§4 Species: anchor prompt to 2nd exon, drop zebrafish

- fetch_species.py: also capture per-species exon coords from Ensembl,
translated into 0-based offsets in the trimmed seq
- species.js: new getPromptWindow() — anchors prefixEnd 35 bp into the
2nd exon (like §1's gene completion); slides prefixStart back by the
user-selected prefixLen; falls back to flat slice when exon 2 isn't
visible. Always render the prompt (no more "click run all" placeholder).
Per-row "{N} bp prompt" note.
- species.json: regenerated with exon data; zebrafish dropped (~450 My
drift made the row look like noise next to mammals + bird)
- demo.html §4 lede/takeaway: reflect new framing and dropped species

assets/js/sections/species.js

@@ -40,6 +40,26 @@
     return Math.max(20, Math.min(blocks, 12) * 10);
   }
 
+  // Choose where the prompt sits inside the species seq. The §1 finding is
+  // that Carbon is most predictive when it's continuing the 2nd exon with
+  // some intron context behind it. We replicate that here: anchor prefixEnd
+  // a bit past the start of exon 2 (35 bp of exon context, like §1) and
+  // slide prefixStart back by the user-selected `prefixLen`. If exon 2
+  // isn't visible in the trimmed seq, fall back to a flat slice from start.
+  function getPromptWindow(s, prefixLen) {
+    const exons = s.exons || [];
+    const exon2 = exons.length >= 2 ? exons[1] : null;
+    if (exon2) {
+      const EXON_CTX = 35;
+      const exonLen = exon2.end - exon2.start;
+      const exonCtx = Math.min(EXON_CTX, Math.max(0, exonLen - 30));
+      const prefixEnd = Math.min(s.length, exon2.start + exonCtx);
+      const prefixStart = Math.max(0, prefixEnd - prefixLen);
+      return { prefixStart, prefixEnd };
+    }
+    return { prefixStart: 0, prefixEnd: Math.min(s.length, prefixLen) };
+  }
+
   function renderRow(s) {
     const wrap = document.createElement("div");
     wrap.className = "species-row";
@@ -47,7 +67,8 @@
 
     const stat = runState[s.species_id] || {};
     const genText = stat.genText || "";
-    const refSlice = s.seq.slice(prefixLen, prefixLen + genLen);
+    const { prefixStart, prefixEnd } = getPromptWindow(s, prefixLen);
+    const refSlice = s.seq.slice(prefixEnd, prefixEnd + genLen);
     let match = 0, total = 0;
     for (let i = 0; i < genText.length && i < refSlice.length; i++) {
       total++;
@@ -55,12 +76,14 @@
     }
     const idPct = total > 0 ? `${((match / total) * 100).toFixed(0)}%` : "·";
     const meanLp = stat.genTokens ? meanLogprob(stat.genTokens) : null;
+    const promptBp = prefixEnd - prefixStart;
 
     wrap.innerHTML = `
       <div class="species-meta">
         <div class="species-name" style="border-left-color:${s.color}">${s.common}</div>
         <div class="species-sub">${s.ortholog_symbol}</div>
         <div class="species-sub">chr${s.chrom} · strand ${s.strand}</div>
+        <div class="species-sub" style="color:#999">${promptBp} bp prompt</div>
         <div class="species-stats">
           <div class="stat-id">${idPct}</div>
           <div class="stat-sub">${total > 0 ? `${match}/${total} bases` : "not run"}</div>
@@ -68,7 +91,7 @@
         </div>
       </div>
       <div>
-        <div class="species-seq" data-role="output">click "run all" to generate</div>
+        <div class="species-seq" data-role="output"></div>
         <div class="species-seq" data-role="ref" style="margin-top:4px"></div>
       </div>
     `;
@@ -76,11 +99,7 @@
     const outEl = wrap.querySelector('[data-role="output"]');
     const refEl = wrap.querySelector('[data-role="ref"]');
 
