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+# MAT discovery: search strategy and the Taphrinomycotina probe (2026-11-14)
+
+Status: exploratory. Nothing is curated or accepted. Source: detector run, job 32090545, code commit 9c4759269f (worktree
+`run-9c47592`), preset v0.9.1, `--withheld-detail-policy on`. Results: `results/2026-11-14_taphrinomycotina_probe/` (HPCC, not committed).
+
+## Goal (user, 2026-11-14)
+Find mating-type loci in lineages with none defined. Chytrids first (Bd the main target, with the depth/heterozygosity comparison),
+Allomyces, then other lineages not yet searched. Do not repeat taxa already found to have no good candidate. Probe Taphrinomycotina.
+
+## What is already done (not repeated)
+- Flank-first scan of 496 BFD genomes (PR #351): Mortierellomycota none; Blastocladiomycota (14 genomes, 3 Allomyces) nothing above
+  chance; Zoopagomycota, Kickxellomycota, Basidiobolus and Chytridiomycota give weak or lineage-specific hits only.
+  The Neocallimastigomycota (25) and Entomophthoromycota genome lists were part of the scan, but the lineage note does not report them.
+- Bd isolate depth/heterozygosity, parent of origin and an idiomorph depth scan (PR #352): no idiomorph candidate.
+
+## Search strategy (proposal; the detector family gate is not changed)
+1. **Detector probe with curated families** on genomes of a lineage close to a curated one. Reads out family, identity, coverage.
+   Treat low identity or low coverage hits as leads only.
+2. **Verify a lead from structure, not score**: the HMG or homeodomain gene must have the domain (Pfam), the genes must be adjacent
+   as in the curated record, and a second genome of the same genus should show the same layout.
+3. **Population signal where isolates exist**: for a species with many isolates (Bd), look for presence/absence or hemizygous
+   windows across isolates (done for Bd; negative).
+4. **Lineages with two or three genomes (Allomyces)**: no population signal is possible. Use the flank-first scan plus a search with
+   pheromone-receptor and HMG-box families, then test layout across the three genomes. I have not run a new Allomyces search.
+5. **Record unsearched lineages before scanning**: compare the BFD phylum/class list with the lists already scanned, scan only the gaps.
+
+## Taphrinomycotina probe
+33 genomes searched (one of 34 was suppressed): Taphrina 13, Schizosaccharomyces 8 searched, 9 listed (not S. pombe, which has curated records),
+Protomyces 8, Saitoella 2, Neolecta 1, Savitreella 1. Pneumocystis is not in `samples.csv` by class and was not run.
+
+| result | genomes |
+|---|---|
+| `mat1` family (Schizosaccharomyces curated), mat1-Mc/Pc/Pi found | 7 of the 8 Schizosaccharomyces genomes searched; none in *S. lindneri* |
+| `PM` family, matMc + matPi (curated from *Taphrina deformans*), idiomorph M, gene only | 4 Protomyces genomes (inouyei, macrosporus, two lactucae-debilis), *Taphrina confusa* |
+| `MAT` family (Pezizomycotina references) | 16 calls across Taphrina, Protomyces, Saitoella, Neolecta |
+| no call at all | 10 genomes: *Taphrina betulina*, *T. communis*, *T.* sp. SM11, *T. wiesneri* (one genome), *Protomyces arabidopsidicola*, *P. gravidus*, *P. pachydermus*, *Saitoella complicata*, *Savitreella*, *S. lindneri* |
+
+Strength of the evidence (identity / coverage to the reference, from `detection_report.yaml`):
+- `PM` calls: matMc 44 to 69% identity at 74% coverage; matPi 42 to 59% at 33 to 89% coverage. Strongest: *Taphrina confusa*
+  (matMc 69.2% / 74.5%, matPi 42.2% / 89.0%). Confidence `medium`. Retracted after the structural follow-up below: the Protomyces calls are not distinguishable from background HMG genes; only the *T. confusa* matMc gene stays a lead.
+- `MAT` family calls: identity 17 to 55%, coverage mostly 10 to 79%, references from Pezizomycotina. I do not treat them as
+  mating-type calls. The 5 *T. deformans* genomes repeat one MAT1-2-1 hit at 44.9% identity and 17.9% coverage.
+- `mat1` calls agree with the curated *S. pombe* family; they are not an independent check.
+
+Not verified: that the `PM` hits contain the HMG domain, that the two genes are adjacent in the same layout as *T. deformans*,
+and that the 10 empty genomes lack a locus (the detector recall for distant lineages is limited: see the holdout notes).
+
+## Next
+- (Done, see the follow-up section) Pfam and gene-order check of the `PM` leads (Protomyces x4, *T. confusa*), then a second look at the 10 empty genomes with the
+  flank-first scan using matMc/matPi as controls.
+- Draft candidate records only after a curator reads the structural check.
+
+## Lineage coverage survey (added 2026-11-14)
+BFD `samples.csv` (23,679 rows) was matched to the genomes in the flank-first scan (496). Scanned: Basidiobolomycota 18, Blastocladiomycota 14,
+Chytridiomycota 83, Entomophthoromycota 9, Glomeromycota 59, Kickxellomycota 177, Mortierellomycota 100, Neocallimastigomycota 25, Zoopagomycota 11.
+Not scanned before and now scanned with the same stage 1 (job 32090926, 141 genomes): Aphelidiomycota 2, Calcarisporiellomycota 1,
+Monoblepharomycota 3, Olpidiomycota 1, Rozellomycota 1, one unclassified, Microsporidia 132. Not scanned because the BFD sample name did not map
+to an annotation folder (name matching is imperfect, so counts are approximate): some Chytridiomycota, Entomophthoromycota, Kickxellomycota and
+Neocallimastigomycota genomes, Sanchytriomycota 2, 31 Microsporidia and 2 Aphelidiomycota. Mucoromycota (Mucoromycotina) has curated MAT records and was not part of this survey.
+
+Result table: `2026-11-14_mat-discovery-tables/gap_lineages_summary.tsv` (same columns as the lineage note of PR #351).
+- Small phyla (9 genomes): no HD1+HD2 locus and no 2xHomeo locus. One `HMG+Homeo` locus each in the Calcarisporiella genome and the Rozella genome, and
+  `sexM/sexP` control hits in 4 genomes. A single genome per lineage; not tested against chance.
+- Microsporidia (132 genomes): 65 genomes have two Pfam Homeodomain genes within 5 genes. Random placement of the same number of genes gives a mean of
+  18.8 genomes (maximum 28 in 200 shuffles), so the adjacency is more than chance. The median genome has 8 Homeodomain-hit genes, 79 of 154
+  neighbouring pairs are on the same strand, and 104 pairs have no gene between them. That fits a tandem-duplicated family, not a MAT locus. No further test done.
+
+## Allomyces probe (added 2026-11-14)
+`scripts/flank_idiomorph_probe.py` (tests in `tests/test_flank_idiomorph_probe.py`). Stage 1 had found 35, 45 and 63 HMG/Homeodomain candidate genes in
+*A. arbusculus* Burma 1F, *A. javanicus* California 12 and *A. macrogynus* ATCC 38327, all as single-gene loci (no adjacent pair). The new test asks, for each
+candidate, whether its flanking genes form a syntenic block in the other genomes and whether the candidate is conserved there, replaced by another
+HMG/Homeodomain gene, or missing.
+- 84 candidate genes; 152 gene-by-genome comparisons were testable. Not conserved (absent or replaced): 56 of 152 = 0.37.
+- Baseline, random non-candidate genes through the same test: 944 of 2,529 = 0.37. The candidates are not more often non-conserved than ordinary genes
+  (per pair 0.19 to 0.48 against 0.13 to 0.54).
+- 15 genes are absent or replaced in both other genomes, for example F5BE82F7_007902 (HMG_box, *A. macrogynus*; absent in both others, 4 flank genes each in a syntenic block).
+  With a 0.37 background rate these are expected by chance; none is a call. F5BE82F7_000331 (*A. macrogynus*, HMG_box with a weak sexP hit, E 9.3e-8) was not
+  singled out by the test.
+- Not tested: gene order beyond 25 genes, divergent alleles that fall below diamond E 1e-5, and assembly gaps. No new Allomyces candidate. Allomyces results are negative.
+
+## Structural follow-up of the PM leads and rescan of the 10 empty genomes (added 2026-11-14)
+Correction: the `PM` calls are in 4 Protomyces genomes plus *T. confusa* (5 genomes), not 5 Protomyces genomes plus *T. confusa* as written above before this edit.
+
+Script `scripts/pm_lead_followup.py` (tests in `tests/test_pm_lead_followup.py`); job 32091035; tables in `2026-11-14_mat-discovery-tables/`
+(`pm_lead_summary.tsv`, `pm_lead_genes.tsv`, `empty_scan_genes.tsv`, `empty_scan_pairs.tsv`). Pfam is `hmg_homeo.hmm` (HMG_box, HMG_box_2, Homeodomain, GA cutoff).
+
+PM leads (gene under each detector hit, tested with Pfam):
+| genome | matMc gene | HMG-box | matPi gene | homeodomain |
+|---|---|---|---|---|
+| *Protomyces inouyei* | F7C0A940_005637 | yes | no gene under the hit | n/a |
+| *P. lactucae-debilis* NRRL YB-4353 | F21A9957_003986 | yes | no gene under the hit | n/a |
+| *P. lactucae-debilis* 12-1054 | F003EF48_006292 | yes | no gene under the hit | n/a |
+| *P. macrosporus* | no gene under the hit | n/a | FCFD2032_003005 | no |
+| *Taphrina confusa* | F57803F5_005977 | yes | no gene under the hit | n/a |
+- In no genome do a matMc gene and a matPi gene sit next to each other. The two-gene `PM` structure is not confirmed anywhere. The matMc genes are HMG-box genes; the matPi hit has no Pfam homeodomain in *P. macrosporus* and no predicted gene in the other four. **[RETRACTED 2026-11-14, see the genome-level matPi search below: matPi is unannotated, not absent; a homeodomain region lies 7 to 14 kb from the matMc-like gene in 4 of these genomes]**
+- The Protomyces hits are not specific. The matMc hits are 44% identical, and the ten genomes with no call also have HMG genes that match the curated mat1-Mc at 46 to 49% (for example *P. gravidus* 46.1%, *P. pachydermus* 48.6%). The Protomyces `PM` calls are indistinguishable from background HMG genes in the same genomes. **[RETRACTED 2026-11-14, see the genome-level matPi search below: the HMG gene is generic, but its adjacency to a homeodomain region is not background]**
+- *T. confusa* is different: its matMc gene is 69.2% identical to the curated *T. deformans* matMc.
+
+Rescan of the 10 genomes with no call (Pfam plus diamond, E 1e-3, against the 14 curated PM and mat1 proteins):
+- Each genome has 5 to 7 HMG-box genes and 2 to 7 homeodomain genes (domain genes per genome 7 to 14). No genome has an HMG and a homeodomain gene, or two domain genes, within 5 genes of each other (`scan_pairs` is empty).
+- *Taphrina wiesneri* CBS 275.28 has a strong matMc-like gene (72.5% identity, E 7.6e-110) that the detector did not report as a locus, because no second gene was found next to it. No other genome has a hit above 50% identity to matMc.
+- Best matPi hits (31 to 55% identity) are generic homeodomain genes that every genome has; they carry no locus information.
+
+Conclusion, with limits: no Taphrinomycotina genome tested shows a two-gene PM locus. A matMc-like gene (about 70% identity to *T. deformans*) is present in *T. confusa* and *T. wiesneri* CBS 275.28 with no partner nearby; the 3 other *Taphrina* genomes with no call have no such gene. I did not look for a matPi that sits far from matMc (the curated record places matMc and matPi on separate contigs of the old assembly), and the layout **[RETRACTED 2026-11-14, see the genome-level matPi search below: a matMc-like HMG gene with a homeodomain region next to it exists in 6 genomes]**
+test cannot see a locus split over contigs. The probe finds no new candidate to curate; the only lead worth keeping is the matMc-like gene in the two *Taphrina* genomes. **[RETRACTED 2026-11-14, see the genome-level matPi search below: the leads are the HMG + homeodomain pairs below]**
+
+## matPi search and positive control (added 2026-11-14)
+Scan of the 5 PM-lead genomes, the 10 no-call genomes and the 4 *T. deformans* genomes for homeodomain genes similar to the curated matPi (job 32091046, 32091068; tables `pm_genomes_scan_genes.tsv`, `taphrina_deformans_scan_genes.tsv`, `empty_scan_genes.tsv`).
+- Positive control: in all 4 *T. deformans* genomes the curated matMc matches an HMG-box gene at 100% identity. The curated matPi matches no gene better than 49.2%, a generic homeodomain gene on a different contig from the matMc gene. The curated *T. deformans* matPi has no exact match in any *T. deformans* genome. The record already says matPi is unresolved; this is a second reason to review it. I did not trace where the curated matPi sequence comes from.
+- Every *Taphrina* genome has one homeodomain gene at 47.6 to 50.0% identity to the curated matPi, including the 3 genomes with no matMc-like gene. *T. confusa* (50.0%) and *T. wiesneri* CBS 275.28 (50.0%) have it on a different contig from the matMc-like gene, as in *T. deformans*. Identity cannot tell a matPi ortholog from the other homeodomain genes (the top hit stays within 2 points of the *T. deformans* value), so I cannot say whether these genes are matPi. No homeodomain gene is closer than 55.2% to the curated matPi in any genome tested (*Protomyces arabidopsidicola* 55.2%).
+- Protomyces genomes with a PM call have no homeodomain gene above the scan threshold for matPi (E 1e-3), apart from the *P. arabidopsidicola* hit above.
+
+## Follow-up of the leads in the other lineages (added 2026-11-14)
+Chance test (`scripts/adjacent_pair_null.py`, 500 random placements per genome; `gap_adjacent_pair_null.tsv`). With 6 lineages and 3 pair types, 18 tests were run: one p of 0.05 or below is expected by chance.
+
+| lineage | pair type | observed genomes | expected mean (max) | p |
+|---|---|---|---|---|
+| Microsporidia (132) | 2xHomeo | 65 | 19.0 (30) | 0.002 (floor of 500 draws) |
+| Microsporidia | HMG+Homeo | 0 | 4.5 (10) | 1.0 |
+| Monoblepharomycota (3) | 2xHMG | 2 | 0.2 (2) | 0.014 |
+| Rozellomycota clade (1) | HMG+Homeo | 1 | 0.0 (1) | 0.050 |
+| Calcarisporiellomycota (1) | HMG+Homeo | 1 | 0.5 (1) | 0.46 |
+| Aphelidiomycota (2), Olpidiomycota (1) | all | 0 | 0.0 to 0.0 | 1.0 |
+
+- **Microsporidia 2xHomeo** is a real excess (65 against 19.0). 55.4% of the pairs are on the same strand and 104 of 154 neighbours have no gene between them. This fits a tandem-duplicated family and not one locus per genome. Not followed further.
+- **Monoblepharomycota 2xHMG** comes from *Hyaloraphidium curvatum* (one adjacent same-strand HMG pair) and *Gonapodya prolifera* (4 separate HMG pairs on 4 contigs). Four pairs in one genome point to a repeated family, not one MAT locus. All genes are annotated as hypothetical proteins. The other *Gonapodya* genome has no pair.
+- **Rozellomycota clade (*Paramicrosporidium saccamoebae* KSL3)**: HMG-box gene FE6F46FC_001951 and homeodomain gene FE6F46FC_001954 on MTSL01000117.1 with two genes between them (the HMG gene on `-`, the homeodomain gene on `+`, divergent). Neither has a hit to the AMF HD1/HD2 or the Mucorales sexM/sexP controls at E 1e-5. This is the only compact HMG+homeodomain arrangement among the new lineages; it is one genome, uncorrected p = 0.05, and cannot be tested across genomes. Not a candidate record.
+- **Calcarisporiella**: pair not above chance.
+- **Aphelidiomycota, Olpidiomycota**: no pair.
+
+## Strategy status (checked against the five steps above)
+| step | status |
+|---|---|
+| 1. Detector probe with curated families | done for Taphrinomycotina (33 genomes) and Antarctolithica earlier |
+| 2. Structural verification of leads | done for PM leads (Pfam, gene order, positive control) and for the new-lineage leads (gene order, products, chance test). Result: no lead survives except the matMc-like gene in two *Taphrina* genomes and the single *Paramicrosporidium* pair |
+| 3. Population signal | done for Bd (negative) |
+| 4. Small-genome-count lineages | done for Allomyces (negative against a random-gene baseline) |
+| 5. Record unsearched lineages | done to the limit set by the data (see the coverage recount and the annotation-free search at the end); the 48 fragmentary assemblies were searched without gene models, with no pair found, which is weak evidence |
+Open: a curator check of the matPi reference of the *T. deformans* record; any test of the *Paramicrosporidium* pair needs a second genome of that clade.
+
+## Genomes that were not in any scan, and what was done (added 2026-11-14)
+The first survey left 65 genomes (target phyla only) outside the 496 + 141 scanned genomes. A name-matching fix and a look at each folder (table `unscanned_genomes_status.tsv`) gave (65 genomes: 3 annotated + 48 skipped + 10 without folder + 4 without proteome; 58 stay unscanned):
+
+| status | genomes | action |
+|---|---|---|
+| annotated, scannable | 3 | stage 1 run (job 32091100): *Homolaphlyctis polyrhiza*, *Vavraia culicis*, *Rhizophagus irregularis* DAOM_181602. Only the Rhizophagus genome has an HD1+HD2 locus: the known AMF locus, so it works as a positive control |
+| BFD annotation skipped (`skipped_too_small`) | 48 | 4 assemblies (three of 11 to 24 Mb in 44 to 495 contigs, and a 1.9 Mb *Synchytrium endobioticum* assembly in 203 contigs) got Augustus gene prediction and stage 1 (below). The other 44 are fragments; they include *Globomyces pollinis-pini* Arg68 (21.4 Mb in 983 contigs, about 22 kb per contig), which I did not predict of hundreds to thousands of contigs (13 Kickxellomycota at about 8 Mb in 1,600 to 2,000 contigs; Microsporidia 0.7 to 7.5 Mb in 278 to 2,245 contigs; Sanchytriomycota 4.2 and 6.3 Mb in 549 and 897 contigs) and were not scanned. A flank-first scan needs several genes per contig |
+| no annotation folder | 10 (Chytridiomycota 4, Entomophthoromycota 2, Glomeromycota 2, Microsporidia 1, one unclassified) | not scanned: no gene models. Includes a *Batrachochytrium dendrobatidis* genome, *Entomophthora muscae*, *Massospora cicadina*, *Gigaspora margarita*, *Mitosporidium daphniae* |
+| folder without proteome | 4 (Entomophthoromycota 1, Microsporidia 3) | not scanned |
+
+Augustus gene prediction (`scripts/augustus_gene_predict.slurm`, `scripts/augustus_proteins.py`, model `rhizopus_oryzae`, not trained on these lineages; jobs 32092338, stage 1 job 32092954; table `augustus_genomes_candidates.tsv`):
+| genome | contigs | genes predicted | HMG/Homeodomain candidates | result |
+|---|---|---|---|---|
+| *Amoeboaphelidium protococcarum* FD95 | 44 | 4,898 | 4 | no HD1+HD2, no HMG+flank, no pair |
+| *A. protococcarum* X5 | 155 | 9,397 | 5 | same |
+| *Rozella allomycis* CSF55 | 495 | 3,527 | 9 | same |
+| *Synchytrium endobioticum* 18_T1 | 203 (1.9 Mb assembly) | 821 | 2 | partial assembly; too little sequence to test |
+The summary count for the four genomes: HD1+HD2 0, HMG+flank 0, 2xHomeo 0, HMG+Homeo 0, sexM/sexP control hits in 2 genomes. The total candidate counts in stage 1 (domain hits plus control hits; 11, 17, 15 and 2) are lower than in BFD-annotated genomes of related lineages (13 to 71: *Olpidium bornovanus* 13, *Aphelidium insulamus* 19, *Gonapodya* 31 and 47, *Calcarisporiella thermophila* 71). That is what a mismatched Augustus model would give, but I did not test it. It suggests that these predicted gene sets miss domain genes, so a negative here is weak evidence. The *Synchytrium* assembly is only 1.9 Mb, so it says nothing about the species. A proper test needs BFD-style annotation of these assemblies (funannotate) or RNA-based gene models.
+
+Coverage conclusion: of the genomes in the target phyla that I could map, every one with gene models has been through at least one stage-1 scan, apart from those listed as not scanned above (58). The lineage conclusions stand only for those. In particular, for Sanchytriomycota, Kickxellomycota fragments, Microsporidia fragments and the Entomophthoromycota without annotation, nothing was tested.
+
+## Coverage recount and final status (added 2026-11-14; supersedes the counts of the two sections above)
+Recount by locus tag (the `LOCUSTAG` column of `samples.csv` against the gene IDs in all stage-1 outputs), which does not depend on folder names. The earlier name-based counts (58 unscanned; 10 genomes without an annotation folder) were partly a naming artefact: for example *Entomophthora muscae*, *Massospora cicadina*, *Gigaspora margarita* and a *Chytridiomycetes* sp. had been scanned in the first run under another folder name.
+- Target phyla in `samples.csv`: 699 samples. After the first two scans, 61 had no stage-1 output by locus tag; 4 of these were the Augustus genomes of the previous section, so 57 were truly unscanned. All 57 lack BFD gene models (`unscanned_by_locustag.tsv`). Every target-phylum genome that has BFD gene models has been through stage 1.
+- Contiguity of the 57 (`unscanned_assembly_stats.tsv`): N50 of 50 kb or more in 5, 20 kb or more in 9; one has no genome file.
+- Seven more assemblies were given Augustus gene models (same caveat: `rhizopus_oryzae` model, not trained on these lineages) and stage 1: both *Globomyces* assemblies (chytrids), two *Mitosporidium daphniae* assemblies and three *Spraguea lophii* assemblies (jobs 32093014, 32093248; stage 1 jobs 32093239, 32093330).
+
+| genome | contigs / N50 | genes | candidates | result |
+|---|---|---|---|---|
+| *Globomyces pollinis-pini* Arg68 | 983 / 51 kb | 8,406 | 17 HMG, 3 Homeodomain | 2xHMG pairs, conserved HMG cluster (below) |
+| *Globomyces* sp. JEL0801 | 800 / 46 kb | 5,960 | 10 HMG, 2 Homeodomain | 2xHMG pairs, same cluster |
+| *Mitosporidium daphniae* (ASM5257605) | 10 / 864 kb | 2,420 | 4 Homeodomain | no HMG gene, no pair |
+| *M. daphniae* UGP1 | 273 / 35 kb | 2,359 | 7 | no pair |
+| *Spraguea lophii* x3 | 143 to 158 / 97 to 99 kb | 356 to 362 | 0 | gene sets far too small (a microsporidian of 5.6 Mb should have about 2,000 genes); not testable |
+
+Globomyces (chytrid) follow-up, with the one genus where two genomes can be compared (`flank_idiomorph_probe.py --ann`, tables `globomyces_probe.tsv`, `globomyces_baseline.tsv`):
+- 32 HMG/Homeodomain candidates; 21 testable; 6 not conserved (0.29) against 112 of 728 random genes (0.15). Six against about 3 expected; I did not compute an exact p (a rough binomial tail is about 0.1), so this is not significant.
+- The 2xHMG excess (2 of 3 genomes, p 0.008 in `adjacent_pair_null_aug2.tsv`) rests on 3 genomes and several tests and is not taken as evidence.
+- The conserved block with an HMG cluster (Glopol1 MU621598.1 genes 7540 to 7545; JEL0801 JADGIX010000364.1 genes 5331 to 5335) holds two HMG gene types. The long type (263 aa) is 99.2% identical between the species and in the same position. The short type (138 aa) is 76.8% identical between the species and occurs as two copies 97.8% identical to each other in Glopol1 and one copy in JEL0801: a species-specific tandem duplication. Both species carry both genes. The cluster is not idiomorph-like. Two of its genes have a weak sexM hit (E about 1e-7); I do not treat that as MAT evidence.
+
+Final coverage: 50 target-phylum genomes remain unscanned (fragmentary assemblies, no genome file, or small N50) and 3 more (*Spraguea* sets) were run but are untestable: 53 genomes with no usable result, and the 1.9 Mb *Synchytrium* assembly (11 genomes in total went through Augustus). The unscanned set is mostly Microsporidia (about 25 after the five run here), 13 Kickxellomycota fragments, and a few Entomophthoromycota, Chytridiomycota and Sanchytriomycota genomes. The lineage conclusions of this note hold for scanned genomes only. A test of the rest needs BFD-style annotation (funannotate) or RNA-based gene models, and assemblies with an N50 below 20 kb are unlikely to help even then.
+
+Validation of the strategy: step 2 (structural verification) was applied in 5 lineages. In Taphrinomycotina it removed the Protomyces leads, in Allomyces it found no excess against a random baseline, in *Globomyces* it explained an apparent difference as a tandem duplication, and in the other new lineages (Rozellomycota, Monoblepharomycota, Microsporidia, Calcarisporiellomycota) it could not test the leads across genomes, because each lineage has one genome or the arrangement looks like a tandem family. For those lineages the claims stay "no evidence", not "absent".
+
+### Why the last 50 genomes are not scanned (checked 2026-11-14)
+`unscanned_assembly_stats.tsv`: of the 50 genomes not run, the median N50 is 5.4 kb (maximum 41 kb) and the median assembly has 938 contigs; one has no genome file. Only three have an N50 above 15 kb: a 0.5 Mb *Vairimorpha* sp. fragment (12 contigs), the *Pleurotus ostreatus* x *Saccharomyces cerevisiae* fusant (not a lineage without a defined MAT) and *Metchnikovella incurvata* (4.6 Mb, N50 17.6 kb). A flank-first scan needs about 11 genes on one contig (a window of 5 on each side), which is a contig of 20 kb or more in these gene-poor genomes. Annotating these assemblies (funannotate or otherwise) would give gene models but not the contiguity the method needs. This is a limit of the assemblies, so the coverage statement stays: no usable result for these 50 genomes.
+
+## Genome-level matPi search: the PM-like pair is present in 6 of 17 genomes (added 2026-11-14; corrects statements above)
+The BFD gene models do not include the homeodomain gene of this locus (the record of *T. deformans* says the same). The curated *T. deformans* matPi is a 181 aa partial protein from the old assembly, and its homeodomain region has no gene model in the BFD annotation either. So an annotation-based search misses it. I searched the assemblies directly.
+
+Scripts: `matpi_tblastn.py` (tblastn of the 4 curated matPi proteins against each assembly), `region_pfam_check.py` (six-frame translation of a region and Pfam), `matpi_hmg_adjacency.py` (distance of every HMG-box gene to the homeodomain-like regions, with a permutation null). Jobs: tblastn and region checks run on the HPCC 2026-11-14; tests in `tests/test_region_pfam_check.py` (4 tests). Tables: `matpi_genome_search_hits.tsv`, `matpi_region_pfam.tsv`, `matpi_hmg_adjacency_pairs.tsv`, `matpi_hmg_adjacency_summary.tsv`, `matpi_hmg_adjacency_null.tsv`. 17 genomes gave hits (3 *T. deformans*, other *Taphrina* 5, *Protomyces* 7, *Savitreella*, *Saitoella*); *T. deformans* JCM22205 has no genome file in the library, and *Schizosaccharomyces lindneri* gave no hit.
+
+- Positive control: in all three *T. deformans* genomes with a genome file the curated matPi matches an unannotated region at 100% identity (E 1e-119). In A2 it lies on the same scaffold as the matMc gene, 40,370 bp away (RHGF01000006.1: matPi 51,688 to 52,236, matMc 92,606 to 93,298). In CBS 355.35 and PYCC 5710 the two sit on different contigs.
+- The top-ranked matPi-like region lies on the same contig as an HMG-box gene in:
+
+| genome | HMG gene | region (identity, E) | distance | Pfam in the region (six-frame ORF) |
+|---|---|---|---|---|
+| *Protomyces inouyei* | F7C0A940_005637 | 45.2%, 2e-18 | 7,165 bp | Homeodomain, 167 aa, E 1.1e-10 |
+| *P. lactucae-debilis* NRRL YB-4353 | F21A9957_003986 | 45.2%, 2e-18 | 7,164 bp | Homeodomain, 151 aa, E 1e-10 |
+| *P. lactucae-debilis* 12-1054 | F003EF48_006292 | 45.2%, 2e-18 | 7,152 bp | Homeodomain, 151 aa, E 1e-10 |
+| *Taphrina confusa* | F57803F5_005977 | 46.5%, 2e-46 | 14,057 bp | Homeodomain, 168 aa, E 1.1e-8 |
+| *T. communis* | F8DCC00A_005608 | 52.4%, 8e-54 | 18,060 bp | Homeodomain, 184 aa, E 1.5e-9 |
+| *T. betulina* | FC6B0312_004634 | 43.0%, 2e-26 | 10,297 bp | no Pfam ORF of 40 aa or more in the region: weaker |
+| *T. deformans* A2 (control) | F891DC7E_001655 | 100%, 1e-119 | 40,370 bp | Homeodomain, 189 aa, E 1.5e-9 |
+Negative control, a 549 bp stretch 20 kb from the A2 hit: no Pfam ORF. *Savitreella* has a pair at 39 kb (not within 20 kb).
+- Permutation null (`matpi_hmg_adjacency_null.tsv`): an HMG gene within 20 kb of a matPi-like region in 6 of 17 genomes; random placement of the same number of HMG genes at random gene positions gives a mean of 0.71 genomes (maximum 5 in 2,000 draws), p = 0.0005 (the floor with 2,000 draws). The genomes are not independent: there are two *P. lactucae-debilis* assemblies, and the three Protomyces offsets are the same (7.15 to 7.17 kb), which is what a conserved locus would give but also what one lineage would give.
+- The 20 kb result includes genomes with no detector call (*T. communis*, *T. betulina*): the detector missed them because only one of the two genes had a model.
+- Not adjacent: *P. macrosporus*, *P. arabidopsidicola*, *P. gravidus*, *P. pachydermus*, *Taphrina* sp. SM11, *T. wiesneri*, *Saitoella*, and two *T. deformans* assemblies (contigs may be broken at the locus).
+
+What this means, with limits. A homeodomain gene is present in these genomes whether or not an HMG gene is next to it (for example *P. gravidus*, *T. communis* have unannotated homeodomain ORFs), so the homeodomain gene alone is not MAT evidence. The evidence is the conserved physical pairing of an HMG-box gene and a homeodomain gene, which is the arrangement of the curated *T. deformans* locus (matMc plus matPi) and of the Pneumocystis PM locus. The HMG genes in Protomyces are only 44 to 49% identical to the curated matMc and could be any HMG gene; the pairing, not the HMG identity, carries the evidence. I did not test that the HMG genes are orthologous across genomes, I did not look at expression, and the mating-type role of this locus in these species is not shown. The candidate set, for a curator: *P. inouyei*, *P. lactucae-debilis* (two assemblies), *T. confusa*, *T. communis* and *T. betulina* (weaker); the orthology section below narrows it to *P. inouyei*, *P. lactucae-debilis* and *T. confusa*.
+Next test (done in the orthology section below): gene models and orthology of both genes.
+
+## Cross-genome orthology of the HMG + homeodomain pair (added 2026-11-14; closes step 2 for Taphrinomycotina)
+Scripts: `pm_locus_models.py` (exonerate gene models and a diamond reciprocal-best-hit test; tests in `tests/test_pm_locus_models.py`). Tables: `pm_locus_homeodomain_models.tsv`, `pm_locus_orthology.tsv`, `pm_locus_orthology_proteins.faa`, `matpi_region_pfam.tsv` (refreshed). A bug found on the way: the ORF end coordinate in `region_pfam_check.py` was one base too high (exclusive reported as inclusive), which shifted the frame when re-extracting a reverse-strand ORF; fixed and tested, and `matpi_region_pfam.tsv` was regenerated. The Pfam hits themselves were unaffected.
+
+Gene models of the homeodomain gene (exonerate protein2genome against the curated matPi proteins; the BFD annotation has none):
+| genome | strand | CDS | aa | exons | Pfam |
+|---|---|---|---|---|---|
+| *T. deformans* A2 (control) | + | 51,694 to 52,236 | 181 | 1 | Homeodomain; reproduces the curated partial matPi |
+| *T. confusa* | - | 181,602 to 182,084 | 161 | 1 | Homeodomain |
+| *T. communis* | - | 80,258 to 80,794 | 179 | 1 | Homeodomain |
+| *T. betulina* | + | 16,268 to 16,750 | 161 | 1 | none |
+| *Protomyces inouyei*, *P. lactucae-debilis* x2 | +/- | 59 aa homeodomain core only | 59 | 1 | Homeodomain |
+The Protomyces models cover only the homeodomain core; the full stop-free ORFs of 151 to 167 aa (six-frame) were used for the orthology test. None of these models has an intron model beyond what exonerate found, and none is supported by RNA.
