:root {
  --font-sans: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif;
  --font-mono: 'SF Mono', 'Fira Code', 'Fira Mono', 'Roboto Mono', monospace;
  --c-text: #1a1a1a;
  --c-text2: #666;
  --c-text3: #999;
  --c-bg: #fff;
  --c-bg2: #f7f7f8;
  --c-border: #e2e2e5;
  --c-border2: #d0d0d4;
  --c-accent: #4f6df5;
  --c-accent-light: #eef1fe;
  --c-match: #22c55e;
  --c-match-bg: #dcfce7;
  --c-mismatch: #ef4444;
  --c-mismatch-bg: #fee2e2;
  --c-gap: #a3a3a3;
  --c-gap-bg: #f3f3f3;
  --radius: 10px;
  --radius-sm: 6px;
}

* { box-sizing: border-box; margin: 0; padding: 0; }

body {
  font-family: var(--font-sans);
  max-width: 960px;
  margin: 0 auto;
  padding: 1.5rem 1rem 3rem;
  background: var(--c-bg);
  color: var(--c-text);
  line-height: 1.5;
}

header { margin-bottom: 1.5rem; }
h1 { font-size: 1.35rem; font-weight: 700; }
.subtitle { font-size: 13px; color: var(--c-text2); margin-top: 2px; }

/* Sections */
.input-section, .results-section {
  background: var(--c-bg2);
  border: 1px solid var(--c-border);
  border-radius: var(--radius);
  padding: 1rem 1.25rem;
  margin-bottom: 1.25rem;
}
.section-label {
  font-size: 11px;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.04em;
  color: var(--c-text3);
}
.section-hint {
  font-size: 11px;
  color: var(--c-text3);
  margin-left: 8px;
}
.results-header {
  display: flex;
  align-items: baseline;
  margin-bottom: 0.5rem;
}
.input-header {
  display: flex;
  align-items: center;
  justify-content: space-between;
  margin-bottom: 0.75rem;
}

/* Sequence input */
.seq-textarea {
  width: 100%;
  padding: 10px 12px;
  font-size: 13px;
  border: 1px solid var(--c-border);
  border-radius: var(--radius-sm);
  background: var(--c-bg);
  color: var(--c-text);
  font-family: var(--font-mono);
  resize: vertical;
  line-height: 1.5;
}
.seq-textarea:focus {
  outline: none;
  border-color: var(--c-accent);
  box-shadow: 0 0 0 2px var(--c-accent-light);
}

/* Buttons */
.btn {
  padding: 7px 16px;
  border-radius: var(--radius-sm);
  border: 1px solid var(--c-border);
  background: var(--c-bg);
  color: var(--c-text);
  cursor: pointer;
  font-size: 13px;
  font-weight: 500;
  transition: background 0.15s, border-color 0.15s;
}
.btn:hover { background: var(--c-bg2); border-color: var(--c-border2); }
.btn-sm { padding: 4px 10px; font-size: 12px; }
.btn-primary {
  background: var(--c-accent);
  color: #fff;
  border-color: var(--c-accent);
  font-weight: 600;
}
.btn-primary:hover { opacity: 0.9; background: var(--c-accent); }

.action-row {
  display: flex;
  align-items: center;
  gap: 10px;
  margin-top: 0.75rem;
  flex-wrap: wrap;
}

/* Scoring controls */
.scoring-controls {
  display: flex;
  gap: 10px;
  margin-left: auto;
  font-size: 12px;
  color: var(--c-text2);
}
.scoring-controls label {
  display: flex;
  align-items: center;
  gap: 4px;
}
.scoring-controls input {
  width: 44px;
  padding: 3px 6px;
  border: 1px solid var(--c-border);
  border-radius: 4px;
  font-size: 12px;
  text-align: center;
  font-family: var(--font-mono);
}

/* Lengths bar */
.lengths-bar {
  display: flex;
  gap: 12px;
  flex-wrap: wrap;
  margin-bottom: 0.75rem;
}
.len-tag {
  font-size: 12px;
  color: var(--c-text2);
  background: var(--c-bg);
  border: 1px solid var(--c-border);
  border-radius: 4px;
  padding: 3px 10px;
}
.len-tag strong {
  color: var(--c-text);
  font-weight: 600;
  margin-right: 4px;
}
.len-name {
  border: none;
  background: transparent;
  font-size: 12px;
  font-weight: 600;
  color: var(--c-text);
  font-family: var(--font-sans);
  padding: 0;
  border-bottom: 1px dashed var(--c-border2);
  outline: none;
}
.len-name:focus {
  border-bottom-color: var(--c-accent);
}