-    if (genText.length === 0 && (stat.status === "idle" || !stat.status)) {
-      outEl.classList.add("empty");
-      outEl.textContent = "click \"run all\" to generate";
-      refEl.style.display = "none";
-    } else if (stat.status === "error") {
+    if (stat.status === "error") {
       outEl.classList.add("empty");
       outEl.style.color = "#b00020";
       outEl.textContent = stat.error || "error";
@@ -88,12 +107,13 @@
     } else {
       outEl.classList.remove("empty");
       const bpl = basesPerLine(outEl);
-      const total = (s.seq.slice(0, prefixLen) + genText);
+      const prompt = s.seq.slice(prefixStart, prefixEnd);
+      const total = prompt + genText;
       const lpRange = stat.genTokens ? lpRangeOf(stat.genTokens) : null;
       const colorOut = (absIdx) => {
-        if (absIdx < prefixLen) return { style: `color:rgb(${PROMPT_RGB.join(",")})` };
+        if (absIdx < prompt.length) return { style: `color:rgb(${PROMPT_RGB.join(",")})` };
         const tok = stat.genTokens && stat.genTokenAtBase
-          ? stat.genTokens[stat.genTokenAtBase[absIdx - prefixLen]]
+          ? stat.genTokens[stat.genTokenAtBase[absIdx - prompt.length]]
           : null;
         const [r, g, b] = logprobRgb(tok ? tok.logprob : null, lpRange);
         return { style: `color:rgb(${r},${g},${b})` };
@@ -102,9 +122,8 @@
 
       // Reference (only the generated span)
       if (genText.length > 0) {
-        const refSpanStart = prefixLen;
-        const refSpanEnd = Math.min(s.length, prefixLen + genLen);
-        const refSeq = s.seq.slice(refSpanStart, refSpanEnd);
+        const refSpanEnd = Math.min(s.length, prefixEnd + genLen);
+        const refSeq = s.seq.slice(prefixEnd, refSpanEnd);
         const colorRef = (absIdx, base) => {
           // absIdx is local to refSeq (starts at 0)
           const genIdx = absIdx;
@@ -132,7 +151,8 @@
   }
 
   async function generateForSpecies(s) {
-    const prompt = s.seq.slice(0, prefixLen);
+    const { prefixStart, prefixEnd } = getPromptWindow(s, prefixLen);
+    const prompt = s.seq.slice(prefixStart, prefixEnd);
     const stat = { genText: "", genTokens: [], genTokenAtBase: [], status: "running" };
     runState[s.species_id] = stat;
     renderAll();
@@ -211,7 +231,7 @@
     entry = SPECIES_DATA.find(x => x.symbol === symbol);
     if (!entry) return;
     els.pills.querySelectorAll(".pill").forEach(p => p.classList.toggle("active", p.dataset.gene === symbol));
-    els.info.innerHTML = `<strong>${entry.symbol}</strong> · same gene, ${entry.species.length} species · prefix from each species' own canonical transcript`;
+    els.info.innerHTML = `<strong>${entry.symbol}</strong> · same gene, ${entry.species.length} species · prefix anchored to the 2nd exon of each species (intron context, then generate into the exon)`;
     runState = {};
     renderAll();
     setStatus("idle");