+
+Orthology test: for each locus protein (the HMG gene next to the homeodomain region, and the homeodomain ORF), the best hit in every other genome among that genome's proteins of the same domain class (all Pfam HMG-box genes, or all homeodomain genes, plus the locus protein), and whether that best hit is the other genome's locus protein and reciprocal. Genomes: 3 Protomyces assemblies, *T. confusa*, *T. communis*, *T. betulina*, *T. deformans* A2.
+- Homeodomain locus protein (6 genomes with a locus ORF; *T. betulina* has none): in all 30 comparisons among these six the best hit is the other genome's locus protein and it is reciprocal. Identity 32 to 53% over 139 to 171 aa: *T. deformans* A2 against Protomyces 32.5 to 34.0%, against *T. confusa* 43.3%, against *T. communis* 52.6%; the Protomyces assemblies are 100% identical to each other over 151 aa. So the unannotated homeodomain gene beside the HMG gene is the same gene in all six genomes, and it is the gene of the curated *T. deformans* matPi region.
+- HMG locus protein: among the Protomyces assemblies, *T. confusa* and *T. deformans* A2 the locus HMG protein is the reciprocal best hit of the others' locus protein in all 20 comparisons: A2 against Protomyces 43.4 to 45.0%, against *T. confusa* 69.2%; *P. inouyei* against the *P. lactucae-debilis* assemblies 99 to 100%. It is also the best hit among the genome's other 5 to 6 HMG genes. So it is the ortholog of the curated *T. deformans* matMc, although the Protomyces identity (44%) is low.
+- *T. communis* and *T. betulina* are different: their adjacent HMG proteins are reciprocal best hits of each other (41.4%) but have no hit (E 1e-3) to the matMc orthologs in the other genomes. The HMG gene next to the conserved homeodomain gene there is not the matMc ortholog (or has diverged beyond detection). The *T. communis* homeodomain gene is orthologous (A2 52.6%).
+
+Result with limits. A matMc-ortholog HMG gene and a matPi-ortholog homeodomain gene lie 7 to 14 kb apart on one contig in three Protomyces assemblies and *T. confusa*, and 40 kb apart in *T. deformans* A2, which matches the fused PM arrangement in the curated *T. deformans* record and in Pneumocystis. This is the structural verification that the detector call lacked. It does not show a mating-type function. What is not shown: expression; that the locus is fused in one copy per strain (homothallic-like) as opposed to two alleles (no allele difference was seen: *P. inouyei* and the two *P. lactucae-debilis* assemblies are 99 to 100% identical at both genes); that the pair is the only copy (the genomes have 5 to 7 HMG genes and 2 to 7 homeodomain-hit genes). *P. inouyei* contig QXDQ01000433.1 is only 36.8 kb long and the HMG gene ends 0.5 kb from its end, so the locus is cut at that contig end. The *P. lactucae-debilis* assemblies are two assemblies of one species and are not independent. Candidate loci for a curator: *P. inouyei*, *P. lactucae-debilis* (two assemblies), *T. confusa* (matMc and matPi orthologs). *T. communis* has the matPi ortholog beside a different HMG gene and *T. betulina* has no Pfam homeodomain ORF there: both are not confirmed.
+
+## Expression of the HMG + homeodomain pair (added 2026-11-14)
+Public RNA-seq exists for two genomes that carry the locus (ENA, library source TRANSCRIPTOMIC): *T. deformans* A2 (SRR8132818, 27,496,815 read pairs, unstranded) and *P. lactucae-debilis* 12-1054 (SRR5576147, 79,174,280 read pairs). Both runs were fetched with `prefetch`, converted with `fasterq-dump`, and both mates matched the ENA read count exactly. Reads were mapped with hisat2 (`--dta`, introns up to 5 kb); depth over every annotated gene and over the unannotated homeodomain region comes from `samtools bedcov`. Scripts: `rnaseq_locus_expression.slurm`, `locus_expression.py` (tests in `tests/test_locus_expression.py`); jobs 32093453 and 32093454; tables `rnaseq_*_locus_expression.tsv`, `rnaseq_*_spliced.tsv`.
+
+| genome (run) | overall alignment | HMG gene (matMc ortholog) | unannotated homeodomain region | spliced reads in the region |
+|---|---|---|---|---|
+| *T. deformans* A2 (SRR8132818) | 91.1% | F891DC7E_001655: 664x, 82.6th percentile | RHGF01000006.1:51,685 to 52,252: 215x, 53.3rd percentile | 66 of 1,676 reads |
+| *P. lactucae-debilis* 12-1054 (SRR5576147) | 56.2% | F003EF48_006292: 1,388x, 79.1st percentile | NW_024468021.1:38,146 to 38,599: 1,432x, 79.8th percentile | 157 of 5,477 reads |
+The percentile is the share of annotated genes of 300 bp or more with a lower mean depth in the same library; mean depth is not corrected for gene length effects or library size, so it only compares genes within one library.
+- Both loci are transcribed in both species. The unannotated homeodomain region is covered at every base (801 of 801 in A2, 551 of 551 in 12-1054) at a depth at or above the median gene. So the homeodomain gene is a real transcribed region that BFD did not annotate, in the genome that carries the curated *T. deformans* matPi and in *Protomyces*.
+- *T. deformans* A2: four short introns (43 to 60 bp; 1,361 to 2,427 reads each) lie 100 to 470 bp downstream of the homeodomain exon (52,342 to 52,392; 52,465 to 52,507; 52,555 to 52,614; 52,658 to 52,710), with depth peaks at 52,300 to 52,400. The run is unstranded, so I cannot say whether these exons belong to the same gene. The curated protein has its homeodomain at the C-terminus, which would put further exons upstream; my single-exon model is therefore not verified, and the full gene structure is open.
+- *P. lactucae-debilis* 12-1054: the strongest junctions in the 4 kb window (39,067 to 40,515) lie 1 to 2 kb from the homeodomain ORF and belong to other genes.
+- Limits: one library per species, conditions unknown; the 12-1054 run aligns at 56.2% (a mixed sample or divergence; not examined); this shows transcription, not a mating role, and no comparison between mating types or conditions was made.
+
+### Transcript assembly at the locus (added 2026-11-14)
+StringTie 3.0.3 on the two alignments (4,910 transcripts in A2, 3,326 in 12-1054), spliced sequences with `gffread -w`, and `scripts/locus_transcripts.py` (Pfam on every ORF of 30 aa or more in the six frames; tests in `tests/test_locus_expression.py`); table `rnaseq_locus_transcripts.tsv`.
+- *P. lactucae-debilis* 12-1054: three minus-strand transcripts (3, 5 and 7 exons; 34,271 to 38,767 or 40,155; spliced length 4.3 to 5.6 kb) span the homeodomain region (38,146 to 38,599). Each contains a homeodomain ORF (135 to 151 aa, E 3 to 5e-10) in a frame of the transcript as written, so the homeodomain ORF is on the same strand as the assembled transcript. The longest ORF of these transcripts (462 aa) carries no Pfam domain. So the homeodomain ORF is part of a spliced transcript, not an isolated exon.
+- *T. deformans* A2: two minus-strand transcripts (4 and 5 exons; 50,131 to 52,842; 2.5 kb spliced) span the region. They contain a 189 aa homeodomain ORF (E 3.3e-9) in the reverse frame (-1) of the transcript as written, that is, on the strand opposite to the assembled transcript. The run is unstranded, so StringTie takes the strand from splice motifs. Two readings fit the data: a plus-strand homeodomain gene overlapped by a minus-strand gene, or a strand mis-assignment. I cannot choose between them. A stranded library, or a long-read transcript, would.
+- A separate plus-strand transcript (38,896 to 39,637; 208 aa ORF) in 12-1054 carries no Pfam domain.
+- What this settles: the homeodomain region is spliced into multi-exon transcripts in both genomes and the homeodomain ORF is present in the spliced sequence. What it does not settle: the strand and the exact exons of the homeodomain gene in A2, the full-length protein in either genome, and whether the transcripts correspond to the matPi gene of Pneumocystis (whose homeodomain is C-terminal).
+
+### Where the curated *T. deformans* matPi sequence comes from (traced 2026-11-14)
+`db/Ascomycota/Taphrinales/5011_unknown-1_PM_combined/proteins.faa` holds a 181 aa matPi. It is identical, residue for residue, to the plus-strand translation of GCA_005281805.1 RHGF01000006.1:51,694 to 52,236 (543 bp, no stop codon, first residue Leu). That span is the tblastn subject range recorded in the record's own 2026-09-18 note. So the curated matPi is the translation of a homology-hit region, not a Met-initiated gene model, which is what the record says ("only a homology-confirmed homeodomain-encoding region was localised"). Consequences: (1) it matches no BFD gene model, because BFD did not annotate this gene; (2) it matches the matPi of Pneumocystis only over the homeodomain (31 to 43% identity, as the record states); (3) the RNA-seq of this note shows the region is transcribed and spliced, so a real gene exists here; its start and strand are not resolved. The record's matPi therefore stays a partial, region-derived sequence. Any change to the record (replace it with a transcript-derived protein, or mark it region-derived) is a curator decision; I changed nothing in `db/`.
+
+### Strand of the homeodomain gene in *P. lactucae-debilis* 12-1054 resolved; A2 still open (added 2026-11-14)
+The public data for these genera are all Illumina (ENA: *Taphrina* 35 runs, *Protomyces* 1 run; no long reads). Strandedness is not recorded in ENA, so I measured it (`scripts/infer_strandedness.py`; test in `tests/test_locus_expression.py`): the orientation of read 1 over 100 to 400 isolated annotated genes of 1 kb or more.
+- *T. deformans* A2 (SRR8132818): unstranded (50.2% of read 1 on the gene strand). The strand of the A2 homeodomain gene cannot be set from this run.
+- *P. lactucae-debilis* 12-1054 (SRR5576147): reverse-stranded (95.4 to 95.8% of read 1 on the strand opposite to the gene, depending on the gene sample). Method check: the annotated minus-strand HMG gene F003EF48_006292 gives 3,039 read-1 forward and 246 reverse, implied strand `-` (92.5%).
+- Over the homeodomain ORF (NW_024468021.1:38,146 to 38,599): 2,748 read-1 forward and 354 reverse, implied strand `-` (88.6%). The upstream 1 kb gives the same strand (1,341 against 478). So in 12-1054 the homeodomain gene is on the minus strand, the same strand as its reverse-strand ORF and the StringTie transcripts, and the same strand as the HMG gene: both genes are transcribed in the same orientation, 7.15 kb apart. Table `rnaseq_Plact_12-1054_strand_check.txt`.
+- Open after this: the exact exons and full-length protein of the homeodomain gene in 12-1054 (the transcripts of the previous section give a candidate), and the strand in A2. A stranded *Taphrina* library or long-read transcripts for either genus would close these; none is public.
+
+### Annotation-free search of the fragmentary assemblies (added 2026-11-14)
+The 48 target-phylum assemblies with a genome file that were not scanned by any gene-order method (Microsporidia 25, Kickxellomycota 13, Entomophthoromycota 3, Chytridiomycota 2, Sanchytriomycota 2, Glomeromycota 1, Neocallimastigomycota 1, one unclassified; the Pleurotus x Saccharomyces fusant and the genome without a file are not included) were searched directly with `scripts/unannotated_genome_search.py` (tests in `tests/test_unannotated_genome_search.py`): tblastn (E 1e-5, SEG off) of 22 HMG-class controls (curated sexM, sexP, matMc, mat1-Mc, matMi) and 87 homeodomain-class controls (Ropars HD1-like and HD2, curated matPi, mat1-Pc, mat1-Pi) against each assembly; hits of one class closer than 2 kb were merged; a pair is an HMG region and a homeodomain region on one contig no more than 20 kb apart. Tables: `annotfree_summary.tsv`, `annotfree_regions.tsv`.
+- 239 HMG regions in 18 genomes (169 of them in one *Gigaspora margarita* assembly, an AMF with a large HMG-box family, as in the Rhizophagus controls) and 47 homeodomain regions in 21 genomes.
+- No genome has an HMG region and a homeodomain region on one contig within 20 kb: 0 of 48 genomes. Per group: Kickxellomycota (13) median 5 HMG and 0 homeodomain regions; Microsporidia (25) median 0 HMG and 2 homeodomain regions; Entomophthoromycota (3) median 2 and 1; Chytridiomycota (2), Sanchytriomycota (2) and Neocallimastigomycota (1) have no or almost no regions.
+- The strongest hits are a *Gigaspora margarita* homeodomain region (E 2.6e-47, 33% identity to a Ropars query), a *Hepatospora eriocheir* region (52%, E 3.9e-13) and the Gigaspora HMG regions (45 to 51%).
+- Limits: the assemblies are fragmented (median N50 5.4 kb), so most contigs are shorter than the pair distance and a pair could not be seen even if the genes were adjacent; the controls come from Mucoromycota and Taphrinomycotina and detect divergent HMG or homeodomain families only weakly in Microsporidia (which have reduced genomes); there is no chance expectation for pairs on fragments. So this result adds presence information for 48 more genomes but is not a test of absence of a MAT-like locus: for these genomes the finding stays "no evidence".
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug2.tsv b/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug2.tsv
new file mode 100644
index 00000000..d74c59a3
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug2.tsv
@@ -0,0 +1,4 @@
+lineage	pair_type	genomes	observed_genomes	expected_mean	expected_max	p	share_same_strand
+Aug2_3genomes	HMG+Homeo	3	0	0.1	1	1.0000	NA
+Aug2_3genomes	2xHomeo	3	1	0.0	1	0.0299	0.0
+Aug2_3genomes	2xHMG	3	2	0.2	2	0.0080	0.333
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug3.tsv b/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug3.tsv
new file mode 100644
index 00000000..830114c6
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/adjacent_pair_null_aug3.tsv
@@ -0,0 +1,4 @@
+lineage	pair_type	genomes	observed_genomes	expected_mean	expected_max	p	share_same_strand
+Aug3_4genomes	HMG+Homeo	4	0	0.0	0	1.0000	NA
+Aug3_4genomes	2xHomeo	4	0	0.0	1	1.0000	NA
+Aug3_4genomes	2xHMG	4	0	0.0	0	1.0000	NA
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/allomyces_baseline.tsv b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_baseline.tsv
new file mode 100644
index 00000000..1deccb4c
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_baseline.tsv
@@ -0,0 +1,19 @@
+genome_A	genome_B	class	genes
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	conserved	399
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	no_synteny	41
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	not_conserved	60
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	conserved	266
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	no_synteny	24
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	not_conserved	210
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	conserved	363
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	no_synteny	48
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	not_conserved	89
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	conserved	198
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	no_synteny	85
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	not_conserved	217
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	conserved	194
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	no_synteny	131
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	not_conserved	175
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	conserved	165
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	no_synteny	142
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	not_conserved	193
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/allomyces_probe.tsv b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_probe.tsv
new file mode 100644
index 00000000..0420350c
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_probe.tsv
@@ -0,0 +1,169 @@
+genome_A	gene	domain	genome_B	class	flank_mapped	region_contig	region_span
+Allomyces_arbusculus_Burma_1F	FA629528_000471	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000013.1	1581-1591
+Allomyces_arbusculus_Burma_1F	FA629528_000695	HMG_box	Allomyces_javanicus_California_12	conserved	9	JADHYU010000004.1	617-625
+Allomyces_arbusculus_Burma_1F	FA629528_000770	HMG_box	Allomyces_javanicus_California_12	conserved	9	JADHYU010000004.1	687-702
+Allomyces_arbusculus_Burma_1F	FA629528_001301	HMG_box	Allomyces_javanicus_California_12	conserved	10	JADHYU010000015.1	1758-1768
+Allomyces_arbusculus_Burma_1F	FA629528_002006	HMG_box	Allomyces_javanicus_California_12	conserved	10	JADHYU010000009.1	1224-1234
+Allomyces_arbusculus_Burma_1F	FA629528_002248	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000034.1	2949-2960
+Allomyces_arbusculus_Burma_1F	FA629528_002316	HMG_box	Allomyces_javanicus_California_12	absent	8	JADHYU010000001.1	224-227
+Allomyces_arbusculus_Burma_1F	FA629528_002370	Homeodomain	Allomyces_javanicus_California_12	conserved	9	JADHYU010000038.1	3124-3133
+Allomyces_arbusculus_Burma_1F	FA629528_002856	Homeodomain	Allomyces_javanicus_California_12	conserved	7	JADHYU010000270.1	8898-8908
+Allomyces_arbusculus_Burma_1F	FA629528_002972	HMG_box	Allomyces_javanicus_California_12	conserved	10	JADHYU010000002.1	342-360
+Allomyces_arbusculus_Burma_1F	FA629528_003412	Homeodomain	Allomyces_javanicus_California_12	absent	10	JADHYU010000178.1	7550-7554
+Allomyces_arbusculus_Burma_1F	FA629528_004436	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000001.1	187-197
+Allomyces_arbusculus_Burma_1F	FA629528_004651	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000084.1	5126-5144
+Allomyces_arbusculus_Burma_1F	FA629528_004909	HMG_box	Allomyces_javanicus_California_12	conserved	6	JADHYU010000042.1	3276-3288
+Allomyces_arbusculus_Burma_1F	FA629528_006029	HMG_box	Allomyces_javanicus_California_12	conserved	9	JADHYU010000180.1	7573-7585
+Allomyces_arbusculus_Burma_1F	FA629528_007241	HMG_box	Allomyces_javanicus_California_12	conserved	8	JADHYU010000014.1	1680-1688
+Allomyces_arbusculus_Burma_1F	FA629528_007273	Homeodomain	Allomyces_javanicus_California_12	absent	3	JADHYU010000258.1	8753-8762
+Allomyces_arbusculus_Burma_1F	FA629528_007501	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000208.1	8079-8088
+Allomyces_arbusculus_Burma_1F	FA629528_007805	Homeodomain	Allomyces_javanicus_California_12	conserved	5	JADHYU010000079.1	4939-4943
+Allomyces_arbusculus_Burma_1F	FA629528_008236	HMG_box	Allomyces_javanicus_California_12	other_domain	6	JADHYU010000189.1	7741-7745
+Allomyces_arbusculus_Burma_1F	FA629528_008543	HMG_box	Allomyces_javanicus_California_12	no_synteny	3		
+Allomyces_arbusculus_Burma_1F	FA629528_008632	HMG_box	Allomyces_javanicus_California_12	conserved	4	JADHYU010000292.1	9145-9148
+Allomyces_arbusculus_Burma_1F	FA629528_000471	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	9	GG745329.1	1598-1606
+Allomyces_arbusculus_Burma_1F	FA629528_000695	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	8	GG745338.1	6744-6752
+Allomyces_arbusculus_Burma_1F	FA629528_000770	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	9	GG745338.1	6674-6683
+Allomyces_arbusculus_Burma_1F	FA629528_001301	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745328.1	719-729
+Allomyces_arbusculus_Burma_1F	FA629528_002006	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745375.1	15222-15238
+Allomyces_arbusculus_Burma_1F	FA629528_002248	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745328.1	256-267
+Allomyces_arbusculus_Burma_1F	FA629528_002316	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	9	GG745328.1	327-335
+Allomyces_arbusculus_Burma_1F	FA629528_002370	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	8	GG745342.1	8105-8112
+Allomyces_arbusculus_Burma_1F	FA629528_002856	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	5	GG745333.1	4466-4473
+Allomyces_arbusculus_Burma_1F	FA629528_002972	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745337.1	6486-6495
+Allomyces_arbusculus_Burma_1F	FA629528_003412	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	10	GG745335.1	5222-5231
+Allomyces_arbusculus_Burma_1F	FA629528_004436	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745328.1	363-372
+Allomyces_arbusculus_Burma_1F	FA629528_004651	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745339.1	7063-7073
+Allomyces_arbusculus_Burma_1F	FA629528_004909	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	7	GG745381.1	15898-15904
+Allomyces_arbusculus_Burma_1F	FA629528_006029	HMG_box	Allomyces_macrogynus_ATCC_38327	absent	8	GG745331.1	3212-3220
+Allomyces_arbusculus_Burma_1F	FA629528_007241	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	7	GG745358.1	12640-12647
+Allomyces_arbusculus_Burma_1F	FA629528_007273	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	9	GG745342.1	8051-8056
+Allomyces_arbusculus_Burma_1F	FA629528_007501	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745352.1	11108-11115
+Allomyces_arbusculus_Burma_1F	FA629528_007805	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	5	GG745347.1	9377-9379
+Allomyces_arbusculus_Burma_1F	FA629528_008236	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	6	GG745331.1	2541-2544
+Allomyces_arbusculus_Burma_1F	FA629528_008543	HMG_box	Allomyces_macrogynus_ATCC_38327	absent	4	GG745337.1	6239-6262
+Allomyces_arbusculus_Burma_1F	FA629528_008632	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	5	GG745359.1	12835-12837
+Allomyces_javanicus_California_12	FAFF0595_000193	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	10	JADHYV010000024.1	4430-4440
+Allomyces_javanicus_California_12	FAFF0595_000342	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	7	JADHYV010000013.1	2953-2970
+Allomyces_javanicus_California_12	FAFF0595_000356	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	4	JADHYV010000013.1	2955-2972
+Allomyces_javanicus_California_12	FAFF0595_000621	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	9	JADHYV010000003.1	691-699
+Allomyces_javanicus_California_12	FAFF0595_000694	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000003.1	765-772
+Allomyces_javanicus_California_12	FAFF0595_001587	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	10	JADHYV010000002.1	465-475
+Allomyces_javanicus_California_12	FAFF0595_001686	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000068.1	7235-7244
+Allomyces_javanicus_California_12	FAFF0595_001764	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	10	JADHYV010000004.1	1295-1305
+Allomyces_javanicus_California_12	FAFF0595_002955	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	9	JADHYV010000009.1	2242-2251
+Allomyces_javanicus_California_12	FAFF0595_003130	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	9	JADHYV010000010.1	2364-2374
+Allomyces_javanicus_California_12	FAFF0595_003281	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	9	JADHYV010000029.1	4904-4918
+Allomyces_javanicus_California_12	FAFF0595_003869	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	10	JADHYV010000004.1	1147-1157
+Allomyces_javanicus_California_12	FAFF0595_004939	Homeodomain	Allomyces_arbusculus_Burma_1F	absent	10	JADHYV010000153.1	8686-8690
+Allomyces_javanicus_California_12	FAFF0595_005132	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	7	JADHYV010000026.1	4645-4655
+Allomyces_javanicus_California_12	FAFF0595_005141	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	5	JADHYV010000026.1	4651-4657
+Allomyces_javanicus_California_12	FAFF0595_005618	HMG_box	Allomyces_arbusculus_Burma_1F	no_synteny	2		
+Allomyces_javanicus_California_12	FAFF0595_007343	Homeodomain	Allomyces_arbusculus_Burma_1F	absent	4	JADHYV010000012.1	2792-2797
+Allomyces_javanicus_California_12	FAFF0595_007578	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	9	JADHYV010000041.1	6020-6032
+Allomyces_javanicus_California_12	FAFF0595_007741	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	6	JADHYV010000112.1	8236-8240
+Allomyces_javanicus_California_12	FAFF0595_008084	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000076.1	7497-7505
+Allomyces_javanicus_California_12	FAFF0595_008621	HMG_box	Allomyces_arbusculus_Burma_1F	absent	5	JADHYV010000172.1	8803-8805
+Allomyces_javanicus_California_12	FAFF0595_008906	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000012.1	2848-2858
+Allomyces_javanicus_California_12	FAFF0595_009145	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000145.1	8625-8630
+Allomyces_javanicus_California_12	FAFF0595_009571	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	4	JADHYV010000009.1	2313-2316
+Allomyces_javanicus_California_12	FAFF0595_009572	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	3	JADHYV010000009.1	2313-2316
+Allomyces_javanicus_California_12	FAFF0595_000193	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745330.1	1840-1847
+Allomyces_javanicus_California_12	FAFF0595_000342	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	6	GG745337.1	6473-6490
+Allomyces_javanicus_California_12	FAFF0595_000356	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	5	GG745337.1	6475-6492
+Allomyces_javanicus_California_12	FAFF0595_000621	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	9	GG745338.1	6744-6753
+Allomyces_javanicus_California_12	FAFF0595_000694	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	9	GG745338.1	6672-6682
