background: rgba(255,255,255,0.1); color: var(--text); border: 1px solid rgba(255,255,255,0.14); }
.upload-button { display: inline-flex; align-items: center; }

.stats-grid {
  display: grid; grid-template-columns: 1fr 1fr; gap: 12px; margin-top: 16px;
}
.stat-card {
  border: 1px solid rgba(255,255,255,0.08);
  border-radius: 14px;
  padding: 12px; background: rgba(255,255,255,0.04);
}
.stat-label { color: var(--muted); font-size: 0.82rem; margin-bottom: 8px; }
.stat-value { font-size: 1.4rem; font-weight: 800; }

.section-header {
  display: flex; justify-content: space-between; align-items: flex-start; gap: 18px; margin-bottom: 14px;
}
.section-header.compact { margin-bottom: 10px; }
.section-header h2 { margin-bottom: 6px; }
.record-summary {
  display: flex; flex-wrap: wrap; gap: 12px; margin-bottom: 12px; color: var(--muted);
}
.record-chip {
  padding: 7px 10px; border-radius: 999px; background: rgba(255,255,255,0.06); border: 1px solid rgba(255,255,255,0.08);
}
.viewer-container {
  overflow: hidden;
  border-radius: 16px;
  border: 1px solid rgba(255,255,255,0.09);
  background: linear-gradient(180deg, rgba(7, 14, 28, 0.96), rgba(8, 16, 32, 0.96));
  cursor: grab;
}
.viewer-container.dragging { cursor: grabbing; }
.viewer-inner { width: 100%; min-width: 0; }
#genomeSvg { display: block; width: 100%; height: 390px; min-height: 390px; touch-action: none; user-select: none; }
.legend { display: flex; flex-wrap: wrap; gap: 10px 16px; margin-top: 12px; color: var(--muted); font-size: 0.92rem; }
.legend-item { display: inline-flex; align-items: center; gap: 8px; }
.legend-swatch { width: 14px; height: 14px; border-radius: 4px; }

/* === CHANGED: tightened PAM candidates table container and row density === */
.table-wrap {
  overflow: auto; max-height: 560px; border-radius: 14px; border: 1px solid rgba(255,255,255,0.08);
}

/* === CHANGED: smaller base font and line-height for the PAM candidates table === */
table { width: 100%; border-collapse: collapse; table-layout: fixed; min-width: 0; font-size: 0.82rem; line-height: 1.1; }

/* === CHANGED: reduced sticky header padding/size to lower overall table height === */
thead th {
  position: sticky; top: 0; z-index: 1; text-align: left;
  background: rgba(13, 21, 40, 0.98); color: var(--muted); font-size: 0.78rem;
  padding: 4px 8px; line-height: 1.05;
}

/* === CHANGED: significantly reduced table row height in PAM candidates table === */
th, td { padding: 2px 8px; border-bottom: 1px solid rgba(255,255,255,0.08); vertical-align: middle; line-height: 1.05; }

/* === CHANGED: compact row behavior remains the same on hover/selection === */
tbody tr { cursor: pointer; }
tbody tr:hover { background: rgba(255,255,255,0.045); }
tbody tr.selected-row { background: rgba(110, 231, 242, 0.16); }

/* === CHANGED: badges inside the PAM candidates table made more compact === */
.badge {
  display: inline-flex; align-items: center; gap: 6px; padding: 2px 7px; border-radius: 999px;
  font-size: 0.74rem; font-weight: 700; line-height: 1;
}
.badge.plus { background: rgba(110, 231, 242, 0.14); color: var(--plus); }
.badge.minus { background: rgba(255, 141, 179, 0.14); color: var(--minus); }
.badge.pattern1 { background: rgba(155, 140, 255, 0.16); color: #c7bcff; }
.badge.pattern2 { background: rgba(91, 228, 155, 0.14); color: var(--green); }
/* === CHANGED: monospace content in PAM candidates table made smaller/tighter === */
.small-mono { font-family: ui-monospace, SFMono-Regular, Menlo, monospace; font-size: 0.78rem; line-height: 1.0; }
.selected-pill {
  display: inline-flex; align-items: center; gap: 8px; padding: 8px 10px; border-radius: 999px;
  background: rgba(255,255,255,0.08); margin: 4px 6px 0 0;
}
.selection-item {
  border: 1px solid rgba(255,255,255,0.08); border-radius: 14px;
  padding: 12px; margin-bottom: 10px; background: rgba(255,255,255,0.04);
}
.selection-header { display: flex; justify-content: space-between; gap: 8px; align-items: center; margin-bottom: 8px; }
.selection-title { font-weight: 800; }
.selection-meta { color: var(--muted); font-size: 0.88rem; }
.selection-seq {
  font-family: ui-monospace, SFMono-Regular, Menlo, monospace;
  word-break: break-all; background: rgba(255,255,255,0.06);
  border-radius: 12px; padding: 10px; margin-top: 8px;
}
.pair-summary {
  padding: 12px; border-radius: 14px; margin-bottom: 12px;
  background: rgba(255,255,255,0.04); border: 1px solid rgba(255,255,255,0.08);
}
.empty-state { color: var(--muted); }
.zoom-readout { margin-top: 8px; color: var(--muted); font-size: 0.92rem; }
.footer { padding: 0 0 24px; color: var(--muted); font-size: 0.92rem; }