data/species.json

@@ -10,6 +10,16 @@
         "strand": -1,
         "length": 1200,
         "seq": "AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGGTCTGTTCCAAGGGCCTTTGCGTCAGGTGGGCTCAGGATTCCAGGGTGGCTGGACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCGTGAAGCATGTGGGGGTGAGCCCAGGGGCCCCAAGGCAGGGCACCTGGCCTTCAGCCTGCCTCAGCCCTGCCTGTCTCCCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGGTGAGCCAACTGCCCATTGCTGCCCCTGGCCGCCCCCAGCCACCCCCTGCTCCTGGCGCTCCCACCCAGCATGGGCAGAAGGGGGCAGGAGGCTGCCACCCAGCAGGGGGTCAGGTGCACTTTTTTAAAAAGAAGTTCTCTTGGTCACGTCCTAAAAGTGACCAGCTCCCTGTGGCCCAGTCAGAATCTCAGCCTGAGGACGGTGTTGGCTTCGGCAGCCCCGAGATACATCAGAGGGTGGGCACGCTCCTCCCTCCACTCGCCCCTCAAACAAATGCCCCGCAGCCCATTTCTCCACCCTCATTTGATGACCGCAGATTCAAGTGTTTTGTTAAGTAAAGTCCTGGGTGACCTGGGGTCACAGGGTGCCCCACGCTGCCTGCCTCTGGGCGAACACCCCATCACGCCCGGAGGAGGGCGTGGCTGCCTGCCTGAGTGGGCCAGACCCCTGTCGCCAGGCCTCACGGCAGCTCCATAGTCAGGAGATGGGGAAGATGCTGGGGACAGGCCCTGGGGAGAAGTACTGGGATCACCTGTTCAGGCTCCCACTGTGACGCTGCCCCGGGGCGGGGGAAGGAGGTGGGACATGTGGGCGTTGGGGCCTGTAGGTCCACACCCAGTGTGGGTGACCCTCCCTCTAACCTGGGTCCAGCCCGGCTGGAGATGGGTGGGAGTGCGACCTAGGGCTGGCGGGCAGGCGGGCACTGTGTCTCCCTGACTGTGTCCTCCTGTGTCCCTCTGCCTCGCCGCTGTTCCGGAACCTGCTCTGCGCGGC",
+        "exons": [
+          {
+            "start": 0,
+            "end": 42
+          },
+          {
+            "start": 221,
+            "end": 425
+          }
+        ],
         "species_id": "homo_sapiens",
         "common": "human",
         "color": "#1a1a1a"
@@ -22,6 +32,16 @@
         "strand": 1,
         "length": 1180,
         "seq": "ACCAGGCAAGTGTTTGGAAACTGCAGCTTCAGCCCCTCTGGCCATCTGCCTACCCACCCCACCTGGAGACCTTAATGGGCCAAACAGCAAAGTCCAGGGGGCAGAGAGGAGGTACTTTGGACTATAAAGCTGGTGGGCATCCAGTAACCCCCAGCCCTTAGTGACCAGCTATAATCAGAGACCATCAGCAAGCAGGTATGTACTCTCCTCTTTGGGCCTGGCTCCCCAGCCAAGACTCCAGCGACTTTAGGGAGAATGTGGGCTCCTCTCTTACATGGATCTTTTGCTAGCCTCAACCCTGCCTATCTTTCAGGTCATTGTTTCAACATGGCCCTGTTGGTGCACTTCCTACCCCTGCTGGCCCTGCTTGCCCTCTGGGAGCCCAAACCCACCCAGGCTTTTGTCAAACAGCATCTTTGTGGTCCCCACCTGGTAGAGGCTCTCTACCTGGTGTGTGGGGAGCGTGGCTTCTTCTACACACCCAAGTCCCGCCGTGAAGTGGAGGACCCACAAGTGGAACAACTGGAGCTGGGAGGAAGCCCCGGGGACCTTCAGACCTTGGCGTTGGAGGTGGCCCGGCAGAAGCGTGGCATTGTGGATCAGTGCTGCACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAAGGCCCACCTCGACCCGCCCCACCCCTCTGCAATGAATAAAACTTTTGAATAAGCACCAAAAAAAAGAGTTCTATAATGAATGAAAAAGGATTGTGTATATAGACATCTTTTTCTCTGGCATTTATTGTCATGTTAGCATACTATTAAACCATTGTTAGGTTGGATGATTATATAATCATGTATGAAGCTTGTGATAAAACACCAGGAATAATTCAAGTATCTGGAATTCTGCTTCCTGCCCAAGAAGGTAGGCAACCGTGTAAATGCCACTGAAGCTACTAGTCTAAAAGTGAGTTATCTCTGTCTTTGTCTTACCCCCTGATGCTGTGATAAAACCCTGACAAGAGCAACTGACTCCTGAGAGGAAGGTTTATTCTAGCTCACAATTCCAGGTTACAAACAGTCCATCCGTAGCAGGGGAGTCACAGCAACAGGAACCTCAGGGAACTGCTCCTATTATCCCCACAATCAAGAATAGTGACCAATAAATAAGTGGATCTTTTCTCAAAAAAAAAAAAAAAAAAAA",
+        "exons": [
+          {
+            "start": 0,
+            "end": 195
+          },
+          {
+            "start": 313,
+            "end": 1180
+          }
+        ],
         "species_id": "mus_musculus",
         "common": "mouse",
         "color": "#2c5aa0"
@@ -34,21 +54,15 @@