+Allomyces_javanicus_California_12	FAFF0595_001587	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	9	GG745329.1	1598-1606
+Allomyces_javanicus_California_12	FAFF0595_001686	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	9	GG745358.1	12640-12647
+Allomyces_javanicus_California_12	FAFF0595_001764	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745328.1	720-729
+Allomyces_javanicus_California_12	FAFF0595_002955	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	10	GG745328.1	256-266
+Allomyces_javanicus_California_12	FAFF0595_003130	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	8	GG745345.1	9191-9198
+Allomyces_javanicus_California_12	FAFF0595_003281	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	9	GG745342.1	7889-7897
+Allomyces_javanicus_California_12	FAFF0595_003869	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	8	GG745330.1	2346-2350
+Allomyces_javanicus_California_12	FAFF0595_004939	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	10	GG745350.1	10348-10356
+Allomyces_javanicus_California_12	FAFF0595_005132	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	8	GG745339.1	7063-7073
+Allomyces_javanicus_California_12	FAFF0595_005141	Homeodomain	Allomyces_macrogynus_ATCC_38327	other_domain	4	GG745339.1	7061-7066
+Allomyces_javanicus_California_12	FAFF0595_005618	HMG_box	Allomyces_macrogynus_ATCC_38327	no_synteny	2		
+Allomyces_javanicus_California_12	FAFF0595_007343	Homeodomain	Allomyces_macrogynus_ATCC_38327	no_synteny	2		
+Allomyces_javanicus_California_12	FAFF0595_007578	HMG_box	Allomyces_macrogynus_ATCC_38327	absent	8	GG745331.1	3209-3220
+Allomyces_javanicus_California_12	FAFF0595_007741	HMG_box	Allomyces_macrogynus_ATCC_38327	other_domain	6	GG745338.1	6834-6838
+Allomyces_javanicus_California_12	FAFF0595_008084	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	6	GG745352.1	11108-11114
+Allomyces_javanicus_California_12	FAFF0595_008621	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	5	GG745337.1	6261-6273
+Allomyces_javanicus_California_12	FAFF0595_008906	Homeodomain	Allomyces_macrogynus_ATCC_38327	conserved	6	GG745333.1	4467-4473
+Allomyces_javanicus_California_12	FAFF0595_009145	HMG_box	Allomyces_macrogynus_ATCC_38327	conserved	6	GG745359.1	12833-12839
+Allomyces_javanicus_California_12	FAFF0595_009571	HMG_box	Allomyces_macrogynus_ATCC_38327	no_synteny	3		
+Allomyces_javanicus_California_12	FAFF0595_009572	HMG_box	Allomyces_macrogynus_ATCC_38327	no_synteny	2		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000262	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000009.1	2242-2251
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000331	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000009.1	2311-2320
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000369	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000024.1	4430-4440
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000725	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	6	JADHYV010000004.1	1295-1305
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001048	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	3	JADHYV010000016.1	3409-3416
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001604	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000002.1	466-475
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001844	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000024.1	4429-4442
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002201	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	4	JADHYV010000004.1	1296-1303
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002352	HMG_box	Allomyces_arbusculus_Burma_1F	absent	4	JADHYV010000004.1	1146-1157
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002543	HMG_box	Allomyces_arbusculus_Burma_1F	absent	6	JADHYV010000105.1	8121-8123
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002626	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	5	JADHYV010000003.1	692-698
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_004133	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000002.1	467-479
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_004473	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	4	JADHYV010000012.1	2848-2856
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_005228	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	7	JADHYV010000016.1	3406-3415
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_005716	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	4	JADHYV010000076.1	7496-7506
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006268	HMG_box	Allomyces_arbusculus_Burma_1F	no_synteny	3		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006492	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000013.1	2966-2974
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006678	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	5	JADHYV010000003.1	765-771
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006750	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000003.1	691-699
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006840	HMG_box	Allomyces_arbusculus_Burma_1F	absent	3	JADHYV010000112.1	8238-8240
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007069	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	10	JADHYV010000026.1	4645-4655
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007894	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000029.1	4904-4918
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007902	HMG_box	Allomyces_arbusculus_Burma_1F	absent	4	JADHYV010000029.1	4915-4923
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008056	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	5	JADHYV010000069.1	7271-7276
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008109	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	6	JADHYV010000010.1	2361-2373
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008423	HMG_box	Allomyces_arbusculus_Burma_1F	other_domain	4	JADHYV010000008.1	2001-2008
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009141	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000069.1	7267-7270
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009194	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	5	JADHYV010000010.1	2363-2374
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009381	Homeodomain	Allomyces_arbusculus_Burma_1F	other_domain	6	JADHYV010000089.1	7805-7807
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_010354	Homeodomain	Allomyces_arbusculus_Burma_1F	no_synteny	4		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_011113	Homeodomain	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000076.1	7497-7507
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_012645	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	8	JADHYV010000068.1	7234-7244
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_012835	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000145.1	8625-8629
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_013092	HMG_box	Allomyces_arbusculus_Burma_1F	no_synteny	1		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_015225	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	6	JADHYV010000008.1	2002-2011
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_015902	HMG_box	Allomyces_arbusculus_Burma_1F	conserved	7	JADHYV010000029.1	4905-4914
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_016404	HMG_box	Allomyces_arbusculus_Burma_1F	no_synteny	3		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000262	Homeodomain	Allomyces_javanicus_California_12	conserved	9	JADHYU010000034.1	2949-2959
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000331	HMG_box	Allomyces_javanicus_California_12	no_synteny	3		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000369	Homeodomain	Allomyces_javanicus_California_12	other_domain	5	JADHYU010000001.1	189-196
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_000725	HMG_box	Allomyces_javanicus_California_12	conserved	6	JADHYU010000015.1	1758-1767
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001048	Homeodomain	Allomyces_javanicus_California_12	absent	5	JADHYU010000169.1	7350-7353
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001604	Homeodomain	Allomyces_javanicus_California_12	other_domain	5	JADHYU010000013.1	1582-1591
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_001844	Homeodomain	Allomyces_javanicus_California_12	conserved	8	JADHYU010000001.1	186-199
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002201	HMG_box	Allomyces_javanicus_California_12	other_domain	3	JADHYU010000015.1	1762-1766
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002352	HMG_box	Allomyces_javanicus_California_12	other_domain	5	JADHYU010000054.1	3863-3874
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002543	HMG_box	Allomyces_javanicus_California_12	conserved	6	JADHYU010000099.1	5619-5623
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_002626	HMG_box	Allomyces_javanicus_California_12	conserved	3	JADHYU010000004.1	614-624
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_004133	Homeodomain	Allomyces_javanicus_California_12	conserved	4	JADHYU010000013.1	1583-1595
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_004473	Homeodomain	Allomyces_javanicus_California_12	conserved	5	JADHYU010000270.1	8900-8906
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_005228	Homeodomain	Allomyces_javanicus_California_12	absent	6	JADHYU010000178.1	7550-7554
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_005716	Homeodomain	Allomyces_javanicus_California_12	no_synteny	2		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006268	HMG_box	Allomyces_javanicus_California_12	conserved	3	JADHYU010000247.1	8621-8624
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006492	HMG_box	Allomyces_javanicus_California_12	conserved	9	JADHYU010000002.1	342-360
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006678	HMG_box	Allomyces_javanicus_California_12	conserved	6	JADHYU010000004.1	688-697
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006750	HMG_box	Allomyces_javanicus_California_12	other_domain	7	JADHYU010000004.1	616-625
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_006840	HMG_box	Allomyces_javanicus_California_12	other_domain	4	JADHYU010000189.1	7741-7745
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007069	Homeodomain	Allomyces_javanicus_California_12	conserved	10	JADHYU010000084.1	5126-5144
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007894	HMG_box	Allomyces_javanicus_California_12	other_domain	6	JADHYU010000042.1	3276-3284
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_007902	HMG_box	Allomyces_javanicus_California_12	absent	4	JADHYU010000042.1	3283-3292
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008056	Homeodomain	Allomyces_javanicus_California_12	no_synteny	3		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008109	Homeodomain	Allomyces_javanicus_California_12	other_domain	6	JADHYU010000038.1	3125-3137
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_008423	HMG_box	Allomyces_javanicus_California_12	absent	6	JADHYU010000009.1	1225-1233
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009141	Homeodomain	Allomyces_javanicus_California_12	no_synteny	0		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009194	Homeodomain	Allomyces_javanicus_California_12	conserved	5	JADHYU010000038.1	3124-3135
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_009381	Homeodomain	Allomyces_javanicus_California_12	conserved	4	JADHYU010000079.1	4933-4941
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_010354	Homeodomain	Allomyces_javanicus_California_12	other_domain	6	JADHYU010000079.1	4935-4943
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_011113	Homeodomain	Allomyces_javanicus_California_12	conserved	8	JADHYU010000208.1	8081-8088
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_012645	HMG_box	Allomyces_javanicus_California_12	conserved	7	JADHYU010000014.1	1679-1688
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_012835	HMG_box	Allomyces_javanicus_California_12	conserved	4	JADHYU010000292.1	9142-9149
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_013092	HMG_box	Allomyces_javanicus_California_12	no_synteny	3		
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_015225	HMG_box	Allomyces_javanicus_California_12	conserved	4	JADHYU010000009.1	1223-1232
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_015902	HMG_box	Allomyces_javanicus_California_12	conserved	5	JADHYU010000042.1	3278-3288
+Allomyces_macrogynus_ATCC_38327	F5BE82F7_016404	HMG_box	Allomyces_javanicus_California_12	no_synteny	5		
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/allomyces_summary.tsv b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_summary.tsv
new file mode 100644
index 00000000..62a3d554
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/allomyces_summary.tsv
@@ -0,0 +1,24 @@
+genome_A	genome_B	class	genes
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	absent	3
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	conserved	17
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	no_synteny	1
+Allomyces_arbusculus_Burma_1F	Allomyces_javanicus_California_12	other_domain	1
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	absent	2
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	conserved	15
+Allomyces_arbusculus_Burma_1F	Allomyces_macrogynus_ATCC_38327	other_domain	5
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	absent	3
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	conserved	17
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	no_synteny	1
+Allomyces_javanicus_California_12	Allomyces_arbusculus_Burma_1F	other_domain	4
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	absent	1
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	conserved	12
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	no_synteny	4
+Allomyces_javanicus_California_12	Allomyces_macrogynus_ATCC_38327	other_domain	8
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	absent	4
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	conserved	17
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	no_synteny	4
+Allomyces_macrogynus_ATCC_38327	Allomyces_arbusculus_Burma_1F	other_domain	12
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	absent	4
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	conserved	18
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	no_synteny	6
+Allomyces_macrogynus_ATCC_38327	Allomyces_javanicus_California_12	other_domain	9
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/annotfree_regions.tsv b/docs/notes/2026-11-14_mat-discovery-tables/annotfree_regions.tsv
new file mode 100644
index 00000000..f8e1b134
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/annotfree_regions.tsv
@@ -0,0 +1,287 @@
+genome	class	contig	start	end	identity	evalue	bitscore
+Tubulinosema_ratisbonensis|GCA_004000155.1_ASM400015v1	HD	RCSS01000177.1	339	773	53.125	3.14e-06	235.5
+Tubulinosema_ratisbonensis|GCA_004000155.1_ASM400015v1	HD	RCSS01000254.1	92	670	50.0	3.88e-11	261.09999999999997
+Vairimorpha_ceranae_BRL01|GCF_000182985.1_ASM18298v1	HD	NW_003313922.1	3505	3663	52.83	4.53e-14	281.5
+Vairimorpha_ceranae_BRL01|GCF_000182985.1_ASM18298v1	HD	NW_003314129.1	3849	4361	46.0	2.73e-10	162.9
+Vairimorpha_ceranae_BRL01|GCF_000182985.1_ASM18298v1	HD	NW_003314238.1	4241	4399	37.736	8.07e-06	320.6
+Spraguea_lophii|GCA_011076965.1_ASM1107696v1	HD	JAABPO010000047.1	12624	13936	55.556	1.52e-14	506.40000000000003
+Spraguea_lophii|GCA_011076965.1_ASM1107696v1	HD	JAABPO010000465.1	230	367	53.488	1.43e-10	261.0
+Spraguea_lophii|GCA_011076965.1_ASM1107696v1	HD	JAABPO010000754.1	268	363	62.5	9.32e-06	42.0
+Spraguea_lophii|GCA_011074935.1_ASM1107493v1	HD	JAABPM010000064.1	12518	13830	55.556	1.52e-14	506.40000000000003
+Spraguea_lophii|GCA_011074935.1_ASM1107493v1	HD	JAABPM010000364.1	230	367	53.488	1.47e-10	261.0
+Spraguea_lophii|GCA_011074935.1_ASM1107493v1	HD	JAABPM010000756.1	1930	2025	62.5	9.38e-06	42.0
+Spraguea_lophii|GCA_011076975.1_ASM1107697v1	HD	JAABPN010000054.1	12623	13935	55.556	1.53e-14	506.40000000000003
+Spraguea_lophii|GCA_011076975.1_ASM1107697v1	HD	JAABPN010000489.1	3090	3227	53.488	1.29e-10	261.8
+Spraguea_lophii|GCA_011074965.1_ASM1107496v1	HD	JAABPL010000046.1	12624	13936	55.556	1.48e-14	506.40000000000003
+Spraguea_lophii|GCA_011074965.1_ASM1107496v1	HD	JAABPL010000457.1	230	367	53.488	1.4e-10	261.0
+Spraguea_lophii|GCA_011074965.1_ASM1107496v1	HD	JAABPL010000745.1	1930	2025	62.5	9.13e-06	42.0
+Spraguea_lophii|GCA_011074945.1_ASM1107494v1	HD	JAABPK010000044.1	12639	13951	55.556	1.5e-14	506.40000000000003
+Spraguea_lophii|GCA_011074945.1_ASM1107494v1	HD	JAABPK010000468.1	230	367	53.488	1.42e-10	261.0
+Spraguea_lophii|GCA_011074945.1_ASM1107494v1	HD	JAABPK010000753.1	268	363	62.5	9.21e-06	42.0
+Spraguea_lophii|GCA_011076955.1_ASM1107695v1	HD	JAABPP010000063.1	12518	13830	55.556	1.51e-14	506.40000000000003
+Spraguea_lophii|GCA_011076955.1_ASM1107695v1	HD	JAABPP010000354.1	230	367	53.488	1.46e-10	261.0
+Spraguea_lophii|GCA_011076955.1_ASM1107695v1	HD	JAABPP010000598.1	2471	2566	62.5	9.53e-06	42.0
+Spraguea_lophii|GCA_011074975.1_ASM1107497v1	HD	JAABPJ010000062.1	12518	13830	55.556	1.5e-14	506.40000000000003
+Spraguea_lophii|GCA_011074975.1_ASM1107497v1	HD	JAABPJ010000352.1	230	367	53.488	1.46e-10	261.0
+Spraguea_lophii|GCA_011074975.1_ASM1107497v1	HD	JAABPJ010000765.1	268	363	62.5	9.29e-06	42.0
+Pseudoloma_neurophilia|GCA_001432165.1_ASM143216v1	HD	LGUB01000056.1	12639	13154	49.231	3.75e-14	193.0
+Pseudoloma_neurophilia|GCA_001432165.1_ASM143216v1	HD	LGUB01000143.1	3567	3848	50.0	1.28e-09	258.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000003.1	12579	12971	38.75	3.37e-09	439.40000000000003
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000016.1	23514	24002	39.744	6.95e-11	407.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000017.1	756	1067	36.364	4.58e-06	100.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000032.1	18425	18790	27.66	7.6e-09	218.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000104.1	18912	19379	49.398	7.27e-18	858.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000110.1	22065	22676	48.78	1.23e-16	756.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000135.1	5997	6413	38.961	1.14e-08	365.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000135.1	10223	10636	39.474	1.18e-08	485.09999999999997
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000135.1	17666	18082	32.941	4.42e-10	112.80000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000198.1	5178	5387	49.123	2.09e-07	259.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000216.1	3223	3558	37.778	9.25e-08	316.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000285.1	2846	3382	34.091	1.64e-08	423.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000318.1	10949	11323	44.776	2.25e-09	260.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000486.1	3962	4120	45.283	7.7e-07	51.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000495.1	11867	12265	35.294	5.3e-07	203.70000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000602.1	12553	12756	32.353	7.19e-06	50.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000603.1	17650	17892	38.961	8.05e-06	99.80000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000630.1	6666	7241	39.726	1e-14	667.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000814.1	4026	4394	39.08	6.67e-15	739.5000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000879.1	267	755	48.052	1.5e-16	897.6999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010000879.1	4741	5121	36.364	3.35e-07	103.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001126.1	19520	19791	50.0	4.29e-07	144.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001150.1	9553	9990	43.333	7.14e-09	438.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001155.1	15913	16350	37.5	6.83e-11	543.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001215.1	13170	13652	44.737	2.81e-16	988.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001232.1	477	806	35.714	2.03e-07	53.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001382.1	11847	12110	37.895	1.25e-08	57.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001422.1	5011	5334	48.052	8.02e-19	873.0999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001480.1	2227	2631	40.789	3.12e-11	419.70000000000005
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001493.1	13047	13403	41.25	2.34e-10	372.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001720.1	2221	2691	44.737	2.82e-17	1029.1999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001769.1	12181	12777	50.649	1.38e-30	1315.9999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001798.1	6667	6981	39.535	7.32e-13	527.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001830.1	1404	1699	52.381	2.14e-08	222.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010001952.1	7693	8196	32.11	2.68e-10	276.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002280.1	5736	6248	49.351	1.28e-19	913.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002280.1	9733	10160	60.0	4.86e-10	477.7000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002491.1	11746	12066	40.0	1.48e-08	380.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002638.1	12765	13130	35.833	6.3e-07	103.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002641.1	13110	13335	91.667	2.38e-06	428.19999999999993
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010002842.1	5491	5925	34.545	4.25e-12	343.90000000000003
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003149.1	14963	15205	37.5	1.68e-08	270.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003161.1	5220	5567	35.227	4e-07	409.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003207.1	6736	7104	36.082	4.42e-09	327.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003442.1	9472	9744	36.25	1.16e-08	263.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003794.1	2632	3087	27.068	2.14e-09	235.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003805.1	11779	12249	45.0	6.47e-11	444.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010003811.1	10049	10540	36.364	6.26e-12	562.6999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010004346.1	4604	4954	43.038	3.76e-10	448.20000000000005
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010004540.1	5750	6286	39.474	6.64e-09	377.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010005231.1	9911	10648	50.0	6.1e-20	1046.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010005630.1	501	908	41.026	1.03e-13	793.4000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010005805.1	3349	3633	37.349	2.51e-07	264.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010005839.1	4252	4656	44.304	6.16e-16	953.1999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010005967.1	3490	3873	39.437	8.69e-11	677.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010006146.1	3522	3902	48.052	5.54e-16	799.4999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010006322.1	3127	3585	34.0	1.19e-09	114.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010006501.1	5568	5948	26.154	3.28e-06	50.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010006531.1	7841	8527	44.737	1.49e-30	1309.1999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010006923.1	11275	11730	42.353	2.02e-11	645.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010007193.1	2027	2419	33.333	1.95e-07	206.79999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010007193.1	8314	8856	29.323	2e-09	218.39999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010007217.1	5774	6088	35.714	1.03e-10	222.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010007374.1	7331	7633	36.047	3.02e-10	514.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010007628.1	9174	9398	42.857	4.11e-08	55.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010008320.1	1261	1656	38.462	3.97e-13	890.7000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010008701.1	921	2504	49.333	1.89e-18	1136.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010009208.1	8186	8701	32.911	3.83e-16	438.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010009432.1	1292	1675	35.106	3.2e-10	489.6000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010009624.1	8834	9211	48.684	1.4e-15	734.8000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010010504.1	4657	5004	36.986	4.3e-10	392.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010010856.1	7459	8034	33.083	1e-08	261.40000000000003
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010010878.1	467	781	40.964	1.48e-11	357.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010011047.1	2852	3156	51.22	5.62e-07	216.00000000000003