/* Alignment block */
.align-block {
  margin-top: 0.75rem;
  background: var(--c-bg);
  border: 1px solid var(--c-border);
  border-radius: var(--radius-sm);
  overflow: hidden;
}
.align-block-header {
  padding: 8px 14px;
  font-size: 13px;
  border-bottom: 1px solid var(--c-border);
  background: var(--c-bg2);
  display: flex;
  align-items: center;
  justify-content: space-between;
  flex-wrap: wrap;
  gap: 6px;
}
.abh-title { font-weight: 600; }
.abh-stats { display: flex; gap: 12px; }
.abh-stat {
  font-size: 11px;
  color: var(--c-text2);
  font-family: var(--font-mono);
}

/* Alignment scrollable view */
.align-view {
  overflow-x: auto;
  padding: 10px 14px;
}
.align-table {
  font-family: var(--font-mono);
  font-size: 13px;
  line-height: 1;
  display: inline-block;
  min-width: 100%;
}

/* Rows */
.align-row {
  display: flex;
  align-items: center;
  white-space: nowrap;
  height: 22px;
}
.ruler-row { height: 16px; }
.align-label {
  width: 100px;
  flex-shrink: 0;
  font-size: 11px;
  color: var(--c-text3);
  text-align: right;
  padding-right: 10px;
  overflow: hidden;
  text-overflow: ellipsis;
}
.align-chars { display: flex; }

/* Residue cells */
.ac {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  width: 18px;
  height: 20px;
  font-size: 13px;
  border-radius: 3px;
  margin: 0 0.5px;
}
/* Reference row: dim for matches, highlighted for diffs */
.ac-dim { color: var(--c-text3); }
.ac-highlight { background: var(--c-mismatch-bg); color: #dc2626; font-weight: 600; }
/* Comparison row */
.ac-same { color: #ccc; }
.ac-mismatch { background: var(--c-mismatch-bg); color: #dc2626; font-weight: 600; }
.ac-gap { background: var(--c-gap-bg); color: var(--c-gap); }

/* Ruler numbers */
.ac-ruler {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  width: 18px;
  height: 14px;
  margin: 0 0.5px;
  font-size: 9px;
  color: var(--c-text3);
  user-select: none;
}

/* Mutations */
.align-mutations {
  padding: 8px 14px;
  border-top: 1px solid var(--c-border);
  display: flex;
  align-items: flex-start;
  gap: 8px;
  flex-wrap: wrap;
}
.mut-label {
  font-size: 11px;
  font-weight: 600;
  text-transform: uppercase;
  letter-spacing: 0.03em;
  color: var(--c-text3);
  flex-shrink: 0;
  line-height: 22px;
}
.mut-text {
  font-family: var(--font-mono);
  font-size: 12px;
  color: var(--c-text2);
  line-height: 1.6;
}

/* View toggle */
.view-toggle {
  display: flex;
  gap: 0;
  border: 1px solid var(--c-border);
  border-radius: var(--radius-sm);
  overflow: hidden;
  margin-left: 8px;
}
.view-toggle button {
  padding: 3px 10px;
  font-size: 11px;
  border: none;
  background: var(--c-bg);
  color: var(--c-text2);
  cursor: pointer;
  font-weight: 500;
  border-right: 1px solid var(--c-border);
}
.view-toggle button:last-child { border-right: none; }
.view-toggle button.active {
  background: var(--c-accent);
  color: #fff;
}

/* Full view: show all letters */
.ac-match-full { background: var(--c-match-bg); color: #15803d; font-weight: 600; }
.ac-mismatch-full { background: var(--c-mismatch-bg); color: #dc2626; font-weight: 600; }
.ac-gap-full { background: #e0e7ff; color: #6366f1; }

/* Footer */
footer {
  margin-top: 2rem;
  padding-top: 1rem;
  border-top: 1px solid var(--c-border);
  font-size: 12px;
  color: var(--c-text3);
}
footer a { color: var(--c-accent); text-decoration: none; }
footer a:hover { text-decoration: underline; }

/* Responsive */
@media (max-width: 600px) {
  .scoring-controls { margin-left: 0; width: 100%; }
  .abh-stats { gap: 6px; }
}