         "strand": 1,
         "length": 1200,
         "seq": "TTGTCTCTTTATGAGAAATCAGCAGGGAGGCCAGCATTGGTGTGAGTGTGTGGATGGAGACAGGCTTCTGGTTATAATTGGTCATTTATTATGACTTTCAAAGCCTGATGAATAAAATATTCCTTTCCTCTTCAGAAGGTCCATTTGCTTCTGTAGTCTTGTTTTCACGTCAAAGGAGCTGAGGGACATAAGATGCCTGATGATAGCTTATTCCTCCCTTGCAACCCCCCCGTGTCTCCTTTGCTTCCTACCTCTAGGCCTCCCCCAGCTCATCATGGCTCTCTGGATCCGATCACTGCCTCTTCTGGCTCTCCTTGTCTTTTCTGGCCCTGGAACCAGCTATGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTGGAGGCTCTCTACCTGGTGTGTGGAGAGCGTGGCTTCTTCTACTCCCCCAAAGCCCGACGGGATGTCGAGCAGCCCCTAGGTAAGTCAGTTCGACCATGACTACATTCATATGCTATATGATGCAAAAAGCAACTGTCTATCTTTGATGGTGACACAAGGAATGTCCTTGGTGGGGAATGCCAGGAATACCTTAAACATACCAACAGCATCATATCACCCATGAAAAGATCGTCAGGCTAAAAAGGCAGGTGGGAGGGCAAGCAGGGAAAGGAGATTTATGAGACAGAAGGAATTGTCACAGAAAGCTCCAAATTTTTTGCTACTCTCTTGGTAGAGAGAGGCTGAAAACAGTGTTATTCCAACATTTGCATGGCAATTACTCTCACCTGGGAGTGATCATGAAAAATAAAGGTGGAAGGAACACAAGAAGCCTCTTTCTGCACCTCTTCTTGACCCACACTACCCCAGTCCTGTTCTGTGACCACATCAAGTGTGGTCATAAAAACCTCCTGCCTTCTGAAGCTGTCCATTCTTGTGCTTAAATGACTTTTTCTTGAATGTTTCCTCCTAATATTTAACCCAAATGTATCTTGTCACAAATTAGTCCTCATCTTCTCAGTAGTGGACAAAAGGAACAGTCTATCATTTCTCCTTCATGGGTGATTTTCAAACAGTTTAAAAATTGCTTCCATGTCTTGTTTTTATCTACTGTGAGCTAAAAGCCCTCAACAGCCCCAGAATTCCTTTTTAGGTCACATATTCTAGCTCTCTGTCTACATAAACTGTTCTGCATTTGGCCCATACCATTACGGAATGGT",
+        "exons": [
+          {
+            "start": 0,
+            "end": 461
+          }
+        ],
         "species_id": "gallus_gallus",
         "common": "chicken",
         "color": "#c08030"
-      },
-      {
-        "ortholog_symbol": "ins",
-        "ensembl_gene": "ENSDARG00000035350",
-        "ensembl_transcript": "ENSDART00000051222",
-        "chrom": "5",
-        "strand": 1,
-        "length": 1200,
-        "seq": "ATCTCCACCACCATATCCACCATTCCTCGCCTCTGCTTCGAGAACAGGTGAGTGTCGAGCGGGATGGTAAATCTACAGAGAATGCGGAGTGTAGCTTGTGTACATGTTTTTGATTAACAGAGATTGTATGTGTGTGTTTGTGTCAGTGTGACCATGGCAGTGTGGCTTCAGGCTGGTGCTCTGTTGGTCCTGTTGGTCGTGTCCAGTGTAAGCACTAACCCAGGCACACCGCAGCACCTGTGTGGATCTCATCTGGTCGATGCCCTTTATCTGGTCTGTGGCCCAACAGGCTTCTTCTACAACCCCAAGAGAGACGTTGAGCCCCTTCTGGGTAAGAAAGTCAAGTAGAGGTGTTTTGACAGTGGAGTAGTAACAGTGGAGTTTTATCATTTTTAAATCCAATTAGCGATCTCCAACTCTGGCAAGAGCACTTTTAGTTTAGTTTAGCGTAGATCATTGAATTGAATTAGACCATTAGCGTCTCGTAAATTTTTTTTTTTGATAATTTCCCTATTGAGTATATAGCTTGAAAATGATAACTTTACTATTCTTTATTTACATTGTGGACTAAGACCAGTGGAAATGAAATGTTGCTGCTTTCTACACTGTAAAAAGCGATTAGTTGCCTTTACCTAAAAAAAGAGAGTGAACTCGTTGCCTTATAATTAAGCAAACTATGTGCATATTATAAAAGTTAAGTCAATGGGTTTTCTGACTTTTTAAAAGTAAAATCAACGGTCACACTTTATTTTGATGGTCCATTTGGTAAATTGCTTCTACATGCCAACTAACTCTCATTAGATTATATGTAGACAGGTTGGGTTTAGGGTTAGGGTTAGTGTAAGTTGACATGTACTTGCAAAGTTTCTTATAGTCAGTTAAATGTCTGTTGAAGGAGCAGTATCAACAGATAATAAGCAGACAGTCTACTAATACTCAAATGGACCATCAAAATAAAGTGTTACCAAATTAACTTGTTGCTTTTGCGGTTGGTTTACTTACTTTTTTAAAGTAAAGTTACTAATCGATTTTTACAGTGTAGGTTAATATCATTCTAGCATAATAATAAAGTAACTTTGCCACTGTATCATGGCTGCAGCCATGGTTCGACAACAAAGTAACTTGCCTAGTTAGCCTAATTAATCTCCACTGTAAAAATATTTGTTAATTAAAATGTAAAAGTTTTTGGTTGATTTATGA",
-        "species_id": "danio_rerio",
-        "common": "zebrafish",
-        "color": "#2a8a8a"