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010011150.1	4768	5100	38.889	1.45e-09	422.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010011210.1	3127	3630	48.611	8.18e-17	880.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010011534.1	5917	6450	45.57	1.67e-13	887.6999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010011647.1	3469	3699	39.241	2.38e-08	160.60000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012033.1	2257	2748	38.806	1.7e-11	742.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012364.1	1283	1639	43.038	1.21e-12	729.8000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012537.1	5036	5338	40.26	6.79e-11	865.8000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012539.1	1278	1721	45.205	1.96e-16	831.4999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012560.1	5256	5666	37.037	9.09e-11	291.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010012947.1	1011	1445	30.201	2.43e-09	109.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010013546.1	4871	5113	29.07	6.9e-06	49.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010013877.1	2910	3188	44.156	6.62e-13	504.80000000000007
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010014558.1	608	1144	48.684	4.82e-17	887.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010014684.1	5261	5611	38.158	9.71e-07	202.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010015199.1	522	905	34.568	4.33e-10	328.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010015544.1	4019	4432	43.243	1.55e-14	647.8000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010015701.1	1392	2003	53.623	2.55e-17	763.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010015842.1	4512	4655	54.167	4.58e-07	52.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010017636.1	5834	6175	37.143	9.32e-08	311.90000000000003
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010018678.1	2581	3192	29.703	3.81e-06	99.69999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010019430.1	2249	2578	35.227	1.16e-08	160.60000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010020813.1	5155	5616	36.842	5.38e-09	436.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010020863.1	514	645	36.364	4.34e-06	49.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010021049.1	3684	4154	41.573	2.98e-15	678.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010021083.1	5220	5621	33.735	1.17e-09	268.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010021900.1	5369	5629	36.709	4.94e-08	267.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010023106.1	1192	1614	31.579	6.32e-07	52.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010024817.1	1854	2219	32.584	2.03e-09	110.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010025481.1	696	1118	35.484	1.15e-06	254.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010026114.1	215	619	44.444	2.9e-15	866.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010027411.1	3274	3630	35.714	2.05e-09	375.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010027719.1	702	1220	45.946	7.84e-17	685.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010028766.1	3958	4425	44.872	1.87e-12	558.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010029431.1	2249	2566	41.558	3e-09	710.8000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010030791.1	1762	2226	42.308	1.53e-12	900.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010030967.1	1607	2110	48.148	8.77e-19	1038.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010031419.1	3068	3310	35.443	9.91e-07	100.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010031783.1	3201	3416	44.444	2.44e-11	66.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010032668.1	3503	3928	42.697	1.09e-13	816.9000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010033009.1	3467	3898	45.333	2.19e-15	757.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010033502.1	2568	3317	44.872	9.06e-14	995.9000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010034252.1	284	622	32.673	4.81e-09	115.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010034707.1	1616	1870	32.941	9.56e-06	49.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010035227.1	2740	3171	23.741	2.58e-10	114.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010035278.1	351	790	55.556	4.58e-10	462.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010035455.1	2025	2498	41.096	7.59e-11	566.5999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010035558.1	1944	2501	39.474	2.03e-12	469.79999999999995
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010036099.1	3180	3587	42.857	1.65e-13	790.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010036161.1	675	1028	40.0	1.65e-11	524.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010036347.1	3478	3990	43.662	2.11e-13	754.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010038517.1	1457	2047	38.462	1e-13	797.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010038660.1	2537	2968	51.389	2.22e-15	850.5000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010039282.1	1890	2405	45.946	5.99e-15	1009.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010039933.1	2284	2625	33.962	2.76e-12	241.89999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010040538.1	3298	3801	36.634	9.4e-11	281.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010041232.1	3804	4091	38.961	7.27e-07	201.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010042131.1	1505	1735	31.169	8.35e-06	48.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010043110.1	1310	1939	43.373	1.58e-12	762.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010043147.1	796	1206	39.683	2.76e-11	665.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010044070.1	2193	2503	53.846	3.09e-06	211.60000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010045530.1	1083	1679	39.474	6.19e-13	772.7000000000002
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010045677.1	8	151	50.0	8.2e-06	50.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010046676.1	1248	1820	38.356	2.81e-12	694.1999999999998
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010047696.1	1346	1783	41.429	3.51e-11	729.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010048326.1	913	1533	42.857	3.84e-13	777.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010048500.1	2237	2533	39.474	6.32e-13	531.1000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010050051.1	1422	1733	45.07	1.08e-14	706.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010052294.1	2934	3293	43.75	9.21e-14	968.0999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010052567.1	1484	2113	44.304	4.53e-13	974.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010052811.1	2023	2649	40.449	9.92e-14	877.9999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010052873.1	2690	2884	34.848	5.73e-06	49.7
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010053271.1	2401	2892	41.026	1.23e-14	990.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010054391.1	704	1314	100.0	6.36e-08	526.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010057856.1	1858	2382	43.836	1.14e-13	951.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010058109.1	1025	1492	37.975	4.77e-11	724.4000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010059547.1	364	918	42.254	2.33e-14	1075.3999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010060774.1	331	726	41.096	2.13e-13	898.5000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010061323.1	865	1431	41.558	9.3e-12	713.1999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010062465.1	2015	2260	54.545	3.01e-21	898.6999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010063162.1	1105	1509	41.892	5.2e-10	570.1000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010063888.1	923	1396	42.683	1.07e-15	926.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010065297.1	1799	2164	47.945	3.22e-15	765.0999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010066738.1	2404	2586	41.818	8.08e-08	104.8
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010066878.1	1172	1596	41.667	4.22e-07	127.1
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010067818.1	445	942	41.892	6.11e-11	736.3
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010071430.1	1208	1384	45.763	3.94e-08	56.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010072267.1	944	1438	41.026	2.22e-12	763.3000000000001
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010072402.1	69	497	42.857	1.15e-11	903.6
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010072924.1	775	1104	30.392	1.8e-07	209.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010074222.1	1746	2093	39.744	1.35e-11	520.2
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010077430.1	1118	1690	42.308	8.56e-14	1134.5
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010077935.1	490	1134	40.0	2.16e-15	1126.8999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010079378.1	3	440	41.892	1.44e-10	846.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010080089.1	1048	1683	39.726	3.51e-12	891.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HMG	CAJVQB010082264.1	139	435	48.101	9.16e-13	556.0999999999999
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HD	CAJVQB010000837.1	13738	13887	50.0	2.65e-09	178.4
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HD	CAJVQB010003192.1	13168	14685	32.634	2.59e-47	6556.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HD	CAJVQB010003463.1	2733	3536	40.824	3.1e-46	6298.0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HD	CAJVQB010003754.1	12317	12619	48.889	8.55e-09	222.9
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	HD	CAJVQB010005229.1	8271	8540	52.0	1.57e-10	184.4
+Spraguea_lophii_42_110|GCA_000430065.1_Sprlop1.0	HD	ATCN01000054.1	2588	3091	51.163	1.27e-10	250.29999999999998
+Spraguea_lophii_42_110|GCA_000430065.1_Sprlop1.0	HD	ATCN01000214.1	9877	11189	55.556	1.11e-14	548.3999999999999
+Spraguea_lophii_42_110|GCA_000430065.1_Sprlop1.0	HD	ATCN01001389.1	913	1431	30.0	1.59e-07	2026.7999999999993
+Microsporidia_sp._MB|GCA_049634765.1_KEMRI_ICIPE_Tes0708gam	HD	JBMNCT010008263.1	842	1351	52.381	1.29e-14	285.8
+Microsporidia_sp._MB|GCA_032191455.1_ICIPE_MspMB_1.0	HD	JAVKTW010000901.1	951	1460	52.381	1.13e-14	285.79999999999995
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010000004.1	104019	104354	43.396	3.16e-10	515.8
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010000297.1	4510	4845	38.596	1.41e-09	247.89999999999998
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010000788.1	194	346	43.137	1.78e-07	49.3
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010001112.1	1723	2145	42.373	1.36e-09	144.0
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010001177.1	1509	1946	33.645	8.69e-07	94.7
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HMG	JANBSK010001274.1	3	140	74.194	1.49e-09	212.89999999999998
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	HD	JANBSK010001037.1	1330	1551	35.821	1.07e-06	89.3
+Coemansia_sp._RSA_551|GCA_027577555.1_UCR_CoemRSA551_1.0	HMG	JANBRC010000032.1	18733	19068	43.396	3.23e-10	515.8
+Coemansia_sp._RSA_551|GCA_027577555.1_UCR_CoemRSA551_1.0	HMG	JANBRC010001001.1	118	555	33.645	1.33e-06	93.9
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000001.1	39629	40051	42.373	1.66e-09	145.2
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000001.1	80214	80549	42.373	1.19e-10	211.10000000000002
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000009.1	18369	18665	36.25	1.77e-11	650.8
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000009.1	25473	25787	54.545	1.09e-25	1253.3999999999999
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000030.1	9050	9535	33.645	3.48e-07	96.7
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	HMG	JANBQT010000529.1	2121	2456	43.396	1.9e-10	517.3
+Hepatospora_eriocheir|GCA_002087875.1_ASM208787v1	HD	LTAI01000236.1	443	730	47.727	7.71e-11	259.2
+Hepatospora_eriocheir|GCA_002087875.1_ASM208787v1	HD	LTAI01000281.1	3076	3324	37.234	9.44e-07	800.4999999999999
+Hepatospora_eriocheir|GCA_002087875.1_ASM208787v1	HD	LTAI01000442.1	370	2837	52.273	3.93e-13	2182.4000000000005
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000011.1	42629	42817	34.921	3.38e-06	46.2
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000023.1	18739	19074	42.373	8.91e-11	211.10000000000002
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000089.1	69	506	33.645	1.42e-06	94.0
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000120.1	3451	3936	38.596	7.98e-11	342.0
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000278.1	1541	1876	43.396	2.29e-10	515.8
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	HMG	JANBTP010000846.1	834	1130	36.25	1.23e-11	650.8
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010000013.1	8507	8653	38.776	2.54e-06	45.1
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010000280.1	4386	4943	55.0	1.29e-24	1207.7
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010000609.1	2043	2480	28.125	1.79e-06	45.4
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010000763.1	414	926	42.105	7.02e-10	336.7
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010001553.1	1095	1298	36.538	1.04e-07	95.9
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	HMG	JANBVC010001600.1	7	663	43.636	1.57e-10	309.59999999999997
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HMG	JANBRL010000002.1	17512	17934	42.373	1.71e-09	145.2
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HMG	JANBRL010000002.1	60745	61080	42.373	1.17e-10	211.10000000000002
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HMG	JANBRL010000016.1	18525	18860	43.396	2.18e-10	516.9
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HMG	JANBRL010000664.1	1339	1527	34.921	4.03e-06	46.2
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HMG	JANBRL010001784.1	921	1313	32.558	6.88e-09	193.0
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	HD	JANBRL010000910.1	979	1200	35.821	1.06e-06	89.69999999999999
+Coemansia_sp._RSA_530|GCA_027577795.1_UCR_CoemRSA530_1.0	HMG	JANBRE010000002.1	135263	135598	43.396	2e-10	517.3
+Coemansia_sp._RSA_530|GCA_027577795.1_UCR_CoemRSA530_1.0	HMG	JANBRE010000131.1	2456	5313	38.596	9.88e-11	446.0
+Coemansia_sp._RSA_530|GCA_027577795.1_UCR_CoemRSA530_1.0	HMG	JANBRE010001197.1	257	694	33.645	1.39e-06	94.0
+Coemansia_sp._RSA_1937|GCA_027578435.1_UCR_CoemRSA1937_1.0	HMG	JANBSY010000004.1	16146	16481	42.373	1.04e-10	211.1
+Coemansia_sp._RSA_1937|GCA_027578435.1_UCR_CoemRSA1937_1.0	HMG	JANBSY010000004.1	56644	57066	42.373	1.45e-09	145.2
+Coemansia_sp._RSA_1937|GCA_027578435.1_UCR_CoemRSA1937_1.0	HMG	JANBSY010000026.1	24973	25458	33.645	3.04e-07	96.7
+Coemansia_sp._RSA_1937|GCA_027578435.1_UCR_CoemRSA1937_1.0	HMG	JANBSY010000068.1	523	675	43.137	1.94e-07	49.3
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	HMG	JANBQU010000001.1	144677	145012	43.396	2.05e-10	517.3
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	HMG	JANBQU010000141.1	1768	4619	38.596	1.02e-10	446.0
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	HMG	JANBQU010000404.1	316	651	42.373	9.75e-11	211.89999999999998
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	HMG	JANBQU010001535.1	1	285	36.264	7.53e-11	450.3
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	HMG	JANBQU010001541.1	931	1092	41.176	1.86e-07	93.9
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010000123.1	5450	5809	37.179	1.86e-10	581.6
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010000287.1	205	393	38.095	8.17e-08	49.3
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010000338.1	1	132	47.727	2.42e-07	93.2
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010000471.1	3276	3467	30.137	8.84e-06	45.4
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010000712.1	3053	3217	44.828	5.7e-06	45.8
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010001496.1	1583	2086	55.0	3.51e-25	1245.8999999999999
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010001825.1	554	1069	41.667	6.18e-09	330.90000000000003
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	HMG	JANBST010001843.1	286	528	30.864	9.78e-06	43.1
+Massospora_cicadina|GCA_006912075.1_UMICH_Mcic_1	HMG	QMCF01060181.1	1866	2354	40.541	1.31e-09	621.3
+Massospora_cicadina|GCA_006912075.1_UMICH_Mcic_1	HMG	QMCF01089905.1	1283	1729	40.0	6.41e-13	684.3
+Massospora_cicadina|GCA_006912075.1_UMICH_Mcic_1	HD	QMCF01026385.1	858	1229	27.273	6.15e-06	317.1
+Coemansia_sp._RSA_1836|GCA_027578595.1_UCR_CoemRSA1836_1.0	HMG	JANBTD010000479.1	153	722	40.385	1.77e-08	524.6
+Coemansia_sp._RSA_1836|GCA_027578595.1_UCR_CoemRSA1836_1.0	HMG	JANBTD010000612.1	157	681	55.0	2.62e-25	1254.0
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010000004.1	13365	13934	40.385	1.82e-08	527.9
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010000348.1	475	834	37.179	1.91e-10	581.2
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010000350.1	4162	4353	30.137	9.99e-06	45.1
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010001016.1	2687	2851	44.828	4.71e-06	45.8
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010001693.1	343	711	38.462	7.25e-08	189.9
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	HMG	JANBTL010002007.1	679	930	35.294	5.92e-06	90.8
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	HMG	JANJYR010000172.1	1796	2155	37.179	1.54e-10	580.8
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	HMG	JANJYR010000388.1	1255	1623	38.462	7.37e-08	189.5
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	HMG	JANJYR010000742.1	495	746	35.294	4.07e-06	91.19999999999999
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	HMG	JANJYR010000968.1	255	671	40.351	2.35e-08	233.3
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	HMG	JANJYR010001005.1	1056	1220	44.828	3.68e-06	45.8
+Agmasoma_carcini_nom._nud.|GCA_029231695.1_Cm_Agmasoma_carcini_1	HD	JAOXFJ010000012.1	381	518	45.652	4.77e-06	44.3
+Agmasoma_carcini_nom._nud.|GCA_029231695.1_Cm_Agmasoma_carcini_1	HD	JAOXFJ010000031.1	2456	2833	56.818	2.03e-13	288.9
+Massospora_platypediae|GCA_006912095.1_Mplat_NP02_megahit	HMG	QKRY011115577.1	651	1001	44.578	3.99e-16	791.4
+Massospora_platypediae|GCA_006912095.1_Mplat_NP02_megahit	HMG	QKRY011271659.1	2507	3157	40.0	3.37e-12	697.8000000000001
+Massospora_platypediae|GCA_006912095.1_Mplat_NP02_megahit	HD	QKRY011380830.1	3051	3209	49.057	2.3e-08	165.6
+Entomophthora_muscae|GCA_900018355.1_Em_KVL-14-118	HMG	FCOS01011921.1	378	974	35.065	3.98e-10	354.70000000000005
+Entomophthora_muscae|GCA_900018355.1_Em_KVL-14-118	HD	FCOS01006535.1	92	427	53.061	1.21e-09	247.3
+Chytridiomycetes_sp.|GCA_023347045.1_ASM2334704v1	HMG	JAJQPJ010000053.1	1321	1704	38.158	9.28e-15	846.5000000000001
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/annotfree_summary.tsv b/docs/notes/2026-11-14_mat-discovery-tables/annotfree_summary.tsv
new file mode 100644
index 00000000..35ebf309
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/annotfree_summary.tsv
@@ -0,0 +1,49 @@
+genome	contigs	bp	hmg_regions	hd_regions	pairs	contigs_with_pair	longest_pair_contig_bp
+Vairimorpha_sp._gmOTU17_SAN00002588|GCA_986194575.1_ilOchDupl1.microsporidian_1.1	12	467395	0	0	0	0	0
+Metchnikovella_incurvata|GCA_003600395.1_ASM360039v1	422	4611157	0	0	0	0	0
+Tubulinosema_ratisbonensis|GCA_004000155.1_ASM400015v1	781	7301063	0	2	0	0	0
+Amoeboradix_gromovi|GCA_018985225.1_ASM1898522v1	549	4221620	0	0	0	0	0
+Vairimorpha_ceranae_BRL01|GCF_000182985.1_ASM18298v1	639	4343874	0	3	0	0	0
+Spraguea_lophii|GCA_011076965.1_ASM1107696v1	847	5510003	0	3	0	0	0
+Spraguea_lophii|GCA_011074935.1_ASM1107493v1	851	5544380	0	3	0	0	0
+Sanchytrium_tribonematis|GCA_018985235.1_ASM1898523v1	897	6251251	0	0	0	0	0
+Spraguea_lophii|GCA_011076975.1_ASM1107697v1	864	5569531	0	2	0	0	0
+Spraguea_lophii|GCA_011074965.1_ASM1107496v1	840	5393868	0	3	0	0	0
+Spraguea_lophii|GCA_011074945.1_ASM1107494v1	844	5442871	0	3	0	0	0
+Spraguea_lophii|GCA_011076955.1_ASM1107695v1	864	5502253	0	3	0	0	0
+Spraguea_lophii|GCA_011074975.1_ASM1107497v1	863	5492815	0	3	0	0	0
+Pseudoloma_neurophilia|GCA_001432165.1_ASM143216v1	654	4254243	0	2	0	0	0
+fungal_sp.|GCA_023347065.1_ASM2334706v1	386	2777346	0	0	0	0	0
+Gigaspora_margarita|GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	82485	477110750	169	5	0	0	0
+Spraguea_lophii_42_110|GCA_000430065.1_Sprlop1.0	746	4271025	0	3	0	0	0
+Microsporidia_sp._MB|GCA_050230985.1_KEMRI_ICIPE_ABN394	938	5163565	0	0	0	0	0
+Microsporidia_sp._MB|GCA_049634765.1_KEMRI_ICIPE_Tes0708gam	1135	6052440	0	1	0	0	0
+Microsporidia_sp._MB|GCA_032191455.1_ICIPE_MspMB_1.0	979	5119153	0	1	0	0	0
+Siphonaria_sp._JEL0065|GCA_027596065.1_ASM2759606v1	681	3658752	0	0	0	0	0
+Coemansia_sp._RSA_2524|GCA_027578135.1_UCR_CoemRSA2524_1.0	1593	8304496	6	1	0	0	0
+Coemansia_sp._RSA_551|GCA_027577555.1_UCR_CoemRSA551_1.0	1625	8564016	2	0	0	0	0
+Microsporidia_sp._MB|GCA_049634785.1_KEMRI_ICIPE_Tes094gam	1198	5703600	0	0	0	0	0
+Coemansia_sp._RSA_921|GCA_027577315.1_UCR_CoemRSA921_1.0	1702	8528317	6	0	0	0	0
+Hepatospora_eriocheir|GCA_002087875.1_ASM208787v1	691	3239267	0	3	0	0	0
+Coemansia_sp._RSA_1287|GCA_027578735.1_UCR_CoemRSA1287_1.0	1347	6467358	6	0	0	0	0
+Coemansia_aciculifera|GCA_027579955.1_UCR_CoacBCRC34181_1.0	1888	8968546	6	0	0	0	0
+Coemansia_sp._RSA_475|GCA_027577635.1_UCR_CoemRSA475_1.0	1831	8821283	5	1	0	0	0
+Coemansia_sp._RSA_530|GCA_027577795.1_UCR_CoemRSA530_1.0	1768	8120245	3	0	0	0	0
+Coemansia_sp._RSA_1937|GCA_027578435.1_UCR_CoemRSA1937_1.0	1622	7474678	4	0	0	0	0
+Coemansia_sp._RSA_788|GCA_027577475.1_UCR_CoemRSA788_1.0	1855	8355062	5	0	0	0	0
+Nosema_rusticus|GCA_046563365.1_FR26_Nr_1	1452	6197048	0	0	0	0	0
+Coemansia_sp._RSA_2052|GCA_027578455.1_UCR_CoemRSA2052_1.0	2097	8900158	8	0	0	0	0
+Massospora_cicadina|GCA_006912075.1_UMICH_Mcic_1	144784	584366494	2	1	0	0	0
+Coemansia_sp._RSA_1836|GCA_027578595.1_UCR_CoemRSA1836_1.0	1795	7263336	2	0	0	0	0
+Coemansia_sp._RSA_1694|GCA_027578655.1_UCR_CoemRSA1694_1.0	2055	8354744	6	0	0	0	0
+Dictyocoela_roeselum|GCA_016255985.1_ASM1625598v1	383	1398123	0	0	0	0	0
+Coemansia_sp._RSA_25|GCA_027478835.1_UCR_CoemRSA25_1.0	1749	6626621	5	0	0	0	0
+Areospora_rohanae|GCA_056822185.1_ASM5682218v1	1428	5284787	0	0	0	0	0
+Anncaliia_algerae|GCA_000313815.1_ASM31381v1	2245	7547728	0	0	0	0	0
+Alternosema_astaquatica|GCA_030386735.1_Fv_Alternosema1	319	1077699	0	0	0	0	0
+Agmasoma_carcini_nom._nud.|GCA_029231695.1_Cm_Agmasoma_carcini_1	305	975333	0	2	0	0	0
+Massospora_platypediae|GCA_006912095.1_Mplat_NP02_megahit	241057	750606274	2	1	0	0	0
+Entomophthora_muscae|GCA_900018355.1_Em_KVL-14-118	2615	7761280	1	1	0	0	0
+Hamiltosporidium_tvaerminnensis|GCA_000180835.1_ASM18083v1	278	720977	0	0	0	0	0
+Neocallimastix_californiae|GCA_975848665.1_SNW_BASALT_bin1877_ASM_v1	101	254788	0	0	0	0	0
+Chytridiomycetes_sp.|GCA_023347045.1_ASM2334704v1	279	707884	1	0	0	0	0
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_2_3_candidates.tsv b/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_2_3_candidates.tsv
new file mode 100644
index 00000000..8048c976
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_2_3_candidates.tsv
@@ -0,0 +1,61 @@
+Globomyces_pollinis-pini_Glopol1	g17	MU621090.1	16			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	1.04e-07
+Globomyces_pollinis-pini_Glopol1	g281	MU621093.1	280	Homeodomain	1.2e-17			
+Globomyces_pollinis-pini_Glopol1	g286	MU621093.1	285	Homeodomain	3.5e-18			
+Globomyces_pollinis-pini_Glopol1	g321	MU621094.1	320	HMG_box	6.8e-13			
+Globomyces_pollinis-pini_Glopol1	g540	MU621097.1	539			choline	AMM63120.1	5.55e-58
+Globomyces_pollinis-pini_Glopol1	g829	MU621102.1	828	HMG_box	3.8e-11			
+Globomyces_pollinis-pini_Glopol1	g1449	MU621115.1	1448	HMG_box	8.9e-13			
+Globomyces_pollinis-pini_Glopol1	g1676	MU621120.1	1675			rnhA	29922_cbs109-16_MAT_Minus|gene2|rnhA	5.87e-33
+Globomyces_pollinis-pini_Glopol1	g1874	MU621125.1	1873	Homeodomain	2.5e-19			
+Globomyces_pollinis-pini_Glopol1	g2478	MU621144.1	2477	HMG_box	5.4e-14	sexP	3108396_ai-2023a_MAT_Plus|gene2|sexP	8.82e-10
+Globomyces_pollinis-pini_Glopol1	g2979	MU621161.1	2978	HMG_box	1e-12	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	1.4e-07
+Globomyces_pollinis-pini_Glopol1	g3739	MU621191.1	3738			tptA	3108396_ai-2023a_MAT_Plus|gene1|tptA	8.09e-16
+Globomyces_pollinis-pini_Glopol1	g3940	MU621201.1	3939	HMG_box	1.8e-14			
+Globomyces_pollinis-pini_Glopol1	g4421	MU621225.1	4420	HMG_box	1.6e-15			
+Globomyces_pollinis-pini_Glopol1	g4450	MU621227.1	4449			glrA	86630_cbs357-93_MAT_Minus|gene2|glrA	4.86e-115
+Globomyces_pollinis-pini_Glopol1	g4511	MU621230.1	4510	HMG_box	9.8e-08			
+Globomyces_pollinis-pini_Glopol1	g4923	MU621256.1	4922	HMG_box	2e-13			
+Globomyces_pollinis-pini_Glopol1	g4928	MU621256.1	4927	HMG_box	1.7e-13			
+Globomyces_pollinis-pini_Glopol1	g5065	MU621265.1	5064			rnhA	3108396_ai-2023a_MAT_Plus|gene3|rnhA	5.53e-32
+Globomyces_pollinis-pini_Glopol1	g5474	MU621297.1	5473			choline	AMM63120.1	7.48e-64
+Globomyces_pollinis-pini_Glopol1	g5476	MU621297.1	5475			choline	AMM63120.1	4.32e-43
+Globomyces_pollinis-pini_Glopol1	g5561	MU621304.1	5560			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	6.1e-26
+Globomyces_pollinis-pini_Glopol1	g5896	MU621335.1	5895			rnhA	3108396_ai-2023a_MAT_Plus|gene3|rnhA	8.54e-27
+Globomyces_pollinis-pini_Glopol1	g6538	MU621409.1	6537	HMG_box	9.8e-09			
+Globomyces_pollinis-pini_Glopol1	g6733	MU621435.1	6732	HMG_box	1.9e-10			
+Globomyces_pollinis-pini_Glopol1	g6855	MU621454.1	6854	HMG_box	5.3e-11	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	2.33e-07
+Globomyces_pollinis-pini_Glopol1	g7055	MU621488.1	7054	HMG_box	1.1e-14			
+Globomyces_pollinis-pini_Glopol1	g7541	MU621598.1	7540	HMG_box	9.1e-11	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	4.06e-07