svg text { font-family: var(--font); }
.feature-label { fill: #eef3ff; font-size: 11px; font-weight: 700; }
.axis-label { fill: #b7c0dd; font-size: 11px; }
.marker-label { fill: #ffffff; font-size: 10px; font-weight: 700; pointer-events: none; }
.pam-marker { cursor: pointer; }
.pam-marker.selected circle, .pam-marker.selected rect { stroke: #fff; stroke-width: 2.2; }
.pam-marker:hover circle, .pam-marker:hover rect { filter: brightness(1.15); }
.feature-box { opacity: 0.94; }
.feature-box:hover { opacity: 1; }

@media (max-width: 1240px) {
  .layout { grid-template-columns: 1fr; }
  .two-up { grid-template-columns: 1fr; }
}

@media (max-width: 760px) {
  .hero { flex-direction: column; align-items: flex-start; }
  .checkbox-group.two-col, .stats-grid { grid-template-columns: 1fr; }
  .section-header { flex-direction: column; }
}



#resultsTable th:nth-child(1), #resultsTable td:nth-child(1) { width: 60px; }
#resultsTable th:nth-child(2), #resultsTable td:nth-child(2) { width: 120px; }
#resultsTable th:nth-child(3), #resultsTable td:nth-child(3) { width: 82px; }
#resultsTable th:nth-child(4), #resultsTable td:nth-child(4) { width: 120px; }
#resultsTable th:nth-child(5), #resultsTable td:nth-child(5) { width: 220px; }
#resultsTable th:nth-child(6), #resultsTable td:nth-child(6) { width: 70px; }
#resultsTable th:nth-child(7), #resultsTable td:nth-child(7) { width: auto; }
#resultsTable th:nth-child(8), #resultsTable td:nth-child(8) { width: 84px; text-align: center; }
/* === CHANGED: tighter wrapping and font size for sequence-heavy PAM candidate columns === */
.wrap-mono { overflow-wrap: anywhere; word-break: break-word; line-height: 1.0; }
.spacer-cell { font-size: 0.78rem; line-height: 1.0; }
.feature-cell { overflow-wrap: anywhere; word-break: break-word; line-height: 1.05; }
.selection-seq { overflow-wrap: anywhere; }
.feature-label { paint-order: stroke; stroke: rgba(8, 13, 28, 0.9); stroke-width: 2px; }


/* === CHANGED: prevent PAM table rows from stretching because long cell content wraps to multiple lines === */
#resultsTable td,
#resultsTable th {
  white-space: nowrap;
}

/* === CHANGED: keep sequence/feature-heavy columns on a single line with ellipsis === */
#resultsTable td.small-mono,
#resultsTable td.spacer-cell,
#resultsTable td.feature-cell {
  overflow: hidden;
  text-overflow: ellipsis;
}

/* === CHANGED: PAM badge + sequence stay inline without increasing row height === */
#resultsTable td:nth-child(2) {
  overflow: hidden;
  text-overflow: ellipsis;
}
#resultsTable td:nth-child(2) .badge {
  vertical-align: middle;
}

/* === CHANGED: feature column should truncate rather than wrap into tall rows === */
.feature-cell {
  white-space: nowrap;
  overflow: hidden;
  text-overflow: ellipsis;
}

/* === CHANGED: spacer and PAM sequence cells should not wrap across lines === */
.wrap-mono,
.spacer-cell {
  white-space: nowrap;
  overflow: hidden;
  text-overflow: ellipsis;
}