       }
     ]
   },
@@ -63,6 +77,12 @@
         "strand": -1,
         "length": 1200,
         "seq": "CTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGGTAAGCTCCTGACTGAACTTGATGAGTCCTCTCTGAGTCACGGGCTCTCGGCTCCGTGTATTTTCAGCTCGGGAAAATCGCTGGGGCTGGGGGTGGGGCAGTGGGGACTTAGCGAGTTTGGGGGTGAGTGGGATGGAAGCTTGGCTAGAGGGATCATCATAGGAGTTGCATTGTTGGGAGACCTGGGTGTAGATGATGGGGATGTTAGGACCATCCGAACTCAAAGTTGAACGCCTAGGCAGAGGAGTGGAGCTTTGGGGAACCTTGAGCCGGCCTAAAGCGTACTTCTTTGCACATCCACCCGGTGCTGGGCGTAGGGAATCCCTGAAATAAAAGATGCACAAAGCATTGAGGTCTGAGACTTTTGGATCTCGAAACATTGAGAACTCATAGCTGTATATTTTAGAGCCCATGGCATCCTAGTGAAAACTGGGGCTCCATTCCGAAATGATCATTTGGGGGTGATCCGGGGAGCCCAAGCTGCTAAGGTCCCACAACTTCCGGACCTTTGTCCTTCCTGGAGCGATCTTTCCAGGCAGCCCCCGGCTCCGCTAGATGGAGAAAATCCAATTGAAGGCTGTCAGTCGTGGAAGTGAGAAGTGCTAAACCAGGGGTTTGCCCGCCAGGCCGAGGAGGACCGTCGCAATCTGAGAGGCCCGGCAGCCCTGTTATTGTTTGGCTCCACATTTACATTTCTGCCTCTTGCAGCAGCATTTCCGGTTTCTTTTTGCCGGAGCAGCTCACTATTCACCCGATGAGAGGGGAGGAGAGAGAGAGAAAATGTCCTTTAGGCCGGTTCCTCTTACTTGGCAGAGGGAGGCTGCTATTCTCCGCCTGCATTTCTTTTTCTGGATTACTTAGTTATGGCCTTTGCAAAGGCAGGGGTATTTGTTTTGATGCAAACCTCAATCCCTCCCCTTCTTTGAATGGTGTGCCCCACCCCGCGGGTCGCCTGCAACCTAGGCGGACGCTACCATGGCGTGAGACAGGGAGGGAAAGAAGTGTGCAGAAGGCAAGCCCGGAGGTATTTTCAAGAATGAGTATATCTCATCTTCCCGGAGGAAAAAAAAAAAGAATGGGTACGTC",
+        "exons": [
+          {
+            "start": 0,
+            "end": 114
+          }
+        ],
         "species_id": "homo_sapiens",
         "common": "human",
         "color": "#1a1a1a"
@@ -75,6 +95,12 @@
         "strand": 1,
         "length": 1200,
         "seq": "TTTCCCCTCCCACGTGCTCACCCTGGCTAAAGTTCTGTAGCTTCAGTTCATTGGGACCATCCTGGCTGTAGGTAGCGACTACAGTTAGGGGGCACCTAGCATTCAGGCCCTCATCCTCCTCCTTCCCAGCAGGGTGTCACGCTTCTCCGAAGACTGGGTAAGTAATTGATGAGCGTGACGAGACCTCTCGGTCACTGGCTCTCTCCGTTTGCATCCATAAAACTAGAGAAAACCGTGGGGTTTGGGGGTGGGGCAGTGGGGGGACTCAGCGCGATGGAGATGGGCGGAATGGAAGCTTGGCGGGCGGGATGAACGGGAGTGTATATGTCAGATGCTGTAGTGAGGGTAGCTGATGATGATGATGTTAGGACCGACGAGCCTCACTGTCATGCACCTGCAAAGTAGAGCATATAGGGACCACTGAGATGGCCTAAGGGGTTTTCTCTCCGCTACGCGTTGTACACACTTATCTGCCCGCTGCTAGGTGATGGAAGCTCCGGAAATAACATGCACAAAGCACCAGGATTTAAGATTTTTCGAGATTCATAGCTTAAGACTTAAGACCCCCCATAGCATCCTAATGAAACCCTGGGTTCCGTTCCTGGATGAGATCGGGGTGATCCGGGGAGCCTTAGCTGCTAAGGTCCCGCAACTTCCGGACCTTTGTCCCTGGAGTGATTTCTTTTTTTTTCCAGCCGCTTCTCGACCCTGCTAGATGAAGAAAATCCAAGAAAAGCCTGAAGCACTAGCGGTGCTAGCCAGAAGTATTTGCCCTCGGGGCCCGACTCAGCCTCTTGGTCTGAAAGGCCCGCCGGCCCTGTTATTGTTTGGCTCCTTTACGTTTCTGCCGCTTGCAGGAGCATTTCCGGTTTCTTGTTTTCGGAGCAGATCACTGCTCGCCCGGCGACGGGGGAGTAGCGAAAGGGGAGAAATGGATTCTAGGCTGGTTCTGTGGTTTGAGGAGGAAAACTGCTGTCCTCGACATCTTATTTTTCTGGATTACTTGGTTATTGCTTTTGCAAAGGAGGAGGTGTTTATTTAAAAGAGTGCGCCGATAGGTCGTTTCTTCCTGCCGGAAAAGCAAATTACCGAGTATCCGGTTTTAGGGTGAGCCATTCCCTTGCTTAACGCATTCCGCGCGTCCTGAAAGCGGAAGGGGCGGGCTTGGGCCCCGGGCGCCCGGCGGTCCTAAGTGCAGTC",
+        "exons": [
+          {
+            "start": 0,
+            "end": 157
+          }
+        ],
         "species_id": "mus_musculus",
         "common": "mouse",
         "color": "#2c5aa0"
@@ -87,21 +113,19 @@
         "strand": 1,
         "length": 1200,