+Globomyces_pollinis-pini_Glopol1	g7543	MU621598.1	7542	HMG_box	1e-09			
+Globomyces_pollinis-pini_Glopol1	g7544	MU621598.1	7543	HMG_box	7.2e-11	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	2.97e-07
+Globomyces_sp_JEL0801_ASM2759588	g794	JADGIX010000014.1	793	Homeodomain	8.4e-18			
+Globomyces_sp_JEL0801_ASM2759588	g801	JADGIX010000014.1	800	Homeodomain	2.5e-18			
+Globomyces_sp_JEL0801_ASM2759588	g2165	JADGIX010000060.1	2164	HMG_box	2.6e-14			
+Globomyces_sp_JEL0801_ASM2759588	g2253	JADGIX010000063.1	2252	HMG_box	7.1e-13	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	1.4e-07
+Globomyces_sp_JEL0801_ASM2759588	g2256	JADGIX010000063.1	2255	HMG_box	7.1e-13	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	1.4e-07
+Globomyces_sp_JEL0801_ASM2759588	g2335	JADGIX010000067.1	2334	HMG_box	4.1e-14	sexP	3108396_ai-2023a_MAT_Plus|gene2|sexP	8.69e-10
+Globomyces_sp_JEL0801_ASM2759588	g2515	JADGIX010000075.1	2514			rnhA	29922_cbs109-16_MAT_Minus|gene2|rnhA	5.83e-33
+Globomyces_sp_JEL0801_ASM2759588	g2873	JADGIX010000094.1	2872			choline	AMM63111.1	8.84e-60
+Globomyces_sp_JEL0801_ASM2759588	g3757	JADGIX010000152.1	3756			rnhA	101119_atcc11807_MAT_Minus|gene1|rnhA	6.03e-31
+Globomyces_sp_JEL0801_ASM2759588	g4138	JADGIX010000183.1	4137			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	3e-18
+Globomyces_sp_JEL0801_ASM2759588	g4690	JADGIX010000243.1	4689	HMG_box	1.4e-10			
+Globomyces_sp_JEL0801_ASM2759588	g4706	JADGIX010000245.1	4705	HMG_box	1.1e-15			
+Globomyces_sp_JEL0801_ASM2759588	g5334	JADGIX010000364.1	5333	HMG_box	4.3e-11	sexM	4837_nrrl1555_MAT_Minus|gene1|sexM	9.06e-08
+Globomyces_sp_JEL0801_ASM2759588	g5335	JADGIX010000364.1	5334	HMG_box	7.5e-10			
+Globomyces_sp_JEL0801_ASM2759588	g5364	JADGIX010000374.1	5363	HMG_box	1.6e-09			
+Globomyces_sp_JEL0801_ASM2759588	g5894	JADGIX010000741.1	5893	HMG_box	1.4e-13			
+Mitosporidium_daphniae_ASM5257605	g56	JBLVQJ010000001.1	55	Homeodomain	1.6e-15			
+Mitosporidium_daphniae_ASM5257605	g98	JBLVQJ010000001.1	97	Homeodomain	1.4e-16			
+Mitosporidium_daphniae_ASM5257605	g332	JBLVQJ010000001.1	331			glrA	3108396_ai-2023a_MAT_Plus|gene4|glrA	1.26e-83
+Mitosporidium_daphniae_ASM5257605	g700	JBLVQJ010000002.1	699	Homeodomain	1.5e-20			
+Mitosporidium_daphniae_ASM5257605	g1043	JBLVQJ010000003.1	1042			rnhA	3108396_ai-2023a_MAT_Plus|gene3|rnhA	7.32e-30
+Mitosporidium_daphniae_ASM5257605	g1911	JBLVQJ010000006.1	1910			rnhA	64495_cbs110-17_MAT_Minus|gene2|rnhA	9.19e-21
+Mitosporidium_daphniae_ASM5257605	g2087	JBLVQJ010000007.1	2086			choline	AMM63120.1	3.95e-42
+Mitosporidium_daphniae_ASM5257605	g2138	JBLVQJ010000007.1	2137	Homeodomain	6.4e-08			
+Mitosporidium_daphniae_UGP1	g426	NW_013546154.1	425			choline	AMM63120.1	3.95e-42
+Mitosporidium_daphniae_UGP1	g474	NW_013546159.1	473			rnhA	64495_cbs110-17_MAT_Minus|gene2|rnhA	9.19e-21
+Mitosporidium_daphniae_UGP1	g1733	NW_013546648.1	1732			rnhA	3108396_ai-2023a_MAT_Plus|gene3|rnhA	7.32e-30
+Mitosporidium_daphniae_UGP1	g1879	NW_013546678.1	1878	Homeodomain	1.6e-15			
+Mitosporidium_daphniae_UGP1	g1927	NW_013546685.1	1926	Homeodomain	6.2e-08			
+Mitosporidium_daphniae_UGP1	g2014	NW_013546695.1	2013			glrA	3108396_ai-2023a_MAT_Plus|gene4|glrA	1.26e-83
+Mitosporidium_daphniae_UGP1	g2158	NW_013546711.1	2157	Homeodomain	1.4e-16			
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_candidates.tsv b/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_candidates.tsv
new file mode 100644
index 00000000..10b75036
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/augustus_genomes_candidates.tsv
@@ -0,0 +1,45 @@
+Amoeboaphelidium_protococcarum_FD95	g2494	JALECJ010000004.1	159	HMG_box	8.5e-12	sexM	4850_vkm-f-921_MAT_Minus|gene0|sexM	2.23e-11
+Amoeboaphelidium_protococcarum_FD95	g2513	JALECJ010000004.1	178			glrA	86630_cbs357-93_MAT_Minus|gene2|glrA	1.98e-20
+Amoeboaphelidium_protococcarum_FD95	g2515	JALECJ010000004.1	180	HMG_box	9.3e-08			
+Amoeboaphelidium_protococcarum_FD95	g2877	JALECJ010000004.1	542			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	3.52e-18
+Amoeboaphelidium_protococcarum_FD95	g102	JALECJ010000006.1	758	HMG_box	8.5e-45			
+Amoeboaphelidium_protococcarum_FD95	g3333	JALECJ010000020.1	1029			glrA	3108396_ai-2023a_MAT_Plus|gene4|glrA	2.82e-11
+Amoeboaphelidium_protococcarum_FD95	g3712	JALECJ010000020.1	1408			tptA	4837_nrrl1555_MAT_Minus|gene0|tptA	2.58e-07
+Amoeboaphelidium_protococcarum_FD95	g2127	JALECJ010000254.1	2385	HMG_box	9.9e-08			
+Amoeboaphelidium_protococcarum_FD95	g733	JALECJ010000257.1	4169			choline	AMM63120.1	1.27e-07
+Amoeboaphelidium_protococcarum_FD95	g846	JALECJ010000257.1	4282			choline	AMM63120.1	5.55e-24
+Amoeboaphelidium_protococcarum_FD95	g1416	JALECJ010000257.1	4852	Homeodomain	8.6e-11			
+Amoeboaphelidium_protococcarum_X5	g83	JALDTO010000013.1	82			tptA	64495_cbs346-36_MAT_Plus|gene0|tptA	6.55e-07
+Amoeboaphelidium_protococcarum_X5	g1379	JALDTO010000098.1	1378	HMG_box	9.4e-08			
+Amoeboaphelidium_protococcarum_X5	g1954	JALDTO010000142.1	1953			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	2.98e-19
+Amoeboaphelidium_protococcarum_X5	g2558	JALDTO010000146.1	2557	HMG_box	6.1e-44			
+Amoeboaphelidium_protococcarum_X5	g3432	JALDTO010000155.1	3431			glrA	86630_cbs357-93_MAT_Minus|gene2|glrA	8.33e-24
+Amoeboaphelidium_protococcarum_X5	g3658	JALDTO010000158.1	3657	HMG_box	1.8e-07			
+Amoeboaphelidium_protococcarum_X5	g3661	JALDTO010000158.1	3660			glrA	86630_cbs357-93_MAT_Minus|gene2|glrA	1.98e-20
+Amoeboaphelidium_protococcarum_X5	g3686	JALDTO010000158.1	3685	HMG_box	4.3e-12	sexM	4850_vkm-f-921_MAT_Minus|gene0|sexM	3.77e-12
+Amoeboaphelidium_protococcarum_X5	g4437	JALDTO010000181.1	4436			glrA	3108396_ai-2023a_MAT_Plus|gene4|glrA	4.25e-12
+Amoeboaphelidium_protococcarum_X5	g4789	JALDTO010000192.1	4788			choline	AMM63120.1	2.49e-24
+Amoeboaphelidium_protococcarum_X5	g4877	JALDTO010000200.1	4876			glrA	101119_atcc11807_MAT_Plus|gene1|glrA	9.89e-48
+Amoeboaphelidium_protococcarum_X5	g5240	JALDTO010000206.1	5239	Homeodomain	1.4e-16			
+Amoeboaphelidium_protococcarum_X5	g5317	JALDTO010000206.1	5316			rnhA	64495_cbs110-17_MAT_Minus|gene2|rnhA	2.12e-16
+Amoeboaphelidium_protococcarum_X5	g6130	JALDTO010000213.1	6129			choline	AMM63120.1	1.41e-13
+Amoeboaphelidium_protococcarum_X5	g6238	JALDTO010000213.1	6237			choline	AMM63120.1	2.49e-08
+Amoeboaphelidium_protococcarum_X5	g8595	JALDTO010000266.1	8594			choline	AMM63120.1	1.04e-07
+Amoeboaphelidium_protococcarum_X5	g8857	JALDTO010000266.1	8856	HMG_box	2e-06			
+Rozella_allomycis_CSF55	g238	KE560505.1	237	HMG_box	1.9e-19			
+Rozella_allomycis_CSF55	g461	KE560636.1	460	HMG_box	1.8e-11			
+Rozella_allomycis_CSF55	g517	KE560662.1	516	Homeodomain	1e-09			
+Rozella_allomycis_CSF55	g564	KE560700.1	563	Homeodomain	1.6e-19			
+Rozella_allomycis_CSF55	g738	KE560785.1	737	Homeodomain	5.3e-18			
+Rozella_allomycis_CSF55	g1503	KE560959.1	1502	HMG_box	1.7e-06			
+Rozella_allomycis_CSF55	g1708	KE561019.1	1707			rnhA	64495_cbs110-17_MAT_Minus|gene2|rnhA	1.42e-14
+Rozella_allomycis_CSF55	g1851	KE561045.1	1850			glrA	101119_atcc11807_MAT_Plus|gene1|glrA	1.87e-19
+Rozella_allomycis_CSF55	g1945	KE561047.1	1944			rnhA	86630_cbs357-93_MAT_Minus|gene1|rnhA	9.68e-34
+Rozella_allomycis_CSF55	g2116	KE561068.1	2115	Homeodomain	3.7e-12			
+Rozella_allomycis_CSF55	g2374	KE561117.1	2373			rnhA	64495_cbs110-17_MAT_Minus|gene2|rnhA	4.25e-66
+Rozella_allomycis_CSF55	g2504	KE561139.1	2503			choline	AMM63119.1	1.44e-77
+Rozella_allomycis_CSF55	g2542	KE561145.1	2541			glrA	86630_cbs357-93_MAT_Minus|gene2|glrA	2.54e-123
+Rozella_allomycis_CSF55	g2710	KE561167.1	2709	Homeodomain	4.2e-09			
+Rozella_allomycis_CSF55	g3485	KE561370.1	3484	HMG_box	6.7e-09			
+Synchytrium_endobioticum_18_T1	g492	LDOR01000072.1	491	HMG_box	4.4e-09			
+Synchytrium_endobioticum_18_T1	g730	LDOR01000148.1	729	HMG_box	2.4e-19			
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_genes.tsv b/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_genes.tsv
new file mode 100644
index 00000000..54a57a3e
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_genes.tsv
@@ -0,0 +1,123 @@
+genome	gene	contig	index	strand	domain	best_control	control_evalue	control_identity
+Protomyces_arabidopsidicola_C29	FB5CF295_003187	QXMI01000156.1	56	-	HMG_box,HMG_box_2			
+Protomyces_arabidopsidicola_C29	FB5CF295_003620	QXMI01000158.1	29	-	HMG_box,HMG_box_2	mat1-Mc	2.39e-19	47.3
+Protomyces_arabidopsidicola_C29	FB5CF295_004315	QXMI01000171.1	6	+	HMG_box,HMG_box_2			
+Protomyces_arabidopsidicola_C29	FB5CF295_002914	QXMI01000153.1	44	+	HMG_box,HMG_box_2			
+Protomyces_arabidopsidicola_C29	FB5CF295_002288	QXMI01000125.1	27	+	HMG_box,HMG_box_2			
+Protomyces_arabidopsidicola_C29	FB5CF295_002678	QXMI01000151.1	49	+	HMG_box,HMG_box_2			
+Protomyces_arabidopsidicola_C29	FB5CF295_000707	QXMI01000042.1	51	-	Homeodomain			
+Protomyces_arabidopsidicola_C29	FB5CF295_000240	QXMI01000021.1	18	+	Homeodomain			
+Protomyces_arabidopsidicola_C29	FB5CF295_004088	QXMI01000168.1	196	+	Homeodomain			
+Protomyces_arabidopsidicola_C29	FB5CF295_001530	QXMI01000092.1	113	+	Homeodomain			
+Protomyces_arabidopsidicola_C29	FB5CF295_002391	QXMI01000125.1	130	+	Homeodomain	matPi	1.79e-19	55.2
+Protomyces_arabidopsidicola_C29	FB5CF295_003784	QXMI01000162.1	20	+	Homeodomain			
+Protomyces_arabidopsidicola_C29	FB5CF295_002492	QXMI01000135.1	90	-	Homeodomain			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_000932	QXDP01000077.1	112	+	HMG_box,HMG_box_2			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_003015	QXDP01000223.1	21	-	HMG_box,HMG_box_2	mat1-Mc	4.86e-19	46.1
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_004222	QXDP01000241.1	80	+	HMG_box,HMG_box_2			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_001018	QXDP01000087.1	85	+	HMG_box,HMG_box_2			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_005936	QXDP01000295.1	69	+	HMG_box			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_001928	QXDP01000134.1	42	+	HMG_box,HMG_box_2			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_000169	QXDP01000022.1	13	+	Homeodomain			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_003104	QXDP01000224.1	44	-	Homeodomain			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_002493	QXDP01000205.1	32	-	Homeodomain			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_003356	QXDP01000229.1	27	+	Homeodomain			
+Protomyces_gravidus_NRRL_Y-17093	F88801A2_005815	QXDP01000284.1	146	+	Homeodomain			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_004146	QXDU01000268.1	18	+	HMG_box,HMG_box_2			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_004825	QXDU01000283.1	0	+	HMG_box,HMG_box_2	mat1-Mc	5.67e-20	48.6
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_000170	QXDU01000011.1	166	+	HMG_box,HMG_box_2			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_002492	QXDU01000177.1	44	+	HMG_box,HMG_box_2			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_002636	QXDU01000197.1	4	+	HMG_box,HMG_box_2			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_002365	QXDU01000169.1	48	-	HMG_box,HMG_box_2			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_005216	QXDU01000297.1	51	-	Homeodomain			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_003137	QXDU01000214.1	66	-	Homeodomain			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_004594	QXDU01000275.1	148	+	Homeodomain			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_004355	QXDU01000272.1	15	-	Homeodomain			
+Protomyces_pachydermus_NRRL_YB-4355	F1AD082B_001889	QXDU01000121.1	86	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_002486	RHDT01000177.1	75	-	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_003070	RHDT01000209.1	208	-	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_005246	RHDT01000298.1	18	-	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_005907	RHDT01000320.1	108	-	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_003968	RHDT01000277.1	54	-	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_002270	RHDT01000158.1	74	+	HMG_box,HMG_box_2			
+Taphrina_sp._SM11_SM11	FE701F89_004203	RHDT01000278.1	60	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_005748	RHDT01000310.1	177	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_003870	RHDT01000276.1	20	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_000756	RHDT01000055.1	127	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_001314	RHDT01000098.1	118	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_003773	RHDT01000274.1	73	-	Homeodomain			
+Taphrina_sp._SM11_SM11	FE701F89_004046	RHDT01000277.1	132	+	Homeodomain	matPi	2.83e-17	47.7
+Taphrina_wiesneri_CBS_275.28	F929528F_001754	RHGK01000007.1	69	-	HMG_box,HMG_box_2			
+Taphrina_wiesneri_CBS_275.28	F929528F_006232	RHGK01000040.1	1	+	HMG_box,HMG_box_2	matMc	7.58e-110	72.5
+Taphrina_wiesneri_CBS_275.28	F929528F_002443	RHGK01000010.1	72	-	HMG_box,HMG_box_2			
+Taphrina_wiesneri_CBS_275.28	F929528F_006331	RHGK01000042.1	26	+	HMG_box,HMG_box_2			
+Taphrina_wiesneri_CBS_275.28	F929528F_003515	RHGK01000015.1	94	-	HMG_box			
+Taphrina_wiesneri_CBS_275.28	F929528F_001601	RHGK01000006.1	137	+	HMG_box,HMG_box_2			
+Taphrina_wiesneri_CBS_275.28	F929528F_004776	RHGK01000024.1	10	+	HMG_box,HMG_box_2			
+Taphrina_wiesneri_CBS_275.28	F929528F_000006	RHGK01000001.1	5	+	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_002814	RHGK01000012.1	8	-	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_004999	RHGK01000025.1	98	-	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_004311	RHGK01000020.1	95	-	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_004626	RHGK01000022.1	134	+	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_004861	RHGK01000024.1	95	-	Homeodomain			
+Taphrina_wiesneri_CBS_275.28	F929528F_002490	RHGK01000010.1	119	+	Homeodomain	matPi	3.18e-18	50.0
+Taphrina_communis_CBS_352.35	F8DCC00A_005415	RHGI01000033.1	20	+	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_001803	RHGI01000006.1	205	+	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_001525	RHGI01000005.1	173	+	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_004874	RHGI01000028.1	95	-	HMG_box			
+Taphrina_communis_CBS_352.35	F8DCC00A_002717	RHGI01000011.1	154	-	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_004125	RHGI01000022.1	15	+	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_005608	RHGI01000035.1	29	-	HMG_box,HMG_box_2			
+Taphrina_communis_CBS_352.35	F8DCC00A_000778	RHGI01000002.1	358	-	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_005890	RHGI01000039.1	44	+	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_004430	RHGI01000024.1	104	-	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_003036	RHGI01000014.1	9	-	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_001740	RHGI01000006.1	142	-	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_002631	RHGI01000011.1	68	+	Homeodomain			
+Taphrina_communis_CBS_352.35	F8DCC00A_001480	RHGI01000005.1	128	-	Homeodomain	matPi	6.85e-18	48.4
+Taphrina_betulina_UCD315	FC6B0312_004909	VWSI01000029.1	77	-	HMG_box,HMG_box_2			
+Taphrina_betulina_UCD315	FC6B0312_002103	VWSI01000009.1	150	-	HMG_box,HMG_box_2			
+Taphrina_betulina_UCD315	FC6B0312_001164	VWSI01000005.1	0	-	HMG_box,HMG_box_2			
+Taphrina_betulina_UCD315	FC6B0312_006079	VWSI01000048.1	25	+	HMG_box,HMG_box_2			
+Taphrina_betulina_UCD315	FC6B0312_004553	VWSI01000026.1	34	+	HMG_box			
+Taphrina_betulina_UCD315	FC6B0312_005188	VWSI01000033.1	6	-	HMG_box,HMG_box_2			
+Taphrina_betulina_UCD315	FC6B0312_004634	VWSI01000027.1	2	-	HMG_box			
+Taphrina_betulina_UCD315	FC6B0312_000540	VWSI01000002.1	195	+	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_006262	VWSI01000056.1	13	+	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_004330	VWSI01000024.1	41	-	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_000920	VWSI01000003.1	257	+	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_004101	VWSI01000022.1	46	+	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_001235	VWSI01000005.1	71	-	Homeodomain			
+Taphrina_betulina_UCD315	FC6B0312_002074	VWSI01000009.1	121	-	Homeodomain	matPi	6.78e-16	47.6
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_002032	JARFMH010000012.1	99	+	HMG_box,HMG_box_2			
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_003075	JARFMH010000023.1	3	-	HMG_box,HMG_box_2			
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_004078	JARFMH010000038.1	42	-	HMG_box	mat1-Mc	2.66e-14	36.4
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_001962	JARFMH010000012.1	29	-	HMG_box,HMG_box_2			
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_002635	JARFMH010000018.1	31	-	HMG_box,HMG_box_2			
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_004890	JARFMH010000066.1	6	+	Homeodomain			
+Schizosaccharomyces_lindneri_SZ1623-FG-A	F602A758_002292	JARFMH010000014.1	112	-	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_005693	AP039714.1	46	-	HMG_box,HMG_box_2			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_002096	AP039694.1	32	-	HMG_box	mat1-Mc	7.59e-18	45.8
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_000256	AP039689.1	255	-	HMG_box,HMG_box_2			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_004512	AP039704.1	44	-	HMG_box,HMG_box_2			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_000516	AP039689.1	515	+	HMG_box,HMG_box_2			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_004465	AP039703.1	178	+	HMG_box,HMG_box_2			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_001063	AP039691.1	29	-	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_001012	AP039690.1	421	-	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_005451	AP039712.1	20	-	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_005041	AP039708.1	71	+	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_004577	AP039704.1	109	-	Homeodomain			
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_000542	AP039689.1	541	-	Homeodomain	matPi	8.23e-15	52.0
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_005560	AP039713.1	22	-		matPi	2.68e-18	50.9
+Saitoella_complicata_NRRL_Y-17804	F6365D46_006468	NW_017567021.1	71	+	HMG_box,HMG_box_2			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_000992	NW_017566993.1	313	+	HMG_box,HMG_box_2			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_006006	NW_017567017.1	89	-	HMG_box	mat1-Mc	2.48e-16	42.7
+Saitoella_complicata_NRRL_Y-17804	F6365D46_004653	NW_017567009.1	78	-	HMG_box,HMG_box_2			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_000063	NW_017566992.1	62	-	HMG_box,HMG_box_2			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_001996	NW_017566997.1	38	+	Homeodomain			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_000083	NW_017566992.1	82	-	Homeodomain			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_003678	NW_017567004.1	74	-	Homeodomain			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_000236	NW_017566992.1	235	-	Homeodomain			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_003912	NW_017567005.1	106	-	Homeodomain			
+Saitoella_complicata_NRRL_Y-17804	F6365D46_002892	NW_017567000.1	178	-	Homeodomain	matPi	2.90e-16	49.1
+Saitoella_complicata_NRRL_Y-17804	F6365D46_005865	NW_017567016.1	99	+	Homeodomain	matPi	4.33e-23	31.6
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_pairs.tsv b/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_pairs.tsv
new file mode 100644
index 00000000..8ba99823
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/empty_scan_pairs.tsv
@@ -0,0 +1 @@
+genome	gene_a	gene_b	contig	genes_between	strand_relation	domains
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/gap_adjacent_pair_null.tsv b/docs/notes/2026-11-14_mat-discovery-tables/gap_adjacent_pair_null.tsv
new file mode 100644
index 00000000..8d9406c2
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/gap_adjacent_pair_null.tsv
@@ -0,0 +1,19 @@
+lineage	pair_type	genomes	observed_genomes	expected_mean	expected_max	p	share_same_strand
+SmallPhyla_9	HMG+Homeo	9	2	0.8	3	0.1796	0.5
+SmallPhyla_9	2xHomeo	9	0	0.5	2	1.0000	NA
+SmallPhyla_9	2xHMG	9	2	0.5	3	0.0559	0.8
+Microsporidia_132	HMG+Homeo	132	0	4.5	10	1.0000	NA
+Microsporidia_132	2xHomeo	132	65	19.0	30	0.0020	0.554
+Microsporidia_132	2xHMG	132	1	0.1	1	0.0778	1.0
+Aphelidiomycota	HMG+Homeo	2	0	0.0	1	1.0000	NA
+Aphelidiomycota	2xHomeo	2	0	0.0	1	1.0000	NA
+Aphelidiomycota	2xHMG	2	0	0.0	1	1.0000	NA
+Monoblepharomycota	HMG+Homeo	3	0	0.2	2	1.0000	NA
+Monoblepharomycota	2xHomeo	3	0	0.0	1	1.0000	NA
+Monoblepharomycota	2xHMG	3	2	0.2	2	0.0140	0.8
+Calcarisporiellomycota	HMG+Homeo	1	1	0.5	1	0.4631	1.0
+Calcarisporiellomycota	2xHomeo	1	0	0.4	1	1.0000	NA
+Calcarisporiellomycota	2xHMG	1	0	0.1	1	1.0000	NA
+Rozellomycota	HMG+Homeo	1	1	0.0	1	0.0499	0.0
+Rozellomycota	2xHomeo	1	0	0.0	1	1.0000	NA
+Rozellomycota	2xHMG	1	0	0.0	1	1.0000	NA
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/gap_lineages_summary.tsv b/docs/notes/2026-11-14_mat-discovery-tables/gap_lineages_summary.tsv
new file mode 100644
index 00000000..a55d07a2
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/gap_lineages_summary.tsv
@@ -0,0 +1,8 @@
+lineage	genomes	with_stage1	HD1+HD2	sexM/sexP	HMG+flank	2xHomeo	HMG+Homeo
+Aphelidiomycota	2	2	0	1	0	0	0
+Calcarisporiellomycota	1	1	0	1	0	0	1
+Monoblepharomycota	3	3	0	1	0	0	0
+Olpidiomycota	1	1	0	0	0	0	0
+Rozellomycota	1	1	0	0	0	0	1
+Unclassified	1	1	0	1	0	0	0
+Microsporidia	132	132	0	0	0	65	0
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/globomyces_baseline.tsv b/docs/notes/2026-11-14_mat-discovery-tables/globomyces_baseline.tsv
new file mode 100644
index 00000000..04b6e719
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/globomyces_baseline.tsv
@@ -0,0 +1,7 @@
+genome_A	genome_B	class	genes
+Globomyces_pollinis-pini_Glopol1	Globomyces_sp_JEL0801_ASM2759588	conserved	257
+Globomyces_pollinis-pini_Glopol1	Globomyces_sp_JEL0801_ASM2759588	no_synteny	192
+Globomyces_pollinis-pini_Glopol1	Globomyces_sp_JEL0801_ASM2759588	not_conserved	51
+Globomyces_sp_JEL0801_ASM2759588	Globomyces_pollinis-pini_Glopol1	conserved	359
+Globomyces_sp_JEL0801_ASM2759588	Globomyces_pollinis-pini_Glopol1	no_synteny	80
+Globomyces_sp_JEL0801_ASM2759588	Globomyces_pollinis-pini_Glopol1	not_conserved	61
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/globomyces_probe.tsv b/docs/notes/2026-11-14_mat-discovery-tables/globomyces_probe.tsv
new file mode 100644
index 00000000..02e4192f
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/globomyces_probe.tsv
@@ -0,0 +1,33 @@
+genome_A	gene	domain	genome_B	class	flank_mapped	region_contig	region_span
+Globomyces_pollinis-pini_Glopol1	g281	Homeodomain	Globomyces_sp_JEL0801_ASM2759588	conserved	10	JADGIX010000014.1	788-800
+Globomyces_pollinis-pini_Glopol1	g286	Homeodomain	Globomyces_sp_JEL0801_ASM2759588	conserved	10	JADGIX010000014.1	793-805
+Globomyces_pollinis-pini_Glopol1	g321	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	7	JADGIX010000060.1	2161-2169
+Globomyces_pollinis-pini_Glopol1	g829	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	0		
+Globomyces_pollinis-pini_Glopol1	g1449	HMG_box	Globomyces_sp_JEL0801_ASM2759588	absent	8	JADGIX010000269.1	4868-4871
+Globomyces_pollinis-pini_Glopol1	g1874	Homeodomain	Globomyces_sp_JEL0801_ASM2759588	no_synteny	0		
+Globomyces_pollinis-pini_Glopol1	g2478	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	10	JADGIX010000067.1	2329-2339
+Globomyces_pollinis-pini_Glopol1	g2979	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	0		
+Globomyces_pollinis-pini_Glopol1	g3940	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	1		
+Globomyces_pollinis-pini_Glopol1	g4421	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	5	JADGIX010000245.1	4703-4708
+Globomyces_pollinis-pini_Glopol1	g4511	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	7	JADGIX010000104.1	3042-3049
+Globomyces_pollinis-pini_Glopol1	g4923	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	0		
+Globomyces_pollinis-pini_Glopol1	g4928	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	1		
+Globomyces_pollinis-pini_Glopol1	g6538	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	1		
+Globomyces_pollinis-pini_Glopol1	g6733	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	6	JADGIX010000243.1	4688-4694
+Globomyces_pollinis-pini_Glopol1	g6855	HMG_box	Globomyces_sp_JEL0801_ASM2759588	absent	3	JADGIX010000292.1	5012-5014
+Globomyces_pollinis-pini_Glopol1	g7055	HMG_box	Globomyces_sp_JEL0801_ASM2759588	no_synteny	0		
+Globomyces_pollinis-pini_Glopol1	g7541	HMG_box	Globomyces_sp_JEL0801_ASM2759588	other_domain	4	JADGIX010000364.1	5331-5335
+Globomyces_pollinis-pini_Glopol1	g7543	HMG_box	Globomyces_sp_JEL0801_ASM2759588	conserved	3	JADGIX010000364.1	5331-5335
+Globomyces_pollinis-pini_Glopol1	g7544	HMG_box	Globomyces_sp_JEL0801_ASM2759588	other_domain	4	JADGIX010000364.1	5331-5335
+Globomyces_sp_JEL0801_ASM2759588	g794	Homeodomain	Globomyces_pollinis-pini_Glopol1	conserved	8	MU621093.1	275-283
+Globomyces_sp_JEL0801_ASM2759588	g801	Homeodomain	Globomyces_pollinis-pini_Glopol1	conserved	8	MU621093.1	282-290
+Globomyces_sp_JEL0801_ASM2759588	g2165	HMG_box	Globomyces_pollinis-pini_Glopol1	conserved	7	MU621094.1	318-325
+Globomyces_sp_JEL0801_ASM2759588	g2253	HMG_box	Globomyces_pollinis-pini_Glopol1	absent	5	MU621161.1	3004-3009