         "seq": "GGCCTGGCCCCCGCACAGCACCTCATCCGGGTGGAGGGGAACCCCCAGGCGCGTTACCACGACGACGAGACCACCAAACGGCCACAGCGTCGTCGTCCCCTATGAGCCCCCCGAGGTACCCCCAAATCACACCCCCCCCATAACCCCCCCCCCCAGACCCCCCTAAAGACCCCCCCAACCCCAATTCCCCCCCCAAGACCCCATAACCTCCCATTGCCATGACCCCCAATCCCCCCCCCATGACCCCATAACCCCTCAATGACCCCCCCCAATGACCCCCCCAATGCCCCCAGCCCCAACCCCCCCCCCCAGTCCCCCCTAAAGACCCCCCCAACCCCAAGACCCCCCACGACCCCATAAGATCCCAATGCCGTGACCCCCCAATCCCCCCCCATGACCCCATAACCCCTCAATGACCCCCCCCAATGACCCCAACCCCAAAATACCCCCCCAGACCCCCCTAAAGACCCCCCCAACCCCAATTCCCCCCCCACGACCCCATAACCTCCCATTGCCATGACCCCCAATCCCCCCCCATGACCCTATAACCCCTCAATGACCCCCCCCCAATGACCCCCAACCCCAAAATACCCCCCCAGACCCCCCCTACAGACCCCCACAACCCCAAGACCCCCCCCCACGAACCCATAACTTCCCAATGCTGTGACCCCCAATCCCCCCCCATGACCCCATAACCCCCCAATGAACCCCAACAGCCCAATGACCCCCAGCCCCAAACCCCCCCCCCAGTCCCCTTTAAGGACCCCCCCCCAACCCCAATTCCCCCCCCACGACCCCATAACCTCCCATTGCCATGACCCCCCATCCCCCCTCATGACCCCATAACCCCTCAATGACCCCCCCCCAATGACCCCCAACCCCAAAATACCCCCCAGACCCCCCTAAAGACCCCCCCAACCCCAAGACCCCCCCCACGACCCCATAACTTCCCAATGCTGTGACCCCCAATCCCCCCCCCATGACCCCATAACCCTTCACTGACCCCCCCCAATGACCCCCAGCCCCAAACCCCCCCCAGTCCCCCTTAAGGACCCCCCCCCCACCCCATAACCCCTCAATGACACCCCCCCCCAATGACCCCCAACCCCAAAATGCCCCCCCTCAGTCCCCCCTAAAGACCCCCCCAACCCCAAGACCCCCCCCCACGACCCCATAACCTCCCATTGCCGTGACCCCCAA",
+        "exons": [
+          {
+            "start": 0,
+            "end": 81
+          },
+          {
+            "start": 82,
+            "end": 115
+          }
+        ],
         "species_id": "gallus_gallus",
         "common": "chicken",
         "color": "#c08030"
-      },
-      {
-        "ortholog_symbol": "tp53",
-        "ensembl_gene": "ENSDARG00000035559",
-        "ensembl_transcript": "ENSDART00000135934",
-        "chrom": "5",
-        "strand": 1,
-        "length": 1200,
-        "seq": "CTGTAACTAGGGGAATCCCCAAAACTCCACGCGGATTTGCTTTGTGGATGTCCAATAACCTCCTTGTTTTGGTCATTCTTTAAGTCGATCGACTACATATCCGGGCAATCCGAAAGTCGATAATCGTAGTTTAGTGGAGAGGAGGTCGGCAAAATCAATTCTTGCAAAGGTAACAAAGCGAAACTTTTATTGACTAGCGTTAGTGGTTTGATCGATCATATTTATTAACGTTAACTAGTGTTTGTAGATTCAGCTGTTTGTATATTAAGTAAAAGTCGGGATTTGGTGTGCAACATCATTGGACCGCTTGTGTGTTGTATTATTGTAACAAACTGACGTCGATTCGATAAAAACTGGTAATGAATTAAGAGTGAAACTCGTATTTCGAACTTTAGGCCCGACATCGCTTTAAACGTTACTAAAACGTTGATGTTAACGTTAGCCGCTAAGCCTGTTAGCTAGCTAACATTAGCTGTCGAAAATGCAAACTTAGAGTTTCAGTATAATAGCTTTAGGTGACTTTTAGAAATCTTATGTACAGGTATGCGCATTTTTATTCATTTTTAGCTATATCTACTTGCGCGACAGAACTGTGAAGCTAATAAGCTAACGTTAAGCGGCATCTTTGCGACTCTGAGCGATCGCCTGTTTTTTAAATTTAAAGTGAATGTACATGTTATATAAATATCACACTTTGCATAAGAAACAACATCCCGACTTTTATTTTAACGTTATAGTAATTTTAGTTGTCGTGATATATTATTTCCCCCCAGGTTTTTATGACTTTCGTGTTTATAATTTCACAGCAATGGCGCAAAACGACAGCCAAGAGTTCGCGGAGCTCTGGGAGAAGAATTTGATGTAAGTTCGCAAGGGTCGCACTCCTGATACACAACGCTCCTCTTTTTCCTGCCTCTCTAAATTTCCCCGTATTTTTGTTAGCAGCCATGTCAGGTTGCTATAATGTACCTGTCTTAATATTTTTGGTGTTTGCTTGTTTAAGATGCATCTGTCGAACGTATTGTTTATCTGGAGTTCTTTGTATGAGCTTCAACAGATTAATACTAATTTCTCTCTCTTCCTTTTCAATTGTCTCAGAAGTATTCAGCCCCCAGGTGGTGGCTCTTGCTGGGACATCATTAATGATGAGGTATTTAAAAAAATAATCTCAAACACCCAGAAATCTCTATTTTCCTCTTT",
-        "species_id": "danio_rerio",
-        "common": "zebrafish",
-        "color": "#2a8a8a"
       }
     ]
   }