+Globomyces_sp_JEL0801_ASM2759588	g2256	HMG_box	Globomyces_pollinis-pini_Glopol1	no_synteny	3		
+Globomyces_sp_JEL0801_ASM2759588	g2335	HMG_box	Globomyces_pollinis-pini_Glopol1	conserved	10	MU621144.1	2472-2482
+Globomyces_sp_JEL0801_ASM2759588	g4690	HMG_box	Globomyces_pollinis-pini_Glopol1	conserved	6	MU621435.1	6727-6733
+Globomyces_sp_JEL0801_ASM2759588	g4706	HMG_box	Globomyces_pollinis-pini_Glopol1	conserved	5	MU621225.1	4418-4423
+Globomyces_sp_JEL0801_ASM2759588	g5334	HMG_box	Globomyces_pollinis-pini_Glopol1	other_domain	4	MU621598.1	7541-7545
+Globomyces_sp_JEL0801_ASM2759588	g5335	HMG_box	Globomyces_pollinis-pini_Glopol1	conserved	4	MU621598.1	7541-7545
+Globomyces_sp_JEL0801_ASM2759588	g5364	HMG_box	Globomyces_pollinis-pini_Glopol1	no_synteny	2		
+Globomyces_sp_JEL0801_ASM2759588	g5894	HMG_box	Globomyces_pollinis-pini_Glopol1	no_synteny	0		
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/matpi_genome_search_hits.tsv b/docs/notes/2026-11-14_mat-discovery-tables/matpi_genome_search_hits.tsv
new file mode 100644
index 00000000..0b224425
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/matpi_genome_search_hits.tsv
@@ -0,0 +1,36 @@
+genome	rank	contig	start	end	best_identity	best_evalue	bitscore	on_matMc_contig	distance_to_matMc_bp	overlapping_gene
+Protomyces_inouyei_NRRL_YB-4354	1	QXDQ01000433.1	28095	28478	45.238	2.2e-18	234.1	yes	7165	-
+Protomyces_inouyei_NRRL_YB-4354	2	QXDQ01000244.1	57755	57916	54.348	3.04e-12	226.1	no	NA	F7C0A940_003233
+Protomyces_macrosporus_NRRL_Y-12879	1	QXDT01000095.1	125508	125669	54.348	4.31e-12	231.2	no	NA	FCFD2032_001987
+Protomyces_macrosporus_NRRL_Y-12879	2	QXDT01000104.1	146491	146739	52.459	4.71e-16	220.7	no	NA	FCFD2032_003005
+Protomyces_lactucae-debilis_NRRL_YB-4353	1	QXDS01000345.1	101593	101979	45.238	2.17e-18	233.0	yes	7164	-
+Protomyces_lactucae-debilis_NRRL_YB-4353	2	QXDS01000405.1	34146	34337	54.348	7.56e-13	230.0	no	NA	F21A9957_005482
+Taphrina_confusa_CBS_375.39	1	RHGJ01000026.1	181602	182075	46.479	2.19e-46	301.0	yes	14057	-
+Taphrina_confusa_CBS_375.39	2	RHGJ01000014.1	247564	247836	54.348	4.74e-14	255.39999999999998	no	NA	F57803F5_004044
+Protomyces_lactucae-debilis_12-1054	1	NW_024468021.1	38152	38538	45.238	2.21e-18	233.0	yes	7152	-
+Protomyces_lactucae-debilis_12-1054	2	NW_024467997.1	438246	438437	54.348	7.77e-13	230.0	no	NA	F003EF48_001800
+Protomyces_arabidopsidicola_C29	1	QXMI01000162.1	62546	62707	56.0	6.19e-13	227.60000000000002	no	NA	FB5CF295_003784
+Protomyces_arabidopsidicola_C29	2	QXMI01000125.1	203158	203487	41.667	9.31e-16	212.59999999999997	no	NA	FB5CF295_002391
+Protomyces_arabidopsidicola_C29	3	QXMI01000135.1	174500	174691	52.174	2.01e-12	181.0	no	NA	FB5CF295_002492
+Protomyces_gravidus_NRRL_Y-17093	1	QXDP01000295.1	280092	280418	47.619	2.66e-16	262.59999999999997	no	NA	-
+Protomyces_gravidus_NRRL_Y-17093	2	QXDP01000284.1	244866	245315	49.057	9.97e-12	230.40000000000003	no	NA	F88801A2_005815
+Protomyces_pachydermus_NRRL_YB-4355	1	QXDU01000294.1	15623	16006	45.238	2.07e-18	234.5	no	NA	-
+Protomyces_pachydermus_NRRL_YB-4355	2	QXDU01000121.1	163650	163847	54.348	2.41e-12	226.9	no	NA	F1AD082B_001889
+Taphrina_sp._SM11_SM11	1	RHDT01000277.1	272246	272452	54.0	1.14e-13	250.0	NA	NA	FE701F89_004046
+Taphrina_sp._SM11_SM11	2	RHDT01000219.1	24554	25030	42.424	4.27e-25	226.7	NA	NA	-
+Taphrina_wiesneri_CBS_275.28	1	RHGK01000010.1	214844	215035	54.348	1.04e-13	253.5	no	NA	F929528F_002490
+Taphrina_communis_CBS_352.35	1	RHGI01000035.1	80258	80755	52.41	8.21e-54	328.0	NA	NA	-
+Taphrina_communis_CBS_352.35	2	RHGI01000005.1	245837	246097	54.348	1.48e-13	254.60000000000002	NA	NA	F8DCC00A_001480
+Taphrina_betulina_UCD315	1	VWSI01000027.1	16268	16762	43.023	2.21e-26	249.0	NA	NA	-
+Taphrina_betulina_UCD315	2	VWSI01000009.1	220061	220222	56.522	1.2e-12	242.70000000000002	NA	NA	FC6B0312_002074
+Taphrina_betulina_UCD315	3	VWSI01000018.1	4287	4493	45.283	4.93e-10	165.60000000000002	NA	NA	-
+Savitreella_phatthalungensis_PYCC_9005	1	AP039689.1	1044038	1044199	52.0	9.96e-14	240.39999999999998	no	NA	FAD3C0EC_000542
+Savitreella_phatthalungensis_PYCC_9005	2	AP039713.1	46052	46267	50.877	4.26e-15	208.39999999999998	no	NA	FAD3C0EC_005560
+Saitoella_complicata_NRRL_Y-17804	1	NW_017567016.1	167097	167699	45.652	1.31e-22	293.8	no	NA	F6365D46_005865
+Saitoella_complicata_NRRL_Y-17804	2	NW_017567000.1	368619	368768	54.545	1.99e-12	187.5	no	NA	F6365D46_002892
+Taphrina_deformans_A2	1	RHGF01000006.1	51688	52236	100.0	1.13e-119	539.4	yes	40370	-
+Taphrina_deformans_A2	2	RHGF01000011.1	218412	218606	54.0	6.36e-14	244.2	no	NA	F891DC7E_002798
+Taphrina_deformans_CBS_355.35	1	RHGG01000037.1	49436	49984	100.0	1.13e-119	539.4	no	NA	-
+Taphrina_deformans_CBS_355.35	2	RHGG01000002.1	531461	531655	54.0	6.4e-14	244.2	no	NA	F7E28AAD_000825
+Taphrina_deformans_PYCC_5710	1	HE965097.1	49998	50546	100.0	1.13e-119	539.4	no	NA	-
+Taphrina_deformans_PYCC_5710	2	HE965036.1	162351	162545	54.0	6.4e-14	244.20000000000002	no	NA	F282FB4B_000488
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_null.tsv b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_null.tsv
new file mode 100644
index 00000000..e7bcbacc
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_null.tsv
@@ -0,0 +1,2 @@
+max_dist_bp	genomes	observed_genomes	expected_mean	expected_max	p
+20000	17	6	0.71	5	0.0005
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_pairs.tsv b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_pairs.tsv
new file mode 100644
index 00000000..5e777bdd
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_pairs.tsv
@@ -0,0 +1,9 @@
+genome	hmg_gene	contig	region_rank	region_identity	distance_bp
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_005637	QXDQ01000433.1	1	45.238	7165
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_003986	QXDS01000345.1	1	45.238	7164
+Taphrina_confusa_CBS_375.39	F57803F5_005977	RHGJ01000026.1	1	46.479	14057
+Protomyces_lactucae-debilis_12-1054	F003EF48_006292	NW_024468021.1	1	45.238	7152
+Taphrina_communis_CBS_352.35	F8DCC00A_005608	RHGI01000035.1	1	52.41	18060
+Taphrina_betulina_UCD315	FC6B0312_004634	VWSI01000027.1	1	43.023	10297
+Savitreella_phatthalungensis_PYCC_9005	FAD3C0EC_000516	AP039689.1	1	52.0	39362
+Taphrina_deformans_A2	F891DC7E_001655	RHGF01000006.1	1	100.0	40370
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_summary.tsv b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_summary.tsv
new file mode 100644
index 00000000..71816b9b
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/matpi_hmg_adjacency_summary.tsv
@@ -0,0 +1,18 @@
+genome	hmg_genes	hmg_genes_near_region	regions_tested
+Protomyces_inouyei_NRRL_YB-4354	7	1	2
+Protomyces_macrosporus_NRRL_Y-12879	6	0	2
+Protomyces_lactucae-debilis_NRRL_YB-4353	7	1	2
+Taphrina_confusa_CBS_375.39	7	1	2
+Protomyces_lactucae-debilis_12-1054	7	1	2
+Protomyces_arabidopsidicola_C29	6	0	3
+Protomyces_gravidus_NRRL_Y-17093	6	0	2
+Protomyces_pachydermus_NRRL_YB-4355	6	0	2
+Taphrina_sp._SM11_SM11	6	0	2
+Taphrina_wiesneri_CBS_275.28	7	0	1
+Taphrina_communis_CBS_352.35	7	1	2
+Taphrina_betulina_UCD315	7	1	3
+Savitreella_phatthalungensis_PYCC_9005	6	1	2
+Saitoella_complicata_NRRL_Y-17804	5	0	2
+Taphrina_deformans_A2	7	1	2
+Taphrina_deformans_CBS_355.35	7	0	2
+Taphrina_deformans_PYCC_5710	7	0	2
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/matpi_region_pfam.tsv b/docs/notes/2026-11-14_mat-discovery-tables/matpi_region_pfam.tsv
new file mode 100644
index 00000000..36c7facd
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/matpi_region_pfam.tsv
@@ -0,0 +1,10 @@
+name	region	orf_frame	orf_start	orf_end	aa_len	domain	evalue
+Protomyces_inouyei_NRRL_YB-4354|matPi_near_matMc	QXDQ01000433.1:27495-29078	1	27984	28484	167	Homeodomain	1.1e-10
+Protomyces_lactucae-debilis_NRRL_YB-4353|matPi_near_matMc	QXDS01000345.1:100993-102579	1	101533	101985	151	Homeodomain	1e-10
+Taphrina_confusa_CBS_375.39|matPi_near_matMc	RHGJ01000026.1:181002-182675	-1	181587	182090	168	Homeodomain	1.1e-08
+Protomyces_lactucae-debilis_12-1054|matPi_near_matMc	NW_024468021.1:37552-39138	-1	38146	38598	151	Homeodomain	1e-10
+Protomyces_gravidus_NRRL_Y-17093|matPi_unannotated_no_matMc_neighbour	QXDP01000295.1:279492-281018	1	279948	280424	159	Homeodomain	8.4e-11
+Taphrina_communis_CBS_352.35|matPi_unannotated_no_matMc_neighbour	RHGI01000035.1:79658-81355	-1	80243	80794	184	Homeodomain	1.5e-09
+Taphrina_betulina_UCD315|matPi_unannotated_no_matMc_neighbour	VWSI01000027.1:15668-17362					none	
+Taphrina_deformans_A2|matPi_near_matMc	RHGF01000006.1:51088-52836	1	51685	52251	189	Homeodomain	1.5e-09
+Taphrina_deformans_A2|negative_control_20kb_away	RHGF01000006.1:71088-72836					none	
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_genomes_scan_genes.tsv b/docs/notes/2026-11-14_mat-discovery-tables/pm_genomes_scan_genes.tsv
new file mode 100644
index 00000000..1d1cc33c
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_genomes_scan_genes.tsv
@@ -0,0 +1,62 @@
+genome	gene	contig	index	strand	domain	best_control	control_evalue	control_identity
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_003944	QXDQ01000317.1	0	+	HMG_box,HMG_box_2			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_005637	QXDQ01000433.1	18	+	HMG_box,HMG_box_2	matMc	9.85e-47	45.0
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_001588	QXDQ01000108.1	271	+	HMG_box,HMG_box_2	mat1-Mc	5.71e-20	48.6
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_003432	QXDQ01000279.1	2	-	HMG_box,HMG_box_2			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_003008	QXDQ01000221.1	19	-	HMG_box,HMG_box_2			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_001266	QXDQ01000107.1	84	+	HMG_box,HMG_box_2			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_004761	QXDQ01000413.1	33	-	HMG_box,HMG_box_2			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_005400	QXDQ01000429.1	50	-	Homeodomain			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_004297	QXDQ01000375.1	18	+	Homeodomain			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_004905	QXDQ01000418.1	10	-	Homeodomain			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_005340	QXDQ01000428.1	14	-	Homeodomain			
+Protomyces_inouyei_NRRL_YB-4354	F7C0A940_003233	QXDQ01000244.1	28	-	Homeodomain			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_000110	QXDT01000009.1	109	+	HMG_box,HMG_box_2			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_003884	QXDT01000114.1	19	-	HMG_box,HMG_box_2	mat1-Mc	2.34e-20	48.7
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_003553	QXDT01000108.1	64	-	HMG_box,HMG_box_2			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_004602	QXDT01000126.1	15	-	HMG_box			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_005905	QXDT01000170.1	178	+	HMG_box,HMG_box_2			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_005774	QXDT01000170.1	47	+	HMG_box,HMG_box_2			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_006117	QXDT01000181.1	159	+	Homeodomain			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_005509	QXDT01000159.1	18	+	Homeodomain			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_003753	QXDT01000112.1	12	-	Homeodomain			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_004535	QXDT01000124.1	20	+	Homeodomain			
+Protomyces_macrosporus_NRRL_Y-12879	FCFD2032_001987	QXDT01000095.1	71	+	Homeodomain			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_006289	QXDS01000428.1	90	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_003986	QXDS01000345.1	65	+	HMG_box,HMG_box_2	matMc	5.55e-46	44.4
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_002866	QXDS01000234.1	24	-	HMG_box,HMG_box_2	mat1-Mc	5.67e-20	48.6
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_006358	QXDS01000429.1	9	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_001070	QXDS01000087.1	61	-	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_004928	QXDS01000393.1	38	-	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_003047	QXDS01000251.1	52	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_000040	QXDS01000011.1	2	-	Homeodomain			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_002544	QXDS01000215.1	17	+	Homeodomain			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_004986	QXDS01000395.1	12	-	Homeodomain			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_004156	QXDS01000380.1	14	-	Homeodomain			
+Protomyces_lactucae-debilis_NRRL_YB-4353	F21A9957_005482	QXDS01000405.1	15	+	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_003754	RHGJ01000013.1	66	-	HMG_box,HMG_box_2			
+Taphrina_confusa_CBS_375.39	F57803F5_004161	RHGJ01000015.1	2	-	HMG_box,HMG_box_2			
+Taphrina_confusa_CBS_375.39	F57803F5_004000	RHGJ01000014.1	74	-	HMG_box,HMG_box_2			
+Taphrina_confusa_CBS_375.39	F57803F5_005977	RHGJ01000026.1	83	+	HMG_box,HMG_box_2	matMc	6.93e-89	69.2
+Taphrina_confusa_CBS_375.39	F57803F5_002637	RHGJ01000008.1	225	-	HMG_box			
+Taphrina_confusa_CBS_375.39	F57803F5_001127	RHGJ01000003.1	351	-	HMG_box,HMG_box_2			
+Taphrina_confusa_CBS_375.39	F57803F5_003604	RHGJ01000012.1	143	+	HMG_box,HMG_box_2			
+Taphrina_confusa_CBS_375.39	F57803F5_001137	RHGJ01000004.1	3	+	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_002097	RHGJ01000006.1	299	+	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_006117	RHGJ01000027.1	97	-	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_004223	RHGJ01000015.1	64	+	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_006217	RHGJ01000029.1	8	-	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_001039	RHGJ01000003.1	263	+	Homeodomain			
+Taphrina_confusa_CBS_375.39	F57803F5_004044	RHGJ01000014.1	118	+	Homeodomain	matPi	1.59e-17	50.0
+Protomyces_lactucae-debilis_12-1054	F003EF48_000425	NW_024467993.1	424	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_12-1054	F003EF48_006292	NW_024468021.1	12	-	HMG_box,HMG_box_2	matMc	8.97e-46	44.4
+Protomyces_lactucae-debilis_12-1054	F003EF48_001932	NW_024467998.1	23	-	HMG_box,HMG_box_2	mat1-Mc	5.67e-20	48.6
+Protomyces_lactucae-debilis_12-1054	F003EF48_001253	NW_024467995.1	358	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_12-1054	F003EF48_000047	NW_024467993.1	46	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_12-1054	F003EF48_005701	NW_024468014.1	71	-	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_12-1054	F003EF48_000189	NW_024467993.1	188	+	HMG_box,HMG_box_2			
+Protomyces_lactucae-debilis_12-1054	F003EF48_000947	NW_024467995.1	52	-	Homeodomain			
+Protomyces_lactucae-debilis_12-1054	F003EF48_004261	NW_024468006.1	17	+	Homeodomain			
+Protomyces_lactucae-debilis_12-1054	F003EF48_000640	NW_024467994.1	154	+	Homeodomain			
+Protomyces_lactucae-debilis_12-1054	F003EF48_005759	NW_024468015.1	14	-	Homeodomain			
+Protomyces_lactucae-debilis_12-1054	F003EF48_001800	NW_024467997.1	199	+	Homeodomain			
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_genes.tsv b/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_genes.tsv
new file mode 100644
index 00000000..7adfedaa
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_genes.tsv
@@ -0,0 +1,48 @@
+genome	locus	gene_index	gene	strand	start	end	domain	evidence
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	13	F7C0A940_005632	-	24577	25071		
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	14	F7C0A940_005633	+	25109	26086		
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	15	F7C0A940_005634	+	26488	26929		
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	16	F7C0A940_005635	-	26952	27714		
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	17	F7C0A940_005636	+	30760	32228		
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	18	F7C0A940_005637	+	35643	36275	HMG_box,HMG_box_2	matMc:44.71% id, 73.6% cov
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1#0	19	F7C0A940_005638	-	36357	36695		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	68	FCFD2032_003000	-	131384	131884		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	69	FCFD2032_003001	+	132005	132997		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	70	FCFD2032_003002	+	133410	133859		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	71	FCFD2032_003003	-	133928	134694		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	72	FCFD2032_003004	-	135912	136228		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	73	FCFD2032_003005	-	144915	146526		matPi:43.9% id, 36.1% cov
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	74	FCFD2032_003006	+	149113	149517		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	75	FCFD2032_003007	+	150376	150993		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	76	FCFD2032_003008	+	155502	157029		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	77	FCFD2032_003009	-	158777	160318		
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1#0	78	FCFD2032_003010	-	161573	163600		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	60	F21A9957_003981	+	98757	99599		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	61	F21A9957_003982	+	100001	100442		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	62	F21A9957_003983	-	100465	101230		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	63	F21A9957_003984	+	104260	105728		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	64	F21A9957_003985	-	106147	108212		
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	65	F21A9957_003986	+	109143	109775	HMG_box,HMG_box_2	matMc:44.12% id, 73.6% cov
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1#0	66	F21A9957_003987	-	109857	110576		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	78	F57803F5_005972	-	143747	144315		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	79	F57803F5_005973	+	145732	146655		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	80	F57803F5_005974	-	161470	162516		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	81	F57803F5_005975	-	162983	163777		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	82	F57803F5_005976	+	165223	166019		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	83	F57803F5_005977	+	166886	167545	HMG_box,HMG_box_2	matMc:69.19% id, 74.5% cov
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	84	F57803F5_005978	+	169362	169845		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	85	F57803F5_005979	-	170517	170994		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	86	F57803F5_005980	+	171994	173827		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	87	F57803F5_005981	-	174359	174804		
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1#0	88	F57803F5_005982	+	175407	176302		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	7	F003EF48_006287	+	18493	20451		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	8	F003EF48_006288	+	20891	21409		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	9	F003EF48_006289	-	22014	22420		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	10	F003EF48_006290	+	26856	28068		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	11	F003EF48_006291	+	28264	30274		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	12	F003EF48_006292	-	30356	31000	HMG_box,HMG_box_2	matMc:44.12% id, 73.6% cov
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	13	F003EF48_006293	+	31919	33984		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	14	F003EF48_006294	-	34403	35871		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	15	F003EF48_006295	+	38904	39666		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	16	F003EF48_006296	-	39689	40130		
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1#0	17	F003EF48_006297	-	40532	41374		
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_summary.tsv b/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_summary.tsv
new file mode 100644
index 00000000..d8772029
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_lead_summary.tsv
@@ -0,0 +1,6 @@
+genome	contig	matMc_gene	matMc_domain	matPi_gene	matPi_domain	genes_between	strand_relation
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1	F7C0A940_005637	HMG_box,HMG_box_2	NA	NA	NA	NA
+Protomyces_macrosporus_NRRL_Y-12879	QXDT01000104.1	NA	NA	FCFD2032_003005		NA	NA
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1	F21A9957_003986	HMG_box,HMG_box_2	NA	NA	NA	NA
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1	F57803F5_005977	HMG_box,HMG_box_2	NA	NA	NA	NA
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1	F003EF48_006292	HMG_box,HMG_box_2	NA	NA	NA	NA
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_homeodomain_models.tsv b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_homeodomain_models.tsv
new file mode 100644
index 00000000..7152de81
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_homeodomain_models.tsv
@@ -0,0 +1,8 @@
+name	contig	strand	cds_start	cds_end	exons	aa_len	score	query	domains
+Protomyces_inouyei_NRRL_YB-4354	QXDQ01000433.1	+	28281	28457	1	59	174.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
+Protomyces_lactucae-debilis_NRRL_YB-4353	QXDS01000345.1	+	101782	101958	1	59	174.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
+Taphrina_confusa_CBS_375.39	RHGJ01000026.1	-	181602	182084	1	161	394.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
+Protomyces_lactucae-debilis_12-1054	NW_024468021.1	-	38173	38349	1	59	174.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
+Taphrina_communis_CBS_352.35	RHGI01000035.1	-	80258	80794	1	179	417.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
+Taphrina_betulina_UCD315	VWSI01000027.1	+	16268	16750	1	161	223.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	none
+Taphrina_deformans_A2	RHGF01000006.1	+	51694	52236	1	181	908.0	5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT	Homeodomain
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology.tsv b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology.tsv
new file mode 100644
index 00000000..513a7fe0
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology.tsv
@@ -0,0 +1,79 @@
+locus_protein	other_genome	best_hit	hit_is_locus_protein	identity	aligned_aa	reciprocal
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	P_lact_12-1054	P_lact_12-1054|HMG_locus|F003EF48_006292	True	99.0	197	True
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	P_lact_YB-4353	P_lact_YB-4353|HMG_locus|F21A9957_003986	True	99.0	197	True
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	T_betulina_315	T_betulina_315|HMG|FC6B0312_004553	False	38.4	73	False
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	T_communis_352.35	T_communis_352.35|HMG|F8DCC00A_004874	False	40.0	75	False
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	T_confusa_375.39	T_confusa_375.39|HMG_locus|F57803F5_005977	True	42.4	172	True
+P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	T_deformans_A2	T_deformans_A2|HMG_locus|F891DC7E_001655	True	45.0	171	True
+P_inouyei_YB-4354|HD_locus|orf27984	P_lact_12-1054	P_lact_12-1054|HD_locus|orf38146	True	100.0	151	True
+P_inouyei_YB-4354|HD_locus|orf27984	P_lact_YB-4353	P_lact_YB-4353|HD_locus|orf101533	True	100.0	151	True
+P_inouyei_YB-4354|HD_locus|orf27984	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	50.8	61	False
+P_inouyei_YB-4354|HD_locus|orf27984	T_communis_352.35	T_communis_352.35|HD_locus|orf80243	True	36.0	139	True
+P_inouyei_YB-4354|HD_locus|orf27984	T_confusa_375.39	T_confusa_375.39|HD_locus|orf181587	True	35.4	147	True
+P_inouyei_YB-4354|HD_locus|orf27984	T_deformans_A2	T_deformans_A2|HD_locus|orf51685	True	32.5	151	True
+P_lact_YB-4353|HMG_locus|F21A9957_003986	P_inouyei_YB-4354	P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	True	99.0	197	True
+P_lact_YB-4353|HMG_locus|F21A9957_003986	P_lact_12-1054	P_lact_12-1054|HMG_locus|F003EF48_006292	True	100.0	197	True
+P_lact_YB-4353|HMG_locus|F21A9957_003986	T_betulina_315	T_betulina_315|HMG|FC6B0312_004553	False	38.4	73	False
+P_lact_YB-4353|HMG_locus|F21A9957_003986	T_communis_352.35	T_communis_352.35|HMG|F8DCC00A_004874	False	40.0	75	False
+P_lact_YB-4353|HMG_locus|F21A9957_003986	T_confusa_375.39	T_confusa_375.39|HMG_locus|F57803F5_005977	True	41.9	172	True
+P_lact_YB-4353|HMG_locus|F21A9957_003986	T_deformans_A2	T_deformans_A2|HMG_locus|F891DC7E_001655	True	44.4	171	True
+P_lact_YB-4353|HD_locus|orf101533	P_inouyei_YB-4354	P_inouyei_YB-4354|HD_locus|orf27984	True	100.0	151	True
+P_lact_YB-4353|HD_locus|orf101533	P_lact_12-1054	P_lact_12-1054|HD_locus|orf38146	True	100.0	151	True
+P_lact_YB-4353|HD_locus|orf101533	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	50.8	61	False
+P_lact_YB-4353|HD_locus|orf101533	T_communis_352.35	T_communis_352.35|HD_locus|orf80243	True	36.0	139	True
+P_lact_YB-4353|HD_locus|orf101533	T_confusa_375.39	T_confusa_375.39|HD_locus|orf181587	True	35.4	147	True
+P_lact_YB-4353|HD_locus|orf101533	T_deformans_A2	T_deformans_A2|HD_locus|orf51685	True	32.5	151	True
+P_lact_12-1054|HMG_locus|F003EF48_006292	P_inouyei_YB-4354	P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	True	99.0	197	True
+P_lact_12-1054|HMG_locus|F003EF48_006292	P_lact_YB-4353	P_lact_YB-4353|HMG_locus|F21A9957_003986	True	100.0	197	True
+P_lact_12-1054|HMG_locus|F003EF48_006292	T_betulina_315	T_betulina_315|HMG|FC6B0312_004553	False	38.4	73	False
+P_lact_12-1054|HMG_locus|F003EF48_006292	T_communis_352.35	T_communis_352.35|HMG|F8DCC00A_004874	False	40.0	75	False
+P_lact_12-1054|HMG_locus|F003EF48_006292	T_confusa_375.39	T_confusa_375.39|HMG_locus|F57803F5_005977	True	41.9	172	True
+P_lact_12-1054|HMG_locus|F003EF48_006292	T_deformans_A2	T_deformans_A2|HMG_locus|F891DC7E_001655	True	44.4	171	True
+P_lact_12-1054|HD_locus|orf38146	P_inouyei_YB-4354	P_inouyei_YB-4354|HD_locus|orf27984	True	100.0	151	True
+P_lact_12-1054|HD_locus|orf38146	P_lact_YB-4353	P_lact_YB-4353|HD_locus|orf101533	True	100.0	151	True
+P_lact_12-1054|HD_locus|orf38146	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	50.8	61	False
+P_lact_12-1054|HD_locus|orf38146	T_communis_352.35	T_communis_352.35|HD_locus|orf80243	True	36.0	139	True
+P_lact_12-1054|HD_locus|orf38146	T_confusa_375.39	T_confusa_375.39|HD_locus|orf181587	True	35.4	147	True
+P_lact_12-1054|HD_locus|orf38146	T_deformans_A2	T_deformans_A2|HD_locus|orf51685	True	32.5	151	True
+T_confusa_375.39|HMG_locus|F57803F5_005977	P_inouyei_YB-4354	P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	True	42.4	172	True
+T_confusa_375.39|HMG_locus|F57803F5_005977	P_lact_12-1054	P_lact_12-1054|HMG_locus|F003EF48_006292	True	41.9	172	True
+T_confusa_375.39|HMG_locus|F57803F5_005977	P_lact_YB-4353	P_lact_YB-4353|HMG_locus|F21A9957_003986	True	41.9	172	True
+T_confusa_375.39|HMG_locus|F57803F5_005977	T_betulina_315	T_betulina_315|HMG|FC6B0312_004553	False	34.7	72	False
+T_confusa_375.39|HMG_locus|F57803F5_005977	T_communis_352.35	T_communis_352.35|HMG|F8DCC00A_004874	False	36.1	72	False
+T_confusa_375.39|HMG_locus|F57803F5_005977	T_deformans_A2	T_deformans_A2|HMG_locus|F891DC7E_001655	True	69.2	172	True
+T_confusa_375.39|HD_locus|orf181587	P_inouyei_YB-4354	P_inouyei_YB-4354|HD_locus|orf27984	True	43.0	100	True
+T_confusa_375.39|HD_locus|orf181587	P_lact_12-1054	P_lact_12-1054|HD_locus|orf38146	True	43.0	100	True
+T_confusa_375.39|HD_locus|orf181587	P_lact_YB-4353	P_lact_YB-4353|HD_locus|orf101533	True	43.0	100	True
+T_confusa_375.39|HD_locus|orf181587	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	56.5	46	False
+T_confusa_375.39|HD_locus|orf181587	T_communis_352.35	T_communis_352.35|HD_locus|orf80243	True	42.9	168	True
+T_confusa_375.39|HD_locus|orf181587	T_deformans_A2	T_deformans_A2|HD_locus|orf51685	True	43.3	157	True
+T_communis_352.35|HMG_locus|F8DCC00A_005608	P_inouyei_YB-4354	none				
+T_communis_352.35|HMG_locus|F8DCC00A_005608	P_lact_12-1054	none				
+T_communis_352.35|HMG_locus|F8DCC00A_005608	P_lact_YB-4353	none				
+T_communis_352.35|HMG_locus|F8DCC00A_005608	T_betulina_315	T_betulina_315|HMG_locus|FC6B0312_004634	True	41.4	116	True
+T_communis_352.35|HMG_locus|F8DCC00A_005608	T_confusa_375.39	none				
+T_communis_352.35|HMG_locus|F8DCC00A_005608	T_deformans_A2	none				
+T_communis_352.35|HD_locus|orf80243	P_inouyei_YB-4354	P_inouyei_YB-4354|HD_locus|orf27984	True	36.0	139	True
+T_communis_352.35|HD_locus|orf80243	P_lact_12-1054	P_lact_12-1054|HD_locus|orf38146	True	36.0	139	True
+T_communis_352.35|HD_locus|orf80243	P_lact_YB-4353	P_lact_YB-4353|HD_locus|orf101533	True	36.0	139	True
+T_communis_352.35|HD_locus|orf80243	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	43.7	71	False
+T_communis_352.35|HD_locus|orf80243	T_confusa_375.39	T_confusa_375.39|HD_locus|orf181587	True	42.9	168	True
+T_communis_352.35|HD_locus|orf80243	T_deformans_A2	T_deformans_A2|HD_locus|orf51685	True	52.6	171	True
+T_betulina_315|HMG_locus|FC6B0312_004634	P_inouyei_YB-4354	P_inouyei_YB-4354|HMG|F7C0A940_003944	False	38.5	52	False
+T_betulina_315|HMG_locus|FC6B0312_004634	P_lact_12-1054	P_lact_12-1054|HMG|F003EF48_000425	False	38.5	52	False
+T_betulina_315|HMG_locus|FC6B0312_004634	P_lact_YB-4353	P_lact_YB-4353|HMG|F21A9957_006289	False	38.5	52	False
+T_betulina_315|HMG_locus|FC6B0312_004634	T_communis_352.35	T_communis_352.35|HMG_locus|F8DCC00A_005608	True	41.4	116	True
+T_betulina_315|HMG_locus|FC6B0312_004634	T_confusa_375.39	none				
+T_betulina_315|HMG_locus|FC6B0312_004634	T_deformans_A2	T_deformans_A2|HMG|F891DC7E_000191	False	33.3	69	False
+T_deformans_A2|HMG_locus|F891DC7E_001655	P_inouyei_YB-4354	P_inouyei_YB-4354|HMG_locus|F7C0A940_005637	True	43.9	173	True
+T_deformans_A2|HMG_locus|F891DC7E_001655	P_lact_12-1054	P_lact_12-1054|HMG_locus|F003EF48_006292	True	43.4	173	True
+T_deformans_A2|HMG_locus|F891DC7E_001655	P_lact_YB-4353	P_lact_YB-4353|HMG_locus|F21A9957_003986	True	43.4	173	True
+T_deformans_A2|HMG_locus|F891DC7E_001655	T_betulina_315	T_betulina_315|HMG|FC6B0312_004553	False	37.5	72	False
+T_deformans_A2|HMG_locus|F891DC7E_001655	T_communis_352.35	T_communis_352.35|HMG|F8DCC00A_004874	False	31.8	129	False
+T_deformans_A2|HMG_locus|F891DC7E_001655	T_confusa_375.39	T_confusa_375.39|HMG_locus|F57803F5_005977	True	69.2	172	True
+T_deformans_A2|HD_locus|orf51685	P_inouyei_YB-4354	P_inouyei_YB-4354|HD_locus|orf27984	True	34.0	144	True
+T_deformans_A2|HD_locus|orf51685	P_lact_12-1054	P_lact_12-1054|HD_locus|orf38146	True	34.0	144	True
+T_deformans_A2|HD_locus|orf51685	P_lact_YB-4353	P_lact_YB-4353|HD_locus|orf101533	True	34.0	144	True
+T_deformans_A2|HD_locus|orf51685	T_betulina_315	T_betulina_315|HD|FC6B0312_002074	False	57.8	45	False
+T_deformans_A2|HD_locus|orf51685	T_communis_352.35	T_communis_352.35|HD_locus|orf80243	True	52.6	171	True
+T_deformans_A2|HD_locus|orf51685	T_confusa_375.39	T_confusa_375.39|HD_locus|orf181587	True	43.3	157	True
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology_proteins.faa b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology_proteins.faa
new file mode 100644
index 00000000..dc2b92ed
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/pm_locus_orthology_proteins.faa
@@ -0,0 +1,196 @@
+>P_inouyei_YB-4354|HMG|F7C0A940_003944
+MEHGSTTKDSTTTRAAAPRAKKEKKDPNAPKKALSSYMLFTQDHRQIVLSENPGIPFGQVGRELGTRWKNLSDADKKPYEDKAKAAKAKYEEEKAAYELENGIAPKKSRAKKEE
+>P_inouyei_YB-4354|HMG_locus|F7C0A940_005637
+MPLGSIEHFSMAEALSMINHSEGWACFIPNGFLPVLVAEEDLAEEVCDGMRRLSSYLIMPTSLEDCRLPSLVVTGITQGLEHPIPAGKPRPPRRPANSFILYRKAKQAELIALYPGISNNEVSRSLGQMWKKEDEQTKQFYQSLAEGLKTQHKALYPDYKYCPKRPKVKNDFQTGTSSPSSCSCTNAGRAASDRQFR
+>P_inouyei_YB-4354|HMG|F7C0A940_001588
+MRPDEVPGRSRERQYSDINLVQQEQPHRSLKRSSTMPELGACPGLTVQPPTPLDMTFGKQHGHPMRAEAEQGPVDTGSLFVGSYRSNASSVFPSGEDSALEDDDAYQRSPAASYDLTASPLSVHAMIRSSASPTLSSVSAPSSRRGSKAKSKQSAEDDQPKRPLNSFMLYRKDKWPTVPNKNHQSISRIIGEMWRNESRETKERYDSLAKQAKANHQALYPGYKFHPKKKKDGKTTSAKTGTPYRQSGSVSDSGVPPAMYSHEDYMRHVQPPFPYGYYPLQPDRSMYGASASTSHLFPTASEARASLAMQQQRSQQGYYAQAPPFRVDTPPRSTTGHSSSDQESPWSVPTAESALRQHHLQVQRRRQQLEEARTLADAEAQAQLDLQHYEWMQAQQTQQAQQAQQQAMLMHQQQQMLPPQELPGQFSGVSSHGVNTPHENLAEPQYDLLSNEYGVPEFMDEHGQIHPTAGLLDLAIYDPNYDGLAAFGPAQGQWSSTTLYDGTGDFGFSDYEHTHGEER
+>P_inouyei_YB-4354|HMG|F7C0A940_003432
+MVEQTNKLQEKYDSVLGCTRLLTEAHAALIRSVKDLNEYVQETHPELDTEASVSTLVAPSNAAPATHEAPVIPGSASKKKEKKEKKVRDPDMPKRPVTAFFHFQNAIRQEMKNSLPDSASAADVQQALAAKWKEMDTEARKPYVAANEEALRAYTREMDTYNKSHGIAPKQAPAKKTTPAAEPSSPNTSPSAEDEEDDVAAASVLQDVPSTPKSSKKRGRPAKKDGQPSAKKVKTPAQEAPAETPKAEKKKKERKKKSAEQSA
+>P_inouyei_YB-4354|HMG|F7C0A940_003008
+MKREVAIGLEQLGLSQYIARLEQEGFDEWASLCDITESDLEALDIKRGHRRILLRHIATIRGHPSTEPLDDGSSDGTGHPEDGTRSRSNSISTRRPSLAFTDAEDSQCQRMMPTKRQYKRHPKVDENAPSRPPSAYVMFANQIREEQRQSKLTFTQIARLAGERWKNLGPAEKVKIEAAADALKQKYVAETNEYRKSVEYQLYQDYLSEFKERAVRHEKPEKLVAPKRTGRKGAPSRHPYSPSAHPSTSPQEAHSAFSRQSSSCDSSSHGQSPAFVMTSTTETRPSEEQKTPLPHLNQWLPSMQEMAEQAVPQHLTGRPPFEQHRLPPLKMSMASQEALPPLIPSAYRGHGVSDPSFFRMAGMDRTY
+>P_inouyei_YB-4354|HMG|F7C0A940_001266
+MADQALPIAPLSESEEIKYRKKCKALKKRINEIEQANDTLITKLARTKRYIQRTRLERAFLLEKLEQIASRDMQAEDEHASPSPPASPGFETYLLQKNPSYLAAHPVSMSPEPGRVSNGHPKPTPTTTGTPAPSKLRIEKPATAHKSKAQAKRDRDPNLPRRPKNAFLRFCDQEREAIKANWQGDETGEPLDLSRELGKVWQAMDDTRRKMYQDQFEEDKLRYERESIAYEAQKKAALEAASNDTLPTAADLQTPATGVTLAEQPRPTGSSPAPPGHADSAMDEDENMTDIEDAEEDEEEEGTDQDSGDNMDEDESGDDAATEDGAGPGQATPSVPKKTSGGGFTAVNSSST
+>P_inouyei_YB-4354|HMG|F7C0A940_004761
+MSIKLMNPLVRLVTRNPAQVRAFATQLGDAPARPSVKKDPSLKIEKDPKFKKPKAVTVPPVQRATKQPPKGGVSAYTLFIKNYASERKAAGERFALTDAIEAYKKMPEEEKAKLLEQVPNVLAERKKLYDAFVNNMSPAEIAAENKVRAGLRKTALAKGKSVSSKLKKIKDPNAPTAPLSAWMRFLQERRSSGAYEDLPMIEITKRASTEWRELSDEARAKYSEEAAKGYEAYKKAKDAYYGQQ
+>P_inouyei_YB-4354|HD|F7C0A940_005400
+MQQLYGFDAAYSNHSAPLMHSPYPHASATGSPPSSAESSPLGLVNGLPRHGRIRAQSLTTKLQSMVGGKSTAHITQQQLNKKRQRATPEQLAVLEEAFDVNPSPNAKQREVISAQIDMTERSVQIWFQNRRAKTKSASKRTSGAHDDSYQHARPGAPSRSFSIDQRMLSEHEAQHLGSNDVTRLNCRSLTIGSWRRVACTLSDLVLYFSHHEPRFTYYINSGASGFKLEFPLTDISKIDLQFLEGQTSKELGRITLTIVKPPVFFMEVPGPGTWSQCTDFTEHQQATLVHTHLLVGPYATLKSALMKMARYHPSVASIMTLADVLQSQPVTATFPVSPDRELFARAGQQAASALEQESNAAGQFARGPGMHRRTRSRSAPIALDFSFLNNENVGGMPNYSFGQRSARPEMNFAQLQQEPTQGFDLSMSGDPYAAAALSASQSIAPGTDYPEMIFTPTTSSTPVFPDGSGIPGWYNTHNAASGYAESPLLSGSGVHSALASPMLPSGSQYGMSSQPSLVAGLQQQHAQTLNDFSMGDPTNEPLMHFPAQSMPDLLNSIPEAETISPPSLQASLAMDGSTGGHAAKLDLGGTLNASTMHGAGLQNAQLAAMVAMNMETNAMIVQQAQQEQEDLQMQDHGMQ
+>P_inouyei_YB-4354|HD|F7C0A940_004297
+MKNMSYGNARSQQLGNGPTSYGEMANVDYHGFDSDYQDAMSPGQKLPGKKNMKRHRLTHDETRFLLNEFARNPHPDGSQRERLVRTVKNLTNRQVQVWFQNRRAKLKRMTEEDAERVLASRRYPSSHGPLGIPRFGGFPGDVSCTEIPSTRTEAIFASSLPPVPSLHQASSSMSTESMSTNVSGSAVPRFREDGYYSGTASPMSYDSGVEPSTPESLVLSPYTMPSTFHHQPHFAARHFTSNFGVSQAPRSVPVTSSPTSRPDVAARTLPEPASLADISVRGWNKSWSLDNHAGGQLPAAPARQRQALPSISHELFGFLGNDDMLSLQSDEKFSTFGQQSYEFASTVGRLEQQYGARTGSLAKDPFTARLSISFDN
+>P_inouyei_YB-4354|HD|F7C0A940_004905
+MSQQDHSTYSPSHAHFPGFNNLGEGRAQMMKQEFDGETQRMQLPFPPVQREALPSLQQLQTMPQSYGQQEQSTGYNSAQQQSFQIPQQTQPAQQASLPQNTGGFNVPHSTFSRHRQGPVPASLPNLGRMEGPFSASNFSPQFSPTQLQSPSASSSFASSSLSQPTSAAQTEGFQSSTGSIKGKRKRASPQQLGLLNQIFDMTFFPSTELRNALGKELGMMPRTVQIWFQNRRQSWRAHKNRSGDATASGDGQTTPTTGEQVEPHSNDNERGGWEVLRSFQNKKATGEIGEYEYMTIPGPVGGTAAPVADQGQSHPLAQHQQQPTSVPQAGILSGLTSPSVLHDFDSRWSSISDYGSSAPSSAGYLHHRSGSISSNPGSASTGTHPYGRSSPRMPSQQAWPRQQSLHAGNGHARSLSTLDLSMQAPPSLPYRHQLSGGYPSLLPLSPTQGTLPPFGNASGMMQGTQQQPQDNRQGYDYTRFGGLPPPPPSSSTAFGRN
+>P_inouyei_YB-4354|HD|F7C0A940_005340
+MDPGSSPQLEPSSQQDGHPAAPTLHQHVLLPAQQAAEQAGKADATATAAADAAAARAKRRRTTGAELAILEDEFAQCDKPDPLARERISKRIGLVEGPGMNGREIQVWFQNKRQAVRKARGSDASLLVVTSGDVPALSASTSTTSLSSSSSDLEKTVWPQVQVVNKGGRGTGYIHLAKRPDTTVVSATAQTKRPRRLASLQLQDLDGHAELHFQPPCAPSPVSPPRIPGAALLTRKFQRLQQQELRADKKRRQLGASRSVSSPALLGERAPHSASVRKQPAARTKLAKSASMAAAGKENVDPHTTLSAQQMADAHQFAGTAQVQGWQGLLLATSARYLPASPSHLRDLPPSASRGNTHGNGQGRRVVSAPATAVSPCKTQPNRQEEGLPGASQETCVDDEEGDVTDHAMSLEECALSLVGLARGS
+>P_inouyei_YB-4354|HD|F7C0A940_003233
+MSDAQDSSFRLPSLTSLIPEEVPQQYSRSDPRWPGTAPQPTAPYDPLERTGGSSMQPGYDYSAYQPGSYFGPSAARDQHHRGSLSSASYVESSRHSSQSTARSSLSSGPDVHGRQPIPAWSDTTTHIQPFSYGAPALQLSPGSRALAYKPEFSPPFPVNHAVPAQRTGPGPLPSIRYSPNSSYASLRRDSVASSIQDEQDHRRDSYPHIMGGGHSPGSGNAQLHDARRGSHPSMSFAPYLTTRPTASTESLPSTASAVDSAGKPKKRRGNLSRKATNMLKTWLNEHVEHPYPSEDEKLALSEQTELTIAQISNWFINARRRILAPRFASKNQSAVWNEIKMNHHIHGGPMPSEGRLEQQQQQQVQLQPSHLPPSVSSSGEGESPELSHAVRDTPLAPATA
+>P_inouyei_YB-4354|HD_locus|orf27984
+LPYHLTRQSVQASTVQTAMDIITMIDEVETDLRMRSVEVSTAIDRFRYIKKELQRLPLDAAVLDTIKAKALTIVDLCAQHRNGSTANVQQNRPHRRAVQKILKAWYLEHLQHPYPNEADKQRLASLTGLTIKQISMWFTNARRRSGTNGDRFMREGVSASLVSLLPY
+>P_lact_YB-4353|HMG|F21A9957_006289
+MEQQVNKKPKQHTNTPQAKDSTTTRAAAPRAKKEKKDPNAPKKALSSYMLFTQDHRQIVLSENPGIPFGQVGRELGTRWKNLSDADKKPYEDKAKAAKAKYEEEKAAYELENGIAPKKSRAKKEE
+>P_lact_YB-4353|HMG_locus|F21A9957_003986
+MPLGSIEHFSMAEALSMINHSEGWACFIPNGFLPVLVAEEDFAEEVCDGMRRLSSYLVMPTSLEDCRLPSLVVTGITQGLEHPIPAGKPRPPRRPANSFILYRKAKQAELIALYPGISNNEVSRSLGQMWKKEDEQTKQFYQSLAEGLKTQHKALYPDYKYCPKRPKVKNDFQTGTSSPSSCSCTNAGRAASDRQFR
+>P_lact_YB-4353|HMG|F21A9957_002866
+MRPDEVPGRSRERQYSDINLVQQEQPHRSLKRSSTMPELGACPGLTVQPPTPLDMTFGKQHGHPMHAEAEQGPVDTGSLFVGSYRSNASSVFPSGEDSALEDDDAYQRSPAASYDLTASPLSVHAMIRSSASPTPSSVSAPSSRRGSKAKSKQSAEDDQPKRPLNSFMLYRKDKWPTVPNKNHQSISRIIGEMWRNESRETKERYDSLAKQAKANHQALYPGYKFHPKKKKDGKTTSAKTGTPYRQSGSVSDSGVPPAMYSHEDYMRHVQPPFPYGYYPLQPDRSMYGASASTSHLFPTASEARASLAMQQQRSQQGYYAQAPPFRVDTPPRSTTGHSSSDQESPWSVPTAESALRQHHLQVQRRRQQLEEARTLADAEAQAQLDLQHYEWMQAQQTQQAQQQAMQMHQQQQMLPPQELPGHLSGVSSHGVNTPHENLAEPQYDLLSNEYGVPEFMDEHGQIHPMAGLLDLAIYDPNYDGLAAFGPAQGQWSSTTLYDGTGDFGFSDYEHTHGEER
+>P_lact_YB-4353|HMG|F21A9957_006358
+MLEQTNKLQEKYDSVLGCTRLLTEAHAALIRSVKDLNEYVQETHPELDTEASVSTLVAPSNAAPATHEAPVIPGSASKKKEKKEKKVRDPDMPKRPVTAFFHFQNAIRQEMKNSLPDSASAADVQQALAAKWKEMDTEARKPYVAANEEALRAYTREMDTYNKSHGIAPKQAPAKKTTPAAEPSSPNTSPSAEDEEDDVAAASVLQDVPSTPKSSKKRGRPAKKDGQPSAKKVKTPAQEAPAETPKAEKKKKERKKKSAEQSA
+>P_lact_YB-4353|HMG|F21A9957_001070
+MKREVAIGLEQLGLSQYIARLEQEGFDEWASLCDITESDLEALDIKRGHRRILLRHIATIRGHPSTEPLDDGSSDGTGHPEDGTRSRSNSISTRRPSLAFTDAEDSQCQRMMPTKRQYKRHPKVDENAPSRPPSAYVMFANQIREEQRQSKLTFTQIARLAGERWKNLGPAEKVKIEAAADALKQKYVAETNEYRKSVEYQLYQDYLSEFKERAVRHEKPEKLVAPKRTGRNGVPPRHPYSPSAHPSTSPQEAHSTFSRQSSSCDSSSHGQSPAFVMTSTTETRPSEEQKTPLPHLNQWLPSMQEMAEQAVPQHLTGRPPFEQHRLPPLKMSMASQEALPPLIPSAYRGHGVSDPSFFRMAGMDRTY
+>P_lact_YB-4353|HMG|F21A9957_004928
+MSIKLMNPLVRLVARNPAQVRAFATQLGDAPTRPRVKKDTSLKIEKDPKLKKLKAVAVPPVQRATKQPPKGGVSAYTLFIKNYASERKAAGERFALTDAIEAYKKMPEEEKAKLLEQVPNVLAERKKLYDAFVNNMSPAEIAAENKVRAGLRKTALAKGKSVSSKLKKIKDPNAPTAPLSAWMRFLQERRSSGAYEDLPMIEITKRASTEWRELSDEARAKYSEEAAKGYEAYKKAKDAYYGQQ
+>P_lact_YB-4353|HMG|F21A9957_003047
+MADQALPIAPLSESEEIKYRKKCKALKKRISEIEQANDTLITKLARTKRYIQRTRLERAFLLEKLEQIASRDMQAEDEHASPSPPASPGFETYLLQKNPSYLAAHPVSMSPEPGRATNGHPKPTPTTTGTPAPSKLRIEKPATAHKSKAQAKRDRDPNLPRRPKNAFLRFCDQEREAIKANWQGDETGEPLDLSRELGKVWQAMDDTRRKMYQDQFEEDKLRYERESIAYEAQKKAALEAASNDTLPTAADLQTPAAGVTSAEQPRPTGSSPAPPGHADSAMDEDENMTDIEDAEEDEEEEGTDQDSGDNMDEDESGDDAATEDGAGPGQATPSVPKKTSGGGFTAVNSSST
+>P_lact_YB-4353|HD|F21A9957_000040
+MQQLYGFDAAYSNHSAPPMHSPYPHASATGSPPSSAESSPLGLVNGLPRHGRIRAQSLTTKLQSMVGGKSTAHITQQQLNKKRQRATPEQLAVLEEAFDVNPSPNAKQREVISAQIDMTERSVQIWFQNRRAKTKSASKRTSGAHDDSYQHARPGAPSRSFSIDQRMLFEHEAQHLGSNDVTRLNCRSLTIGSWRRVACTLSDLVLYFSHHEPRFTYYINSGASGFKLEFPLTDISKIDLQFLDGQTSKELGRITLTIVKPPVFFMEVPGPGTWSQCTDFTEHQQATLVHTHLLVGPYATLKTALMKMARYHPSVASVMTLADVLQSQPVTATFPVSPDRELFARAGQQAASALEQESNAAGQFARGPGMHRRTRSRSAPIALDFSFLNNENVGGMPNYSFGQRSARPEMNFAQLQQEPTQGFDLSMSGDPYAAAALSASQSIAPGTDYPEMTFTPTTSSTPVFPDGSLIPGWYNTHNAASGYAESPLLSGSGVHSALASPMLPSGSQYGMSSQPSLVAGLQQQHAQTLNDFSMGDPTNEPLMHFPAQSMPDLLNSIPEAETISPPSLQASLAMDGSTGGHAAKLDLGGTLNASTMHGAGLQNAQLAAMVAMNMETNAMIVQQAQQEQEDLQMQDHGMQ
+>P_lact_YB-4353|HD|F21A9957_002544
+MTLATHGRCGEHLSHSMENMSYGNARTQQLGNGPTSYGEMANVDYHGFDSDYQDAMSPGQKLPGKKNMKRHRLTHDETRFLLNEFARNPHPDGSQRERLARTVKNLTNRQVQVWFQNRRAKLKRMTEEDAERVLASRRYPSSHGPLGIPRFGGFAGDVSCAEIPSTRTEAIFASFLPPVPSLHQASSSMSTESMSTNVSGSAVPRFREDGYYSGTASPMSYDSGVEPSTPESLVLSPYTMPSTFHHQPHFAARHFTSNYGVSQAPRSVPVTSSPTSRPDVAARTLPEPASLADISVRGWNKSWSLDNHAGGQLPAAPARQRQALPSISHELFGFLGNDDMLSLQSDEKYSTFGQQSYEFASTVGRLEQQYGARTGSLAKDPFTARLSISFDN
+>P_lact_YB-4353|HD|F21A9957_004986
+MSQQDHSTYSPSHAHFPGFNNLGEGRPQMVKQEFDGETQRMQLPFPPAQREALPSLQQLQTMPQSYGQQEQPTGYNSAQQQSFQIPQQPQPTQQVSIPQNTGGFNVPHSTFSRHRQGPVPASLPNLGRMEGSFSASSFSPQFSPTQLQSPSASSSFASSSLSQPTSAAQTEGFQSSTGSIKGKRKRASPQQLGLLNQIFDMTFFPSTELRNALGKELGMMPRTVQIWFQNRRQSWRAHKNRSGDATASGDGQTTPTAGEQVEPHSNDNERGGWEVLRSFQNKKATGEIGEYEYMSIPGPVGGSGAPVADQGQSHPLAQHQQQPTSVPQAGILSGLTSPSVLHDFDSRWSSISDYGSSAPSSAGYLHHRSGSISSNPGSASTGTHPYGRSSPRMPSQQAWPRQQSLHTGNGHARSLSTLDLSMQAPPPLPYRHQLSGGYPSLLPLSPTQGILPPFGNASGMMQGTQQQQQDNRQGYDYTRFGGLPPPPPSSSTAFGRN
+>P_lact_YB-4353|HD|F21A9957_004156
+MDPGSSTQLEPFSQHDGHPAAPTLHQHVLLPAEQAGKADATATAAADAAAARAKRRRTTGAELAILEDEFAQCDKPDPLARERISKRIGLVEGPGMNGREIQVWFQNKRQAVRKARGSDASLLVVTAGDVPALSASTSTTSLSSSSSDLEKTVWPQVQAVNKGGRGTGYIHLAKRPDTTGLSATAQTKRPRRLASLQLQDLDGHAELRFQPPCAPSPVSPPRIPGAALLTRKFQRLQQQELRADKKRRQLVAARSVSSPALLGERAPHSASVSKQSAARTKLAKSTSMAAAGKENVDPHTTLSAQEMADAHEFAGTAQVQGWQGLLLATSARYLPASPSHLRDLPPSASRDNTHGNGQGRRVVSAPATAVSPCKIQPNRQEEGLPGASQETCVDDEEGEVMDHAMSLEECALSLVGLARGS
+>P_lact_YB-4353|HD|F21A9957_005482
+MEVMSDAQDSSFRLPSLTSLIPEEVPQQYSRSDPRWPGTAPQPTAPYDPLERTGGSSMQPGYDYSAYQPGSYFGPSAARDQHHRGSLSSASYVESSRHSSQSTARSSLSSGPDVHGRQPIPAWSDATTHTQPFSYGTPALQLSPGSRALAYKPEFSPPFPVNHAVPAQRTGPGPLPSIRYSPNSSYASLRRDSVASSIQDEQDHRRDSYPHIMGGGHSPGSGNAQLHDARRGSHPSMSFAPYLTTRPTASTESLPSTASAIDSAGKPKKRRGNLSRKATSMLKTWLNEHVEHPYPSEDEKLALSEQTELTIAQISNWFINARRRILAPRFASKNQSAVWNEIKMNHHIHGGPMPTEGTLDQQQQQQVQLQPSHLPPSVSSAGEGESPELSHAVRDTPLAPATA
+>P_lact_YB-4353|HD_locus|orf101533
+TAMDIITMIDEVETDLRMRSVEVSTAIDRFRYIKKELQRLPLDAAVLDTIKAKALTIVDLCAQHRNGSTANVQQNRPHRRAVQKILKAWYLEHLQHPYPNEADKQRLASLTGLTIKQISMWFTNARRRSGTNGDRFMREGVSASLVSLLPY
+>P_lact_12-1054|HMG|F003EF48_000425
+MEQQVNKKPKQHTNTPQAKDSTTTRAAAPRAKKEKKDPNAPKKALSSYMLFTQDHRQIVLSENPGIPFGQVGRELGTRWKNLSDADKKPYEDKAKAAKAKYEEEKAAYELENGIAPKKSRAKKEE
+>P_lact_12-1054|HMG_locus|F003EF48_006292
+MATSMPLGSIEHFSMAEALSMINHSEGWACFIPNGFLPVLVAEEDFAEEVCDGMRRLSSYLVMPTSLEDCRLPSLVVTGITQGLEHPIPAGKPRPPRRPANSFILYRKAKQAELIALYPGISNNEVSRSLGQMWKKEDEQTKQFYQSLAEGLKTQHKALYPDYKYCPKRPKVKNDFQTGTSSPSSCSCTNAGRAASDRQFR
+>P_lact_12-1054|HMG|F003EF48_001932
+MRPDEVPGRSRERQYSDINLVQQEQPHRSLKRSSTMPELGACPGLTVQPPTPLDMTFGKQHGHPMHAEAEQGPVDTGSLFVGSYRSNASSVFPSGEDSALEDDDAYQRSPAASYDLTASPLSVHAMIRSSASPTPSSVSAPSSRRGSKAKSKQSAEDDQPKRPLNSFMLYRKDKWPTVPNKNHQSISRIIGEMWRNESRETKERYDSLAKQAKANHQALYPGYKFHPKKKKDGKTTSAKTGTPYRQSGSVSDSGVPPAMYSHEDYMRHVQPPFPYGYYPLQPDRSMYGASASTSHLFPTASEARASLAMQQQRSQQGYYAQAPPFRVDTPPRSTTGHSSSDQESPWSVPTAESALRQHHLQVQRRRQQLEEARTLADAEAQAQLDLQHYEWMQAQQTQQAQQQAMQMHQQQQMLPPQELPGHLSGVSSHGVNTPHENLAEPQYDLLSNEYGVPEFMDEHGQIHPMAGLLDLAIYDPNYDGLAAFGPAQGQWSSTTLYDGTGDFGFSDYEHTHGEER
+>P_lact_12-1054|HMG|F003EF48_001253
+MLEQTNKLQEKYDSVLGCTRLLTEAHAALIRSVKDLNEYVQETHPELDTEASVSTLVAPSNAAPATHEAPVIPGSASKKKEKKEKKVRDPDMPKRPVTAFFHFQNAIRQEMKNSLPDSASAADVQQALAAKWKEMDTEARKPYVAANEEALRAYTREMDTYNKSHGIAPKQAPAKKTTPAAEPSSPNTSPSAEDEEDDVAAASVLQDVPSTPKSSKKRGRPAKKDGQPSAKKVKTPAQEAPAETPKAEKKKKERKKKSAEQSA
+>P_lact_12-1054|HMG|F003EF48_000047
+MKREVAIGLEQLGLSQYIARLEQEGFDEWASLCDITESDLEALDIKRGHRRILLRHIATIRGHPSTEPLDDGSSDGTGHPEDGTRSRSNSISTRRPSLAFTDAEDSQCQRMMPTKRQYKRHPKVDENAPSRPPSAYVMFANQIREEQRQSKLTFTQIARLAGERWKNLGPAEKVKIEAAADALKQKYVAETNEYRKSVEYQLYQDYLSEFKERAVRHEKPEKLVAPKRTGRNGVPPRHPYSPSAHPSTSPQEAHSTFSRQSSSCDSSSHGQSPAFVMTSTTETRPSEEQKTPLPHLNQWLPSMQEMAEQAVPQHLTGRPPFEQHRLPPLKMSMASQEALPPLIPSAYRGHGVSDPSFFRMAGMDRTY
+>P_lact_12-1054|HMG|F003EF48_005701
+MSIKLMNPLVRLVARNPAQVRAFATQLGDAPTRPRVKKDTSLKIEKDPKLKKLKAVAVPPVQRATKQPPKGGVSAYTLFIKNYASERKAAGERFALTDAIEAYKKMPEEEKAKLLEQVPNVLAERKKLYDAFVNNMSPAEIAAENKVRAGLRKTALAKGKSVSSKLKKIKDPNAPTAPLSAWMRFLQERRSSGAYEDLPMIEITKRASTEWRELSDEARAKYSEEAAKGYEAYKKAKDAYYGQQ
+>P_lact_12-1054|HMG|F003EF48_000189
+MADQALPIAPLSESEEIKYRKKCKALKKRISEIEQANDTLITKLARTKRYIQRTRLERAFLLEKLEQIASRDMQAEDEHASPSPPASPGFETYLLQKNPSYLAAHPVSMSPEPGRATNGHPKPTPTTTGTPAPSKLRIEKPATAHKSKAQAKRDRDPNLPRRPKNAFLRFCDQEREAIKANWQGDETGEPLDLSRELGKVWQAMDDTRRKMYQDQFEEDKLRYERESIAYEAQKKAALEAASNDTLPTAADLQTPAAGVTSAEQPRPTGSSPAPPGHADSAMDEDENMTDIEDAEEDEEEEGTDQDSGDNMDEDESGDDAATEDGAGPGQATPSVPKKTSGGGFTAVNSSST
+>P_lact_12-1054|HD|F003EF48_000947
+MQQLYGFDAAYSNHSAPPMHSPYPHASATGSPPSSAESSPLGLVNGLPRHGRIRAQSLTTKLQSMVGGKSTAHITQQQLNKKRQRATPEQLAVLEEAFDVNPSPNAKQREVISAQIDMTERSVQIWFQNRRAKTKSASKRTSGAHDDSYQHARPGAPSRSFSIDQRMLFEHEAQHLGSNDVTRLNCRSLTIGSWRRVACTLSDLVLYFSHHEPRFTYYINSGASGFKLEFPLTDISKIDLQFLDGQTSKELGRITLTIVKPPVFFMEVPGPGTWSQCTDFTEHQQATLVHTHLLVGPYATLKTALMKMARYHPSVASVMTLADVLQSQPVTATFPVSPDRELFARAGQQAASALEQESNAAGQFARGPGMHRRTRSRSAPIALDFSFLNNENVGGMPNYSFGQRSARPEMNFAQLQQEPTQGFDLSMSGDPYAAAALSASQSIAPGTDYPEMTFTPTTSSTPVFPDGSLIPGWYNTHNAASGYAESPLLSGSGVHSALASPMLPSGSQYGMSSQPSLVAGLQQQHAQTLNDFSMGDPTNEPLMHFPAQSMPDLLNSIPEAETISPPSLQASLAMDGSTGGHAAKLDLGGTLNASTMHGAGLQNAQLAAMVAMNMETNAMIVQQAQQEQEDLQMQDHGMQ
+>P_lact_12-1054|HD|F003EF48_004261
+MTLATHGRCGEHLSHSMENMSYGNARTQQLGNGPTSYGEMANVDYHGFDSDYQDAMSPGQKLPGKKNMKRHRLTHDETRFLLNEFARNPHPDGSQRERLARTVKNLTNRQVQVWFQNRRAKLKRMTEEDAERVLASRRYPSSHGPLGIPRFGGFAGDVSCAEIPSTRTEAIFASFLPPVPSLHQASSSMSTESMSTNVSGSAVPRFREDGYYSGTASPMSYDSGVEPSTPESLVLSPYTMPSTFHHQPHFAARHFTSNYGVSQAPRSVPVTSSPTSRPDVAARTLPEPASLADISVRGWNKSWSLDNHAGGQLPAAPARQRQALPSISHELFGFLGNDDMLSLQSDEKYSTFGQQSYEFASTVGRLEQQYGARTGSLAKDPFTARLSISFDN
+>P_lact_12-1054|HD|F003EF48_000640
+MSQQDHSTYSPSHAHFPGFNNLGEGRPQMVKQEFDGETQRMQLPFPPAQREALPSLQQLQTMPQSYGQQEQPTGYNSAQQQSFQIPQQPQPTQQVSIPQNTGGFNVPHSTFSRHRQGPVPASLPNLGRMEGSFSASSFSPQFSPTQLQSPSASSSFASSSLSQPTSAAQTEGFQSSTGSIKGKRKRASPQQLGLLNQIFDMTFFPSTELRNALGKELGMMPRTVQIWFQNRRQSWRAHKNRSGDATASGDGQTTPTAGEQVEPHSNDNERGGWEVLRSFQNKKATGEIGEYEYMSIPGPVGGSGAPVADQGQSHPLAQHQQQPTSVPQAGILSGLTSPSVLHDFDSRWSSISDYGSSAPSSAGYLHHRSGSISSNPGSASTGTHPYGRSSPRMPSQQAWPRQQSLHTGNGHARSLSTLDLSMQAPPPLPYRHQLSGGYPSLLPLSPTQGILPPFGNASGMMQGTQQQQQDNRQGYDYTRFGGLPPPPPSSSTAFGRN
+>P_lact_12-1054|HD|F003EF48_005759
+MDPGSSTQLEPFSQHDGHPAAPTLHQHVLLPAEQAGKADATATAAADAAAARAKRRRTTGAELAILEDEFAQCDKPDPLARERISKRIGLVEGPGMNGREIQVWFQNKRQAVRKARGSDASLLVVTAGDVPALSASTSTTSLSSSSSDLEKTVWPQVQAVNKGGRGTGYIHLAKRPDTTGLSATAQTKRPRRLASLQLQDLDGHAELRFQPPCAPSPVSPPRIPGAALLTRKFQRLQQQELRADKKRRQLVAARSVSSPALLGERAPHSASVSKQSAARTKLAKSTSMAAAGKENVDPHTTLSAQEMADAHEFAGTAQVQGWQGLLLATSARYLPASPSHLRDLPPSASRDNTHGNGQGRRVVSAPATAVSPCKIQPNRQEEGLPGASQETCVDDEEGEVMDHAMSLEECALSLVGLARGS
+>P_lact_12-1054|HD|F003EF48_001800
+MEVMSDAQDSSFRLPSLTSLIPEEVPQQYSRSDPRWPGTAPQPTAPYDPLERTGGSSMQPGYDYSAYQPGSYFGPSAARDQHHRGSLSSASYVESSRHSSQSTARSSLSSGPDVHGRQPIPAWSDATTHTQPFSYGTPALQLSPGSRALAYKPEFSPPFPVNHAVPAQRTGPGPLPSIRYSPNSSYASLRRDSVASSIQDEQDHRRDSYPHIMGGGHSPGSGNAQLHDARRGSHPSMSFAPYLTTRPTASTESLPSTASAIDSAGKPKKRRGNLSRKATSMLKTWLNEHVEHPYPSEDEKLALSEQTELTIAQISNWFINARRRILAPRFASKNQSAVWNEIKMNHHIHGGPMPTEGTLDQQQQQQVQLQPSHLPPSVSSAGEGESPELSHAVRDTPLAPATA
+>P_lact_12-1054|HD_locus|orf38146
+TAMDIITMIDEVETDLRMRSVEVSTAIDRFRYIKKELQRLPLDAAVLDTIKAKALTIVDLCAQHRNGSTANVQQNRPHRRAVQKILKAWYLEHLQHPYPNEADKQRLASLTGLTIKQISMWFTNARRRSGTNGDRFMREGVSASLVSLLPY
+>T_confusa_375.39|HMG|F57803F5_003754
+MPKDTKPRTVKRDVTKRAKKDPDAPKRALSSYMLFAQDQRSVVQQENPNIAFGEVGKVLGQKWKALTDSEKKPYEDRAGEEKKKYEKLKAQYEADNPKAGKKSGAKKVTKKAKSDDDESA
+>T_confusa_375.39|HMG|F57803F5_004161
+MNGALNSSSIHGTQFADFNRKYQIVLSSCRLLTEAQSALDRSITDFVSVAQALDPDVNVQAFAMEAGQGSIPPRTVVSRTPSKGGKRTKVTNLSSPTTGTADVRTSTQSAAPALLTQAEPRSDTELVGESSSSSIIPGKKQKKIRDPDLPKRPMSAFFLFQNAVRNSVKSAMPEESKGAEIQKAISEKWKELDDESRQPYNEKYENELQDYEARLATYKQDHGLPQRPKSSSTRSDVKNRTPVKTNQANDDDAAAASIVSQVTDPKVIAEAQKTSKKRARTTELEGQKVVKSPRKSEKASDEKKLVLTPDCCLGC
+>T_confusa_375.39|HMG|F57803F5_004000
+MADPNNAYGRSTKIELSISEETKYRKKCRDLKRRINEVEVSNEGLVTKLARTKRYIRRARLERAFLLERLEAQVPKNSQGSDGSPSPPASPALESYSLEPVQPALDNGNSPDPIRRSASPADSRQHTPTYDFPIASAISNAAAAHIANQKERKGSPAPGGSNSTKKIKPPKDPNAPKRPKNAFLLFCEIERDSVRAAADPGNGETVDIARELGRVWADMNDDARKPYRDMYEEDKVRYEKEMSTYEKPKHMAATTPIKPEDYQDKIEIELPTLPNPSPRPKVGGFTAVNRA
+>T_confusa_375.39|HMG_locus|F57803F5_005977
+MTFGEIKNYPTRDALACLNNSQGSAYFVPDGYEPILISQKELTDEVRVEIRRATAYLRLPIALHECRLPTYIVTSRKITTESVAQSVTTSPAKNPPRPPNAFILYRKSKQAEVLAQQQGISNNDVSRIIGTMWRTETEVVRDSFQRFAEEVKLQHKIQYPDYRYKPRRALMKPGTGCCLDKRTPHRRVTLQESPTVCSLETHTSHEPTLLAEEDFPLYY
+>T_confusa_375.39|HMG|F57803F5_002637
+MVTNKLHLAQTTVSAPQVVLEPPTPFLHSTNPETLLTSSVSQELEHAMHTDYRESIALSRSPDSLFVGDLPLSQSATLTHAASICTSRSASPQRPPSRGATPRSRNKTKKLDAEENFVKRPLNSFMLYRKDNQHNIPTNNHQSISRIIGDMWRKETAETKNFYDVLAKEERERHLRDNPGYKFQPKKKKKEGKLLRPELKERHSSGNLDEGQRNMMLQPFDSTQPLQPRQTQSSPLKQRQVPRARNQPDLNPSLGQSSQGHQFADQAMYRELPPQYAHYAGQLQYFSEQAQQSEQSHGALLRDPQDWSLATHQQPDYRSYQTQALYQETLPSDATTCWPEPYPFLDYNMPPTFAEWEHARGSDTPLLQEESLQADFQQMYNNETMLSSEQTCDEQDFVPNHIKYGDPFDFTVGNPSGSCWEIEPEYLPQLYNF
+>T_confusa_375.39|HMG|F57803F5_001127
+MSVFRTVFSKETRLNVTLVRFATTEAVRKPRKNAAAAPPVPKAKAMKTPSSSSVTPYRLFIQQFAEERKNAGEKWLLQNAAEAYKKLPESEKSKLLEQIPELIKQRKVIYEEFVSKLSPSDIVAENKTRAALRKERIAAGKSVKNLAPILDKNAPTRPGGSYVLWAQQARQDAQYSGMSITDQAKALGEKWKALAENEKAEWTSKAKQLREEYEKKKAEYYGS
+>T_confusa_375.39|HMG|F57803F5_003604
+MLSGRSNLAEDFSRLGLSEYLQRFSDEGFTDWSSIADITESDLAALGVRLGHRRTLYREIATLRGYPQTERLENLPKHAPGILLNSASEESRTAYEGSISGSDGQTSPASIETAPQKRRYKRHPKADDNAPIRPPSAYVLFANVIREEQKDSNLSFTQLARLVGERWKNLKSAEKEAIESQAAEVKRRYTAEVGVYKKSPEYAQYQAYLREFKQRVLKDERPEKLEPPRKAQRTNDRQSPAPRSIITAGVRDPTDHRKTRGEPEHDQRGLKPLPDSPFTIPSILHEGARRGDDRVLPSLDYVYNFGNKEQSAPLSERPGVANYNSRPILPRPEFPGPMDNIITNSMYSNSPQWHEESRQRKQQLDWPSSTDQPGRLPSFHGSTVTHDSFAKR
+>T_confusa_375.39|HD|F57803F5_001137
+MSQLIDNDVLGEHSPPDRRLIICEQNSGQSRPSFTSTSFTLRAEAEDHAHRQAGSAESSTSSSPRHSISSNRARSLSLNIKSSQARSTAHVTQQQINRKRQRATPEQLSVLEDAFAANPSPNARMRESISTQINMTERSVQIWFQNRRAKTKSMYRKGAPDEMTLSHASFDMRPSLPGRSWSIDQGMFPNHMMLSNSPQISQIGPVQSFTTRLNCRSLTIGSWRRVACTSSDLICYFSHLEPLFTYYVNSGATGFKIEFPISAIVKIHLTYVAAVNTHEMGRALITLDSCPIFFMEIPSSGAWRQCTDFTENQQGTNERHHNLVGPYQHLKDALIQLLSVHKEMIDCVTFEDANSMDFGVPISSQAVNIAQANAMALRSDDGSTNAVVGRLLQASTPEIRGPARSGHRRTRSRSAPIAVDLSWMNPTHVDDLTKYNYGLRTFNVVPETRYAPEIPSASNSITFDGSDGLYTPATVATSSYQDTWYTSSYANTPLLDAECSQLGSPLAPGGPQFDLDFNGSQIDVYSSFADLGTGMTVTSTLPYHSATANISMPDLPRLDSVPEIPTLDDVPLSEPRGIVDQPYPTMYGQTSSVHNYPIQQ
+>T_confusa_375.39|HD|F57803F5_002097
+MRLRSLSQRGASNKSSDKGSKQVTTTLEDSPCDRQQVSSPSYYRADVPDNQGEMITSASTNYYYDDHRQNRWQQSSDDANNMHNSYEYHQGSPQGYRALQPEDHDAPPDQAIGAFVRNAPLDSYEDSPRDLNAGHIDTQTYPVNDELYADGRRNIPYRDYHGTESGHGLADASPTSTADSPDDTSASMERDMPIVKPFNKKNLKRHRLSHSETRFLLNQFGQNPHPDAAQRVVLSKQISNLSVRQIQVWFQNRRAKLKRMSASDADRMLSTRSYPEGYGPKGFESKPGRPNTPLRTSPDLEPTDAHYTEEDHEDAQSLQPKNISAAIPQYFNHSNLSIHDQSVGLAPYYSRPYLRSPLINENQIHSHYMQTGQVSNLNDETNPTYGEAQLARVVQTPTSLTPAYENVNYGFQTRSPALQNARVYYTRPYPATHPVYAPRSVNSTSEYNDSPVMTPVVQSPYRPYDSRSYYNSATMAAQNFDGGAIRQMYSSSDQASAYQVPEQGNTYVPTAIVPRPLGYSQQAMLGTEIGETRSLDTPASSPDGSYHQAPQMQRESKCGYASINETRSENNEYMETAQGYAQENRQQLNVSQQIEAYEHQIHQPTYSSSHQEYGTDFVPDVTEQD
+>T_confusa_375.39|HD|F57803F5_006117
+MAEVSQETTFDAINNDAAQGNAVDTEEATLADAGLEPPWANEPLLPDATPTTSKAVLTEGQEPEASAISASASTELDGSEGKPTDGNVDTTAAVRDDDQAMQQFKGQIQMHYPQMTPHGPQPYYHDPAIHAQYHYPHPQSGYMNQISNPPGTKAKRKRASPHQLALLNQIFEYTFFPSTELRNAIGKELGMAPRTVQIWFQNRRQAWRSTKVVNADGSESTSAKSNDNERGGWEVLRSFQARRANGEIQEYEYMAIPSPSNAANGQDGRVVGGYSLVPYHPGMMQVALSSNDQFNSSMQQVPMPLPHTPRPNANLVMGPPHPQQFPRPPSPPPPPTVPQTVQDSSLGVTVDQTDEKDTTSSSNDGTAAVPTTDAIETRVDAPDEGTTVLDNVDPSLENADDSSLAIMPDTTTTTTKKTTATERKVTESQGKEHTTTVQE
+>T_confusa_375.39|HD|F57803F5_004223
+MDPRLQDELKVEESTNQHDESHATNDLPAPPANVEDATTEHIDDQGEHTAFLPSLQFASGNDLSSIANYDPRHVASDALRTGEEDAAAQTFDHWPTDTQTQVQNDSGLHDVNTYVQGDSANQFSQAGNPSDYQQDAQQQQSHQQQQQQQQHMQQQQHHLQQQQQHHQHQHHPQHPHHHGGTPYDRPILGASYGTYDGSKPKRKRASPQQLTLLNNIFEMTYFPSSDLRLAIGKELDMVPRSVQIWFQNRRSLWRAKAGQILNENKQRKEELVATGLTADEADAKITADRAESAARQIADQRANDAVEYAINGSNGSLAYALHGANVSQISAATVDDGSVTRDDEAGAWSVLQAFHQARTGVMIQQGHPPMPQRPEAEQQQQQQQQQQQQQQQQTAQQQQQQEV