demo.html

@@ -804,14 +804,14 @@ print(f"delta = {delta:+.2f}  (less likely if negative)")</code></pre></div>
   <div class="section-num">§4 · Species</div>
   <div class="section-title">It knows who's who</div>
   <p class="lede">
-    The same gene (insulin, p53) exists in mouse, chicken, zebrafish, but the surrounding
-    sequence has accumulated different mutations along each lineage for hundreds of millions
-    of years. Feed Carbon the opening ~400 bp of each species' copy of the gene and ask it
-    to continue. Each continuation should match <em>that species'</em> real DNA better than
-    another species' would. How well that holds tracks how recently the lineages split: the
-    model nails closely-related species (mouse, chicken, even though they're ~300 My from
-    human) and starts to drop on zebrafish, where 450 My of independent evolution has
-    smudged the patterns the model was trained to expect.
+    The same gene (insulin, p53) exists in mouse and chicken, but the surrounding sequence
+    has accumulated different mutations along each lineage for hundreds of millions of
+    years. For each species we hand Carbon up to ~400 bp leading into the 2nd exon and
+    ask it to continue inside the exon. Each continuation should match <em>that species'</em>
+    real DNA better than another species' would. The model handles closely-related species
+    well (mouse, chicken, even though they're ~300 My from human); the further you go back
+    in evolutionary time, the more the surrounding sequence drifts and the harder this
+    setup becomes.
   </p>
   </div>
 
@@ -860,9 +860,9 @@ print(f"delta = {delta:+.2f}  (less likely if negative)")</code></pre></div>
       given and continues in that species' style; identity to that species' reference often
       runs 65–90% on the next 60 bp. Cut the prefix to 200 and the signal collapses to
       near-random: a few hundred bases is what it takes to "lock in" on a lineage.
-      Zebrafish stays the hardest case across the board; ~450 My of independent evolution
-      is enough divergence that a 400 bp prefix doesn't pin down the genome as confidently
-      as it does for mammals and birds.
+      The gap between mouse and chicken is where you can read the evolutionary signal: 300+
+      My since the last common ancestor is enough drift that a 400 bp prefix still locks
+      Carbon in, but the per-base identity sits a notch below mouse.
     </p>
   </div>
 
@@ -892,7 +892,7 @@ def continue_species(species_prefix):
     )
     return r.choices[0].text
 
-# species_prefixes = { "human": ..., "mouse": ..., "chicken": ..., "zebrafish": ... }
+# species_prefixes = { "human": ..., "mouse": ..., "chicken": ... }
 with ThreadPoolExecutor() as pool:
     results = dict(zip(species_prefixes, pool.map(continue_species, species_prefixes.values())))
 

scripts/fetch_species.py

@@ -23,7 +23,9 @@ SPECIES = [
     {"id": "homo_sapiens",       "common": "human",     "color": "#1a1a1a"},
     {"id": "mus_musculus",       "common": "mouse",     "color": "#2c5aa0"},
     {"id": "gallus_gallus",      "common": "chicken",   "color": "#c08030"},
-    {"id": "danio_rerio",        "common": "zebrafish", "color": "#2a8a8a"},
+    # Zebrafish dropped: ~450 My from human, the model usually can't pick up
+    # the lineage from ~400 bp of context and the row looks like noise next
+    # to mammals + bird.
 ]
 PREFIX_LEN = 1200  # cap on returned seq length per species (only ~200 will be fed as prompt)
 
@@ -56,9 +58,11 @@ def fetch_for(symbol, species_id):
 
     chrom = g["seq_region_name"]
     strand = g["strand"]
-    t_start = ct["start"]
-    t_end = ct["end"]
+    t_start_full = ct["start"]
+    t_end_full = ct["end"]
+    exons_genomic = [(e["start"], e["end"]) for e in ct.get("Exon", [])]
 
+    t_start, t_end = t_start_full, t_end_full
     # Cap fetched length so the JSON stays small
     if t_end - t_start + 1 > PREFIX_LEN:
         if strand == 1:
@@ -75,6 +79,24 @@ def fetch_for(symbol, species_id):
     else:
         seq = revcomp(plus_seq)
 
+    # Translate exons from genomic coords into 0-based [start, end) offsets in
+    # `seq`. For + strand seq[i] = plus pos t_start + i. For - strand seq is
+    # revcomp(plus_seq), so seq[i] = plus pos t_end - i. Exons that fall
+    # outside the trimmed window are clipped or dropped.
+    exons_seq = []
+    seq_len = len(seq)
+    for e_start, e_end in exons_genomic:
+        if strand == 1:
+            s = e_start - t_start
+            e = e_end - t_start + 1
+        else:
+            s = t_end - e_end
+            e = t_end - e_start + 1
+        s = max(0, s); e = min(seq_len, e)
+        if e > s:
+            exons_seq.append({"start": s, "end": e})
+    exons_seq.sort(key=lambda x: x["start"])
+
     return {
         "ortholog_symbol": g.get("display_name", symbol),
         "ensembl_gene": g["id"],
@@ -83,6 +105,7 @@ def fetch_for(symbol, species_id):
         "strand": strand,
         "length": len(seq),
         "seq": seq,
+        "exons": exons_seq,
     }