+>T_confusa_375.39|HD|F57803F5_006217
+MDQYSIGRMDEPTRRRRRTTTLELEILETEFAKCDKPSISERDRISDVISRTDIDGPGMNGREIQVWFQNKRQAIRRAQGAYPLCEPMSERAKTRLANEQLFGIKLDTSRQDDTTPPGSFTSPEESSSSQNAGTPFTVPRYGLTTPKSSLMIRDRRAQLVLSDTGDGHAEVMFSPTPLKPSSPPRVPLLITPIRTPLSRKIAARSASSPALLALRTPTVSKGHDTVVQDSTDAIMTTTPLQATSTNTLGSLKSLKRSHSLISSPNMHRTKEPHAQKQRQSISKTTSHAGLGRGKENIPPLSSFTMPQHANNIQGSSGDSYGRDIRRIQSENLGQSWSTVPASSPSVAVRTTPMRLKPAITSSSPKSTTTREVQPLLPKKMSAEECALSLVSLAHGG
+>T_confusa_375.39|HD|F57803F5_001039
+MDEEQWRLLEQMFNQTPKPTVAQKEHIAARLKLASSVVRSWFTDRRTKAKEDKLVEERQAWAALENAHHVSPLEQHVVDQTRTIDHRAQSEASYASLARSLYAAAACMPTTDTDYEQSLPPSPAFPYSGSFSSYTPTTASAPSFDMSDSYMMRRSDSQFSTVTTPGEFPEQSAFPFYQSTYMPTAQAAANTMIYGVSQEPLQVEAPKLRPRLQRTLTAPEQVAAARPIPRRTISGIYGNENDMNETPKIRRRPKLSHLGIGMARSRSSLGYDESEYPGPRRPAASREFPYPITPVRRIHSAVAVPTLSTMSTYSPTSSQSKSSPESIYDDKGSGMLGLHSSSMQFPPSPISPEHAGMLPHSGKTSCFTLANDPIPEDGFTPPSTPLSVLNPSSENILAGHHNMTNTHWTVEASKLGHDNVDFMYNDITTLNDIFTDQELALHSF
+>T_confusa_375.39|HD|F57803F5_004044
+MAAEAKGSQPQGHSKNGLIPEYSRKNKAAMPHPAASSKNETTTSAFPLQNQLPRDQHTVGSSSSNMQNDASRHWGHGHFSRPEPIQTQRYDLSRSSYDRDVVSEHGPLSGMMGRGDRTSLTSPYTDVSRSSSYSMGQSPLSSTIPSMSSHWSVPYDVSQQATQNSYQISGAASTTNNSSSSSGSRPHFSPPFPLRASVPLKSPIYTTAPQPSPDMRGNGLDNANGLRANESLHLTRNGGYHQDGLTPTYRDNGYAGSLPRSNLLNHGAPAMHSSFDLSQRRPSLSNPVQHHTTPYDRQIPPASFQSQMSPSQAQSYAQPPHQVYQDYAMSDPSKPKRRRGNLPKSTTALLRTWLYDHTNHPYPSEDEKNQLAAQTGLTINQISNWFINARRRILQPSDMQKGLTHQASGPAVQSHATGSMPRAQTTAPQSMYMSRPKSPHAHASGIALQPPYEH
+>T_confusa_375.39|HD_locus|orf181587
+SCQMSGRAASLGHIYDEVKGIHTSICSGSYTCMDDAETTLCAVGTLIRNMKPMRTSEEKELVTLIGNTARQIMDTCADVRQRQHIVWPALKDHKRARESRRVALLKAWYTAHLDYPYPSETEKLSLSLNTGLSIRQICMWFINARRRSQNGRKYLAEQVSEAIQAALR
+>T_communis_352.35|HMG|F8DCC00A_005415
+MPKDTKPRTIKRDVAKRAKKDPDAPKRALSSYMLFAQDQRSVVQSENPNIAFGMSSSLLSTLNLKYLRSLRMLANALREVIRCEVGKVLGQKWKALTDSEKKPYEDRAAEEKKKYEKAKAQYEVENPKAGKSKGVKKTAKKHDDDESA
+>T_communis_352.35|HMG|F8DCC00A_001803
+MAGTVPQSSLVQGDRFAEFHRKYQIVRAPANFVLVVAILTSEQVLSSCRLLTEAQSALDRSITDFVSIAQTLNPEADANYPQISISSTTPAKRAAETIQSRAKDSGSSDISGKAAADSEGPLKKQKKVRDPDLPKRPMSAFFLFQNAVRNSVKSAMPEESKGADIQKAISEKWKELDDESRQPYNEKYEEEVRDYEAKLATYKQDHGIVQPVKSAKKGLSNPDSSSSSLPAISGNSNQATNDDAAAAASIASKAAAASKTKAMSPKESKTKARTSEKAKSPKKNEQSTEEKK
+>T_communis_352.35|HMG|F8DCC00A_001525
+MADPNNAYGHSAVAELSISEETKYRQKCRDLKRRINEVEASNEAIVTKLARTKRFIRRARLERAFLLERLEGQAPKDSLGSDGSPSPPASPSLESYSLDALHGSFDNAQSPDALRRSGSPSDSRQHTPTHDYSVPSAISNAASAHIANQKDRKGSPAPGASNSTKKIKPPKDPNAPKRPKNAFLLFCEIERDSVRAAADPGTGETVDIARELGRVWAEMNDDARKPYRDMYEEDKVRYEKEMSTYEKPKSLATPIKPEDQVEKVEAEIQTPVNPLPNPSPRPKVGGFTAVNRA
+>T_communis_352.35|HMG|F8DCC00A_004874
+MSHDLPYSHAALDKHQLLTEVPAHFSYAAMGPDGLAMTNMTHDSELSRFHERRELHQTARSAMGSPHTNSICQQELNSSRTASPSRPPSRATTPRSRTKTKKVEPDANFVKRPLNSFMLYRKDNQHNIPTNNHQSISRIIGDMWRKETAETKNFYDVRAKEEREKHLLQHPGYKFQPKKKKKETKAVRPELSSRQSTTSVYSNDLDQSSVVYDQPDFHRAPLETTEQHFHFPMPRHESQAGSPARSTSYFAQSTHPLQQDEHYPSSGMHHHKLPSHYAHYAEQPQFHHAQLPTGYHDRQDAGVMLRDPQDWNVLSNQYHSAASAALYPQQQGQEIAPPEPECPWPESYSLLDYNMPATFGQWEDMRMADMPIFQEALQTDFTYPLIEQELGYPLVDPGDELDFIPNHMKHNNDMSSSSFFVTGELKDTWEIEHVDPQSYPA
+>T_communis_352.35|HMG|F8DCC00A_002717
+MSALRNVVRVESRPSVALARFATTEAVKRPRKNAAAAAAPAPRLKAMKTPKSPSSVTAYRLFIQKFAEERKSSGEKWLLQNAAEAYKQLPESEKAKLVEQIPELIAQRKAIYEEFISKLSPSDILAENSTRAKLRKERIAAGKSVSNLAPILDKNAPTRPGGPYILWAQEARQAPEYKELTLTEQARALGEKWKALAENEKAEWHDKAKKLRSEYEQKKAEYYGGS
+>T_communis_352.35|HMG|F8DCC00A_004125
+MLSMRNNLSDDFARLGLSEYLKRFTDEGFTDWSSIADITESDLAALGVKLGHRRTLYREIATLRGYPQSERLEDIPKPAPGSLPSSINEENRSPCDVSASGSDGQTSPSSYVEAVPQKRRYKRHPKPDDNAPTRPPSAYVLFANVIREEQKDSNLSFTQLARLVGERWKSLAASEKEAIESQAAEVKRRYTAEVAVYKKSPEYHQYQAYLREFKQRVLKDERPEKLEPPRKAQRTMNQQHPAPHAIVAHGARDHNDHNGMKVEHDHENRGVRQGSSGPFTIPSILQDGSRRGDDRILPSLDYVYKFGAQDQYGPMNEKPCLQPYAARPILPRPEFPGPMDNVLPTAMYNNGSQWNEEVRLRSLPMERPRSTVEGQPPIMHRGPGTHNGYANR
+>T_communis_352.35|HMG_locus|F8DCC00A_005608
+MKIVLMQHGSRRTKKGKSIPIMTEVYSDDDEIKAPHDRTQPDISTSQPLKRSSNAFFQYRSDPLIKERWTQKSGKHQQRHVVQDISTEWNALSASEKLPYEQKALRASELYKRNLHKQKLKERQNDTTPPSRQASTHANGRLENPIASWYTPLLQYQEQLPESIIPFDNAVKFTEAQAVVRHPPFPQGCFSVPSYAVDHQSIPLDSSTLQFEFQGRLWPFSDLEESQAQTTEYDWSRDLSWMSLAAPS
+>T_communis_352.35|HD|F8DCC00A_000778
+MQEVDLDASNIRPSNEHLSSIGFNLNHGDKQCNIHFDGAPQESRAGLDSRNLSYTRPTSSDSSTSSSPRRHDAGHRSRSLSLSTKSVHHRSTAHVTQQQINKKRQRATPEQLNVLEDAFACNPSPNARMRENISSQINMTERSVQIWFQNRRAKIKLLHRKCEPDEMVHQAFNNVRPSPPGRSYSIDPGLFQIHSNTVMRQHHEASAECITKFNCRSLTIGTWRRVACNSNDLICYFSNAELSFTYYINNGSSGFKIEFPLASVLSIALDYVSTPHTNEMGRIVISLTSSPIFFMELLSTEIWKQCTDFTENEQGTTVLSHAIVGPYQQLKHSLTQLAAVHNDAIDKICLADGSKMTIDGEFGQETARTLMTSTKQSEESGMIHNDFSSSLRPGSSLTLQVPQRGTHRRTRSRSAPIMVDLSWLHHGHSMETSNYNQDTSDSSMVAPQLYNIQPSPMSQHLSSQNSFYNSATATSPCFPEAWYATSYTNTPLLDAHCSQLNSPIVPDGAQFELPLTTSQLRPYTSFTEMDHATGINMHSVPNGQSLSNHPAIGSSHLEDYPDMLTTIQQQYATTNSFQALVTPTNVMHESFAQQDNHSPFV
+>T_communis_352.35|HD|F8DCC00A_005890
+MRLRSLSLRLAEQKAAEQKADKSCKATVASPCEATQKSSPMYYRPDGADNQEEMKASASTNCYYDDHEQIQVQQSGSTTDNMHGSYLYHEDEEVGPYLCQQQSAAESSQQACEQANTIADRNAASDVTYAGLARQFVADEDTTEQYDGKGGVYYHEEGQPVPYQDYVGTDSAEDEYNASPTSTEHDRDDACRSVERDVPKPINKKNLKRHRLSHSETRFLLNQFGQNPHPDAAQRVLLSKQINGLSVRQIQVWFQNRRAKLKRMSASDADRMLSTRSYPDGYGPQGFETHLTRQESSREGSPCVTKVDAAYVSQDYSEAHGLQPKNDAPATSSPYPVRNISSVYRRPNIRSPLMAQHMPSYSAQTRQTGFTREGTNSPYSEVTMSRDPGSPQASPAQYDGAAYALAGRTSAAAQGSARFIYGRPYPATHAMYAPRSMQINNGYITSPEDSPAIVQSPYRPYHMADQRAYYSPSLLAAQTYENTGYRQAYAMAEQVNAYQAPGQDGPYVLTNVQTRPLGYNQHVNPGMENLYSELRDKRAVQASTSNSDDNYNPAPPMQREVKCVYPDAERIETDQEQFLDAPHYYGREQHSPMDIKQHEMTYAAQIQQATYQQHQACPQDYGSEEYIPDPVVQEQDHSQEEADH
+>T_communis_352.35|HD|F8DCC00A_004430
+MTEVSPEAKIPTETPAMVELETQPTDNKTSATDPPPWADEPLLPDVAEVGTTKEEQAGENADTSEQIIDGSKDSTTQDTVQPHEQIAQQVQIDMPNDIQAVQQFNGQHPMHYAQMAPHGPQPYYHDPMIQAQYYHPHPQSGFMNQIPNPPGTKAKRKRASPHQLALLNQIFEYTFFPSTELRNAIGKELGMAPRTVQIWFQNRRQAWRSTKTVNADGTESPAPKSNDNERGGWEVLRSFQARRANGEIQEYEYMAIPSPSQVAAGATGTGSGGVGGAANGTPGRVVAGYNLVPYHPGMMQVALSSNDQFNSSMQQVPMPLPHTPRPVPYPQSYQPPPPTLPVTDDSDAPTDPAATAMAATAATNQHTDTSVETKDSTTTAEGDRGNVEQGATTLDGKPADLTTNTTPSNTVDNRGDGGGGRVGGGGIPDENLDPSLQDASTTTTTTTTTEEPLVEDASDSHATVEVSV
+>T_communis_352.35|HD|F8DCC00A_003036
+MDQYSGRSDEPTRRRRRTTTLELEILENEFAKCDKPSISERDRISDLISRTDVDGPGMNGREIQVWFQNKRQAIRRAQGAYPLCEPMSDRARARLANEQLFGIKLDSASHDQTTPPGSFTSPEDSGSSQVAGTPYTAPRFGLTTPKNSAVVRDRRAQLVLSDVGDGHAEVMFSPTPLKPSSPPRVPALITPIRTPLSRKIAARSASSPALLSLRTPSVSNNQGSAMKDATARTNNLATPTQSETTVPLSTLRSLKRPHSFVSTPDTHKSTEQPSHKKRQTISKTIVHHDIGRGKENIPPPTAFPAPRLPGTSTEPSSDSYGRDIRRIQSENLGHTWPSVPGSPLESMRTMPARVKPRAIQFPAKDDAGTSNVPQKKMSAEECALSLVSLAHAS
+>T_communis_352.35|HD|F8DCC00A_001740
+MEHMDPQIQDDPKVEKSAEQNDEPNATNELPTPEPNHDAATSVNVEDQGEHTAFLPTLHFTSGNDLSGIAQYEAQHTSDEPLRSGDGEHTEQAYDHWPSDTQTQIQNDGALQNVNHFGPGDSANQFAQGSEQNEYNQNASQAEQNQQHQSHEHQQQEQQQQQQNHLHIQEQHQQQQQQQQPPPLQHYQQHHPHFHQHPHHGGTPYDRPILGASYGTYDGSKPKRKRASPQQLTLLNNIFEMTYFPSSDLRLAIGKELDMVPRSVQIWFQNRRSLWRAKAGQILNENKQRKEELMATGLSEAEADAKVTSDRAEAAARQIADQRANDAVEYAINGNHGSLAYALHGANVNQNPSAMVDDGSITRDDEAGAWSVLQAFHQARTGVLVQQGHPPMPQRPEFQQEHQHQHQQPPPHHESLQQEGHEMHQQQQQQHQQSQLQSQEQLQQPQEQAV
+>T_communis_352.35|HD|F8DCC00A_002631
+MDESQQRFLEQVFNQTTKPTVAQKDQLASRLKVSSAVVRAWFSARRSKAKEDKLVEEQQTWAALENAHQVSPPEQAAVIHAQSVDHRAQSEASYASLARSLYAAAACMPTQNDSEYDHSMPPSPAFHYGGSQSGYSPTSTTAPSFGMSDSSVMMMRSESQYSNFTTPGEMADLSSFPFYQSTHLPTSHAAASSMIYDAPKTFMPIEAPSMRPRLQRTWTAPEPASARPIPRRTISNSFGTGGQENDLSEPPRIRRRPKLSPLGVGMARSRSSLGYDDSASPSTRRPAASKEFPYPITPVRRIASAVCVPTLSSMTTYSPGSSQSSNSPETIYQDRNTKDNNIMGLGVTAHLPPSPISPEHVGMLTQQSNMSSFKLQNVPIPEDSYTPPPTPLSALTTNAENILAGHYDMTSDWSVEPSKLTSGGIPNNMDFMYNDITTLNDIFTDQELAMHSY
+>T_communis_352.35|HD|F8DCC00A_001480
+MRLASKGKTAQERKRKSKRQKKRFGEDSQEQEYSLKKKAAMPQPSPAAQNDTPTSAFPPQNQQSKEFKVQSSLPSSSTMQQNDNTRQWNAMHYTRPEPIQTQRYDLGRPSYDRDMAEHGPLSGLMSRSERSSLTSPYMDASRSSSYSLSQQSPLSSTVPSMSGQWNVPYDMAQQTTQNSYHVPGSSSMSSSLPSAESSSRPHFSPPFPNRASLPLKSPIYTTAPQPSTELRGSGLNGHLRPYEPMQSPRTGVSYHHHDQSPPLAYRDTAYAGSFPRSGFLNHNAPAPTPSSDYSQHRPSLPTSISHHGSTPYDRQMPSAGFPSPAAASQTHSYAHPGHQVYQEFAMADASKPKRRRGNLPKSTTALLRTWLYDHTNHPYPSEDEKNQLAAQTGLTINQISNWFINARRRILQPSDMQKGLTHQGHTPQNSQAQVGSSQPRAQNITSQSLYVPHPRSPAHHASSVALQPPYER
+>T_communis_352.35|HD_locus|orf80243
+TRLFPSIHQIAHHIMLSFREKQLQHAYERFDQVCKTITSTIPDVTSEAISEAITTFAVTNHLVQRFIPPLSLYEQEIIELIGVCSRRVMDICCEGLEQSNMQSPIVADPDRSPGRSRVTILKSWYTQHLDYPYPSEADKAALVSSTGLSNRQVCMWFINARRRSHKGQKFVAEQVSDAVRAILS
+>T_betulina_315|HMG|FC6B0312_004909
+MPKELKPKATKRETGKRAKKDPDAPKRALSSYMLFAQDQRSVVQSEQPDITFGEVGKVLGAKWKALSPSDKKPYEDRAAEEKKKYEKAKAQYEVENPKEKAGKKAAPKKAAKKAPSSEEEEDEDDD
+>T_betulina_315|HMG|FC6B0312_002103
+MADPNNTYGRPAAQELSTSEEAKYKKKCRDLKRRISEIETGNESLVTKLARTKRFIQRVRLERAFLLEKLEDSNPKRVSGSDGSPSPPPSPSLEQYSLDPVNTLGESMGSPDPSRRSMSPPFSRQHTPTHETPSYGDMSAISHTSAARKGGAATGRASPVPQAKKVKVPKDPNAPKRPKNAFLLFCEIERDSVRAAAYTGNGETVDIARELGRVWAEMNDEARKPYRDMYEDDKQRYEKDMAAYEGAKSAKLAVKAVEAPVESTPGIPPPASTASPAPRVGGFTAVNRS
+>T_betulina_315|HMG|FC6B0312_001164
+MVAATDTSSASREQMVSFNDKYQIVLSSCRLLTEAQSALDRSIKDFVAVAETINPNLNVGYTSPVSSPSSGALSAAKDVHESSSVQNGQDSVAATTGGDVPNKKEKKTRDPDMPKRPASAFFLFQNAIRNSVKAAMPDESKGVDIQKAVSDKWKDLDEAGRKPYNDQHERETQEYEARITAYNREKGIAVKPKTAARNVSSKSAEKPTGNDQQGSDDDAAAASLVQDPATNTSAAATPKSSKKRRKSGTENIKKDKTPKKVDKVPEEKKKKRKKTDTNAN
+>T_betulina_315|HMG|FC6B0312_006079
+MFSNTVPKIMERTRIVAHFSAQNARAIRQYATPSGQAVSKTVKKAAPIPKPTARRSPSAHQRLSSYNIFIQKFAEERKKTGEKFLLQNATAAYKALPESEKSKLLEQLPELISQRKAIYDEFVSKLSPGEIAEENKIRAGLRKSRIALGKSVRNLAPIVDPNAPTRPLSAFFLYMKDARKDTDLTGMTIAEQSKSLGEKWKQLAEAEKERYIQEAKKDLVAYQEKKKEYYGSS
+>T_betulina_315|HMG|FC6B0312_004553
+MSSCLTRPAGRASDRVPQKHFKQNAFKANSCGIQSAAMFPAMTLEPPTPCQLLEPGMELGEEISNLNHSLQPDQYLSRDWSSFSTERLSYDSSAFSDSSSRAGFSSPPASPSRPSSVNSSPHRKGSSGRVKKADADFVKRPLNSFMLYRKDHQHCIPTNNHQSISRIIGDMWRKETAETKNRYDNLAKSERERHLLEHPGYKFQPRKRRECKVAKGSPKLLKKHCSIESDEVDHGTIQFKHVEGRPGTLQPSTRKKPQAQTMERTPIQHNSWVSHMPFPISGAYPPTESEASGSLDTPDQSGLYGGMVDYFSFSTVNDTLPAVSPLRDPPEWHGVQPISIRPIAAPMQRLPEMSWHQIDGGEYTLAQGPSTSEAESLRQAMSPSFLQWEEQQIHLHQQRRDLDDGRFGSSLTSQFYDDEALFQAIDLNHPGYFPDYNAEFQPSGEFAPNQMHSYWEMESIMYQ
+>T_betulina_315|HMG|FC6B0312_005188
+MAADTSLADDFVRLGLAEYIEKFIDEGFEDWTSIADITESDLAALGVKLGHRRTLFRQIATLRGHPKSEPLDDNVFNSDYGCYHTGEENPQTGSLNGSGSDCLTSPATHTLSIPSKRRYKRHPKADDNAPIRPASAYVLFANQVREQQKDCNLNFTQLARLVGDRWKNLGTAEKEAIEAQAGEAKKQYNAEVANYKKSREYQLYQDYLVEFKERALKDEKPEKLEPPKKSQKLNIHDSPDVAPSYPYQSVHRSVDQIPSLPPAGRQFFALPSLIREPPGVHPPGGILPPPAGYATEYASPAVARTPESFSRQTHLPYPLPIHPLSQSGEPRSYDARPRLPSIRTEHSKKDNCPPRSFADHRDNTRR
+>T_betulina_315|HMG_locus|FC6B0312_004634
+MKLCSSQIPRPLTGQSKSQERNSGAACELKIVLMEHQTRVNKTGRLVRVMNEVYTGPEPSENAYAIALGEHVHTRSPFDKPNNAFFQYRADPVVKSRHHNKPGLLQESQIVRDIAEEWKSLSDREKLPYERKASMAAYEHKRKLQLVRHSGSVPKATKTGRWNAQKAPYMQGKTQSFENRSSINVSPTLQSHQGDSWKQPTFQLGHTAPEAFSTSTCCELDTTLDFFGWSAFARNPLYDDYPWLSMGADEVDSFMESFEYLQKTGDPSIAFDYSCVL
+>T_betulina_315|HD|FC6B0312_000540
+MSHNNMVPLEYQQTYGGKAYGKDAPAIPSDRPNAAPEALANMSLNGHYPDSQHLDSTNFEEMAVPQDESPNSSNGSSPRPQLHGNRARALSLNTRGSHSRSTAHMTQQQINKKRQRATPEQLIVLEEAFVMNPSPNAKMRELISSQISMTERSVQIWFQNRRAKTKLLNKRGTFDDLGFRQAPYGLRPGLPARSFSIDQSPLEEYRFQGPSQQSASTEADFTRFSCRSLTIGTWRRVACTSNDLICYFSKTEPKFTHYINSGASGFKIEFAIASVAKFDLRYAQQNDLKELGRATITLSRAPLFFIETPAGGWKQCIDFTENVQATTVFAHAMVGPYQHLKRSFTDLASTYKETIGLMTFEDLETAPIPEQLAPPLAFEQNYPAIATRTSQSAGFTTPDGQALRRNPTNALFMDNSNMSSRGSHRRTRSRSAPMTVDFSQIVNQSNVGGMPGYSFGQQSIRIDPTYRPKTDLTPSSSTTGAYDYGDSLYTPTASGTPNYQEPWYMPSYANTPLLDAERSQLGSPMIPAPAQFDLSAGTLPPESFSPGYPLLAQGVGAATMPHLVNANHSMPELPRLDRVVEIPATGQSQFSSLQNLAQNQLSAALDPSQMDFSDMPPAQPHGGPDFLMIDRN
+>T_betulina_315|HD|FC6B0312_006262
+MNRSEPASQGNMETQIASSIHYTVNESNNLPPLSASVPANLLYDNKEEHSPGRSTYDDGGADHRVHNSTTTDPNAVGAFYIQSSVQVDKANYEETPSSSQIITSNESIESQPIQEARSSDTGVGSYHSDLPPGPDYRQDVTEYDSEEEGYTLSTSPAPADHSQANDNMTRPKPFSKKNLKRHRLSHSETRFLLNQFGQNPHPDAVQRCLLAKQINGLTARQIQVWFQNRRAKLKRMSAADADRMLSTRSYPDGYGPQGFTDRSTISQETTHPMSYAQSVEGVYTGHLYLDRHLYHSRSTPPVIVHHPSATPSFVGHESARTPQSAVYPSHYDRGMSHSPLPDRSIQRRFEIRSTYGGNQSQYPDARAVQGRESAPATVSTYDRNYGQSHHRPAQMQFNMQENIDRNYNLLPHYPSSAPPVSQYTSLTSSPFLQPEHGQYWSNREYQGHGSQDGRLRPFNHENACLLKDDGSRLNNSTYELQAVPGTYLSPSPSSRVTPSFGYNTMEQSATGDPEYSDVRHSSHDQYQSHTTDEYRTAVHQHDVHYYYGTEAHLKHENDELQEARRLFQQQKQGVDQGQECPRVPSTSYADAHGSMYAQTGHAQGQFDAIEIEEAAATPNDRAAYVSAQEESVPMNS
+>T_betulina_315|HD|FC6B0312_004330
+MDPYASRIDEPTRRRRRTTTLELEILEMEFAKCDKPSISERERISDRISRTDIHGPGMNGREIQVWFQNKRQAIRRAQGAYPNCEPLSDRAKARLANEQLFGIKLGPPRNEQTTPPNSFTSPDDSGSSGKPAYSSFTISQYGMPTPPISSATRERRAQLVLSDLGDGHAEVMFSPTPLKPSSPPRVPVLITPIRTPLSRKIAARSASSPALFGTSVARLNKMTGSALMDSTNTSISSFTTPTAPSSANNLGALKSLKRPHSFVADARTSSKHNREEVALSSSKKRTPASKSASHHNLGRGKENVPPILPALTTPSTPAATNRGSHERSRSSVMGPLETGYGQSARKAHLEHSSLEGVAKPSVSAHVRHAQSEESGVSRPGQTGHKQKKMSAEECALSLVSLAHGM
+>T_betulina_315|HD|FC6B0312_000920
+MSESYGKQSSTDGSSMATDISNTSPPPPWTVERKSRDRIHLPQPPYRLGNQGLLPPIHDSLTAALNPLPQQTPRSEVHQQDEDKPSMDPAGALGANAQALSGQAHPQQGTATAQYPTGPNHGQQQQQQQQQPQYYQDAIPQPPQPSLRMQHPQSSYLGQVPNPPGMKAKRKRASPQQIALLNQIFEYTFFPSTELRNAIGKELNMAPRTVQIWFQNRRQSWRAQKNRDGVGNPLKSNDHERGGWEVLRSFQSKRATGEIQEYDYLSCSASGSSMPSMQQDPRGQSDVFSVAIASNFPQPYPPAAVSSNTYFNAQMSDPSVPMPHAPHNSTHQQTQTMTSQPHQHHQHQQQQQQQHEQYHHHQHPQQHQHQYQQHQHQQTHTTSFT
+>T_betulina_315|HD|FC6B0312_004101
+MAIIVDEYQRRTLEQLFSQTSKPSAPQREAVAEALNLPVRAVQTWFAERRTKAKADKRIEELQTRTALENAHHISSREASAIPTNQNTNHKTQSDASYASLARSLAAAAACMPQPDALYDRSYPSSPVFHLNMGFPMYSPTNSSFDTSASMVRSDSQYSNFSATTNGDLDQPDYSFFPDHSGYMPTPATNCDTMVYDHLEMRPSTNEMHRSRPRLQRTWTAPESLQQRPLPRRTIVSTSPGDVPQATEPVLIRRRPKLSPLGIGMARSRSSLGYEQSEYPYSVRRATALSDFPCPMTPVRRIASAAAVPTMATMRSFSTTSQDSTGTKGDSGLASSIATQDCLASNIQFPPSPISPEHNVHGTPSSAYKITSFELPHLPIGEDSFTPPPTPLSALTGSAENALAGGYEDTWTSDFSKLSGLDLTNNDLIIADLFHDQEMGVVSF
+>T_betulina_315|HD|FC6B0312_001235
+MDHMDPQLQSVGVQQQHQQQHQHQHDQDTQQQSTNEIPEQRPQEIQVKAAEDAEEQHEHPAFHPSLHYTSGNDLSSIANYNPQHAAGGPIRSGEGDPTGQSFDHWPADTQSQHVQEDVSLQNANQFAQVEQNNQFVPAPDHQYVHDGHQQQQQHHQHQHQHGGSPYERQTPGASYGTYDGSKPKRKRASPQQLTLLNNIFEMTYFPSSDLRLAIGKELDMIPRSVQIWFQNRRSLWRSKAGQILSENKQRKDELLASGMTEAQADAKVTADRAEAAARQIADQRANDAVEYAINGSNGSLAYALHGANTNTVAPGSVDDGSITRDDEAGAWSVLQAFHQARTGVLVQQGHAHPNAHMHMQHQHQHQQHHPHQPQHHLQQQHQHQLPLPLPQQSQAEPMQGQPMHESQQEQQQQPSPGPGTASVERPQEPQLPSGV
+>T_betulina_315|HD|FC6B0312_002074
+MPRAQYESASVGTTQQDTPVAPSSENLRRWDQLRYSMPDQSAPVKRVDVNQPYSQYDRETSDHASFSSVGMGRSDRSSMTSSSNYNSGDSRSNSYSASQRSSVPSMNGQWGMPSYEQQASAPASMPMPMSNANTYQYPLCSPSMIPATARPQFSPPFPHRQSLPTHGGMQKHPEYSSIQHQPLIIDSRTPNLRHFPEPMQSPRSLVPYSEQAHRQPQQSNSPPTPYSETSPFPMGSYQGPSYIAQSMPPYVYPNRRNSVSNLLQPHSTPYDRQLPSYMSQPTYAGPILETAGLNSSMQHKPKRRRGNLPKSTTTLLRSWLYDHTNHPYPSENEKNRLAAQTGLTINQISNWFINARRRILQPSDMKPATGSLQPSSHQEPKAYAHGSTARSSSGESEGIVIQPPYHSR
+>T_deformans_A2|HMG|F891DC7E_000191
+MPKDTKPRTVKRDVTKRAKKDPDAPKRALSSYMLFAQDQRSVVQQEHPNIAFGEVGKVLGQKWKALTDSEKKPYEDRAAEEKKKYEKAKAQYEVENPKAGKTKGAAKKTAKKSKSDDDESA
+>T_deformans_A2|HMG|F891DC7E_002483
+MASNSTHSSQTNAERFADFHRKYQIVLSSCRLLTEAQSALDRSITDFVSIAQGLDPKVHAQYPILPNNSASPLQPATEVSQSQLKGKSGDSSDTVSKNSTASDAPIKKQKKVRDPDLPKRPMSAFFLFQNAVRNSVKSAMPEESKGTDIQKAISEKWRDLDDDSRQPYNERYENDVRDYEAKLATYKQDHGIPRSAKDIVAKGDAITEPKPDFVKKTDQVTNDDDAAAASIASKAAAASKSATATPKDSKKRARTNEKAKSPKKVEKPTEEKKDKKKRKKSLSTTG
+>T_deformans_A2|HMG|F891DC7E_002753
+MADPNNAYGQSTTTELSISEETKYRKKCRDLKRRINEVEASNEGLVTKLARTKRFIRRARLERAFLLERLEAQAPKDSQGSDGSPTPPASPSLESYSLDAMQGTFDNAQSPDPLRRSGSPGDSGHHTPTHDYSIPSAISNAASAHIANQKERKGSPAPGANNSTKKIKPPKDPNAPKRPKNAFLLFCEIERDSVRAAADPGTGETVDIARELGRVWAEMNDDARKPYRDMYEEDKVRYEKEMSTYEKPKNLATPIKPEDHTEKVEPEIQTPSNPSPRPKVGGFTAVNRA
+>T_deformans_A2|HMG_locus|F891DC7E_001655
+MSFGELRNYSTKDALTRLNSSEGKAYFIPDGYEPILIAQSQLTDEVRGEIRRTTAYLRLPVALNECRLPSYIVTTRKTARDQILRLDTQIPVKNPPRPPNAFILYRKSKQAEISAQNEGISNNDVSRIIGNMWKGECDLIRQEFQRCAQEVKFQHKLQYPDYRYKPRKAITKSVPINRAAVASNASSRTHVSRDIPSHLGMLAGCLLHPEHRNGKDAHLYDLGFTNNSLSH
+>T_deformans_A2|HMG|F891DC7E_000442
+MNHDLSFSHVPLSDRQFIGDSPTPFGYVALESNNLANFNMMHESDRSTLSEFRALSPVARSTIDSSIVGGTTQQLLSTGQPSATLSLKTLPQDPPSRTTTPRARAKAKKVLTDVNFVKRPLNSFMLYRKDNQHNIPTNNHQSISRIIGDMWRKETAETKNFYDVRAKEEREKHLLQHPGYKFQPKKKKKETKASRPEPKSRQSPAGIHSHEPTIVPASYDQQDGNLEPPEQTEQPFNFSTLLDENFSTVLDEPQQSLQSRTAACTTWSSYQHEGEHYSEPGNQHELPLHYAHYTGQVQYMDTQVPTNYQEPHGSGAMLKDPQDWNILSNQCHYAASAALYPHQAHANQPGAEAQWPESYNSLDYNMPATFSEWENMRMAEMPMLQQGLETEYPYHHEQDMGFPSHDAYDEQDFMPNHMKHNDMLLFAPTELKGSWEVEHVESQLYQF
+>T_deformans_A2|HMG|F891DC7E_004878
+MRSNLADDFARLGLSEYLTRFIEEGFTDWSSIADITESDLAALGVKLGHRRTLYREIATLRGYPQSERLEDIPKPVPGSLPSSVNEENRSPCDVSASGSDGQPSPASYVDAVPQKRRYKRHPKPDDNAPTRPPSAYVLFANVIREEQKDTNLSFTQLARLVGERWKNLAAAEKETIESQAAEVKRRYTAEVGVYKKSPEYHQYQAYLREFKQRVLKDERPEKLEPPRKAMRTMNPHSPAAHTMVLPNSRDHGDHPSTRNEHEHDPRSTRQGSGAPFTIPSILQDGPRRGDERVLPSLDYVYNFGTQDQYNSLNEKACLPVYAARPILPRPEFPGPMDNILPTAMYNKGPQWNEEVRRRSLPTERPSSTNECRPSAVPCGQGLQNDSYVNR
+>T_deformans_A2|HMG|F891DC7E_003603
+MTALRLFARHETQPSIALVRFATTEAVKRPRKNAVAPPTPKLKAMKTPNNSAVTAYRLFIQKFAEEQKNAGEKWLLQNAADAYKKLPDSEKAKLVEQIPELIAQRKAIYEEFVSKLSPSEILAENQKRTALRKERIAAGKSVKNLAPILDKNAPTRPGGPYILWSKEARQAPEFKDQTLTEQAKALGEKWKALAENEKAEWHEKAKQLRSEYEQKKSEYYGSS
+>T_deformans_A2|HD|F891DC7E_006258
+MQSYDQGSAALCPNNDYRSSAGHNSNNEDEFNNLYFGNTSQAAAHELEIGDHVQMQVESSESSTSSSPQRYNTGNRLRSLSLNTKNMHYRSTAHVTQQQINKKRQRATPEQLNVLEDAFACNPSPNARMRENISNQINMTERSVQIWFQNRRAKIKLLHRKSGPEEIIDQATSTIRPGLPERSYSIDTGLYQGHGSTFMEDTQEYSTGTVQDTRSSFAYSARTCYKAQLSFFNYSSGSTGFKIEFPLKSIINIDLSYIPTPNTKEMGRAIVSLSSSPIFFMELSSSGVWKQCTDFTENQQGTNVLLHAIVGPYQHLKQSLARLTVIHNDIQNRITIEDIHNEGISQESMISSVEPSEQYLATSNSQHNDSRPVMLPFTPETLRESARGSHRRTRSRSAPIAVDFSWLNHGHSIDTPGYISGQNHPSMLARQTYGGIPTPVSQAMSLDCSDEFYSPSVPTPSCYADTWYASSYANTPLLDTSCSRLGSPMLAGGAHFDIPLVTSQVDPYMNFTEMRNTTGTIIHSLPEHTRSVNLSMPDLPHLDSVPEIPVANQEQYSLAESFQALISPPCMAPIDYLQDSGQLPPG
+>T_deformans_A2|HD|F891DC7E_006106
+MRLRSLSLRLAEQKAADEKAGKSGPATSDPPCESRQVSTPMYYRVDGADNQDEMNTSASTNCYYGDHDQIQVQQSGCTSDNMHGSYLYHENVEVESYLCQQQAANDGSQACEQAGDEVKHNAGPECAYTGLDQQFAATQDTTQAYAGKDGIFSTEGCRNPPYQDYMGLDSAEEDLNGSPTSTDHEEDDASRSMERDIPKPINKKNLKRHRLSHSETRFLLNQFGQNPHPDAAQRVLLSKQINGLSVRQIQVWFQNRRAKLKRMSASDADRMLSTRSYPDGYGPQGFENQAKRQESPQDASPCLTKADISFPSQECSEAHVLQPKTDSASLSQYPIRNISSVYRRPQLRSPLTSQPSSSYSAQSRQLGFVRDGTNSPYPEAATSRGAPSPQGSPAQYDATTYGLPLRASAVQSSARFVYGRPYPSPHAMYGPRSVQTNNSFVNSPEDTPVVQSPYRPYSMADQRGYYTPSLLATPTYQDTGYRQVFNVAEQVSDYHAPGQDGPYIMTTAQPHPLGYNQHVPANMDNLYSDVRAIRSHQMTSSSPEDNYHQAPPMQREVKCAYPDDENTRSIHEDYVDTPQYYGRDQNDCMESKQHEMTYAAHLQQATFHQRQVCQQDYNSDDYIPDPVVQERDQAQETA
+>T_deformans_A2|HD|F891DC7E_001028
+MAEVRLEVPAQTDSTTIVEAEEEATDKMLTATDAPPWADEPLLPNVTAPDATRDDQAPDMANEEGKEPDTTKSTMEEVTEQTSNQTDGHDQVSLPNDMQAVQQFNGQYPIHYPHMTPHGPQPYYHDPMMQAQYHHHHLHPHSGFLNQMPNPPGTKAKRKRASPHQLALLNQIFEYTFFPSTELRNAIGKELGMAPRTVQIWFQNRRQAWRSTKTINADGTESATPKSNDNERGGWEVLRSFQARRANGEIQEYEYMAIPSPSQAGGGANGEGARVVGGYSLVPYHPGMMQVALSSNDQFNSSMQQVPMPLPHTPRPMPIGYPGPPAPAPTTTATTTTTMTTTKTMAGQSEGDVVPVAVQGAAHDQAETGTAPEVDGPGLPPSHLDPSLQDAPPEDPSVEPDGTPVDPGRAT
+>T_deformans_A2|HD|F891DC7E_002419
+MDPQLQEDLKVEKPAEQSEAPDATNELPSPEPDIETATPVQVDEQGEHAAFLPTLQFTSGNDLSSIAHYDAQQSGEESLTTGNEEPTSQTFDHWPTDTQTQIQNDGPLQEVNHFVQGDSANQFAQASDQNEYNQNVSQDQQQQQQHLQQQHQFQHQQQQQQQQHYPQQHHPHFHQHPHHHGGTPYDRPILGASYGTYDGSKPKRKRASPQQLTLLNNIFEMTYFPSSDLRLAIGKELDMVPRSVQIWFQNRRSLWRAKAGQILNENKQRKEELMATGLTDAEADAKVTSDRADAAARQIADQRANDAVEYAINGNNGSLAYALHGANMNQNPSGLIDDGSVTRDDEAGAWSVLQAFHQARTGVLVQQGHHPMPQRPESQQQQHQQPPQHQQGQQASQELQAEQPQQQEQHV
+>T_deformans_A2|HD|F891DC7E_004077
+MSGLMDQYSGRMDEPTRRRRRTTTLELEILENEFAKCDKPSISERDRISDLINRTDVDGPGMNGREIQVWFQNKRQAIRRAQGAYPLCEPMSERAKSRLSNEQLFGIKLDSPRHDQKTPPGSFTSPEDSSSSQSASTPYGAPHYGLTTPKNSANVRDRRARLVLSDVGDGHAELMFSPTPLKPSSPPRVPALITPIRTPLSRKIAARSASSPALLALRTPNVRDTQSSAMKDTTNVINNWASPSKTGLAVPLSTLRSLKRPHSFVTTPEVHKIKEAQSQKKRQTSSKAMVQRDIGRGKENIPPPASFPTPRILGSSTDSSGDSYGREIRRIQSENLGHTWPSMPVSSPSESMRTMPPRSSMKVTQTPAKDSLNKAEMPQKKMSAEECALSLVSLAHGS
+>T_deformans_A2|HD|F891DC7E_003686
+MDESQQRLLEQLFCQTPKPTVAQKEQIAAKLNVSNAVIRAWFSVRRSKAKEDKLVEEQQAWAALENAHQVCPLEQLAISQAQPVDHRAQSEASYASLARSLYAAAACMPTTENDYEPSMPPSPAFHYSGSQSAYSPTSATAPSFGMSDSSMMMMRSDSQYSNFTTPGEMADLSSFPFYQSSYLPTPQAAANSMIYDAPQTYMPVEAPSIRPRLQRTWTAPEQAPARPLSRRTVSTSYGSFGTENDHSEPIRIRRRPKLSPLGIGMSRSRSSLGYEDSGSPSARRPAASKDFPYPITPVRRIASAVAVPTLSTIPTYSPTSSQSGNSPESVYQDRHGSVGEISAANPHFPPSPISPEHVGVLIQQGNMSSFKLQGVPIPENSYTPPATPLSALTTNSENILAGHYDMAGDWNVEASKLGNTNDMDLLYNDITTLNDIFTDQELALHSY
+>T_deformans_A2|HD|F891DC7E_002798
+MPQPSSPSQTDTPTSVYTLQSQQPKDLKSRSSAPSSSAMHNDNSRNWNSIHQYSRPEPIQTQRYDLGRPQYDRDLADHSPSSSLVSRSDRTSLTSPYMNASRSSSYSISQPSPLSNTIPPMSNQWNAPYDLSQHSTQNSYQMTGPSSLSSSVPSGIGGSSGSSSAIRPHFSPPFPNRASLPLKSPIYTTAPQPPVESRTSSMHNGLRPYEPLQSPRIGLPYHHEEAPPMNYRDNTYGGTFSANGYLNHNAPAATSPIEYSQRRPSLPTAAQHHATPYDRQVSTGGFHPPVPSSQSHSYSQPGQQVYQEYTMGDASKPKRRRGNLPKSTTALLRTWLYDHTNHPYPSEDEKNQLAAQTGLMINQISNWFINARRRILQPSDMQKGLMQQSHASQNGSVQSTASQPRIHNAASQGPYVSQPRSPSQHASSVVLQPPYER
+>T_deformans_A2|HD_locus|orf51685
+PSTLDTRLSNKTFQQYTDLRIRIMLLSRVSELRHAYERVDDIRRSLCNTSHIVIAEFMETLSSIDDVIQRLLPLESQTEQDLIQVIGISSRHVMDICSDRLQQQGMATVTISNSGRLKSQNRISILKSWYTSHLEYPYPSETEKMSLASSSGLTIRQVCMWFINARRRSHKGQKFVAEQVSDAVRRIIS
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_locus_expression.tsv b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_locus_expression.tsv
new file mode 100644
index 00000000..d7e0505b
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_locus_expression.tsv
@@ -0,0 +1,3 @@
+name	length	mean_depth	percentile_among_genes	genes_with_depth_ge_1
+F003EF48_006292	645	1388.40	0.791	0.999
+Plact_12-1054_matPi_region	454	1431.73	0.798	0.999
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_spliced.tsv b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_spliced.tsv
new file mode 100644
index 00000000..c9561b46
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_spliced.tsv
@@ -0,0 +1 @@
+Plact_12-1054_matPi_region	reads_overlapping=5477	spliced_reads=157
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_strand_check.txt b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_strand_check.txt
new file mode 100644
index 00000000..81986f5f
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Plact_12-1054_strand_check.txt
@@ -0,0 +1,4 @@
+genes used 100; read1 same-strand 27602, opposite 575693; share same 0.046; library: reverse-stranded
+HMG_gene_F003EF48_006292	read1_forward 3039	read1_reverse 246	implied_strand -
+HD_ORF	read1_forward 2748	read1_reverse 354	implied_strand -
+HD_flank_upstream	read1_forward 1341	read1_reverse 478	implied_strand -
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_locus_expression.tsv b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_locus_expression.tsv
new file mode 100644
index 00000000..a61bd091
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_locus_expression.tsv
@@ -0,0 +1,3 @@
+name	length	mean_depth	percentile_among_genes	genes_with_depth_ge_1
+F891DC7E_001655	696	663.57	0.826	0.986
+Tdef_A2_matPi_region	568	215.18	0.533	0.986
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_spliced.tsv b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_spliced.tsv
new file mode 100644
index 00000000..9ac8a2d5
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_Tdef_A2_spliced.tsv
@@ -0,0 +1 @@
+Tdef_A2_matPi_region	reads_overlapping=1676	spliced_reads=66
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_locus_transcripts.tsv b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_locus_transcripts.tsv
new file mode 100644
index 00000000..f1c06c27
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/rnaseq_locus_transcripts.tsv
@@ -0,0 +1,7 @@
+transcript	strand	exons	span	tx_len	longest_orf_aa	pfam_hits(aa,frame,domain,evalue)
+ST_Tdef_A2.1155.1	-	5	50131-52842	2505	350	[(189, -1, 'Homeodomain', '3.3e-09')]
+ST_Tdef_A2.1155.2	-	4	50131-52842	2558	350	[(189, -1, 'Homeodomain', '3.3e-09')]
+ST_Plact_12-1054.2348.1	-	7	34271-40155	5648	462	[(151, 3, 'Homeodomain', '4.8e-10')]
+ST_Plact_12-1054.2348.2	-	3	34271-38767	4414	462	[(151, 2, 'Homeodomain', '3.6e-10')]
+ST_Plact_12-1054.2348.3	-	5	34271-38767	4318	462	[(135, 2, 'Homeodomain', '3.3e-10')]
+ST_Plact_12-1054.2349.1	+	4	38896-39637	627	208	none
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/taphrina_deformans_scan_genes.tsv b/docs/notes/2026-11-14_mat-discovery-tables/taphrina_deformans_scan_genes.tsv
new file mode 100644
index 00000000..94e68d53
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/taphrina_deformans_scan_genes.tsv
@@ -0,0 +1,57 @@
+genome	gene	contig	index	strand	domain	best_control	control_evalue	control_identity
+Taphrina_deformans_A2	F891DC7E_000191	RHGF01000001.1	190	-	HMG_box,HMG_box_2			
+Taphrina_deformans_A2	F891DC7E_002483	RHGF01000009.1	192	+	HMG_box,HMG_box_2			
+Taphrina_deformans_A2	F891DC7E_002753	RHGF01000011.1	70	-	HMG_box,HMG_box_2			
+Taphrina_deformans_A2	F891DC7E_001655	RHGF01000006.1	38	+	HMG_box,HMG_box_2	matMc	4.06e-172	100
+Taphrina_deformans_A2	F891DC7E_000442	RHGF01000002.1	82	+	HMG_box			
+Taphrina_deformans_A2	F891DC7E_004878	RHGF01000025.1	43	+	HMG_box,HMG_box_2			
+Taphrina_deformans_A2	F891DC7E_003603	RHGF01000016.1	7	+	HMG_box,HMG_box_2			
+Taphrina_deformans_A2	F891DC7E_006258	RHGF01000048.1	3	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_006106	RHGF01000042.1	8	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_001028	RHGF01000003.1	313	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_002419	RHGF01000009.1	128	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_004077	RHGF01000019.1	6	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_003686	RHGF01000016.1	90	-	Homeodomain			
+Taphrina_deformans_A2	F891DC7E_002798	RHGF01000011.1	115	+	Homeodomain	matPi	8.15e-18	49.2
+Taphrina_deformans_CBS_355.35	F7E28AAD_005932	RHGG01000034.1	12	+	HMG_box,HMG_box_2			
+Taphrina_deformans_CBS_355.35	F7E28AAD_002651	RHGG01000009.1	190	+	HMG_box,HMG_box_2			
+Taphrina_deformans_CBS_355.35	F7E28AAD_000779	RHGG01000002.1	219	-	HMG_box,HMG_box_2			
+Taphrina_deformans_CBS_355.35	F7E28AAD_006266	RHGG01000044.1	1	+	HMG_box,HMG_box_2	matMc	4.06e-172	100
+Taphrina_deformans_CBS_355.35	F7E28AAD_003144	RHGG01000012.1	93	-	HMG_box			
+Taphrina_deformans_CBS_355.35	F7E28AAD_001919	RHGG01000006.1	76	-	HMG_box,HMG_box_2			
+Taphrina_deformans_CBS_355.35	F7E28AAD_004165	RHGG01000018.1	7	+	HMG_box,HMG_box_2			
+Taphrina_deformans_CBS_355.35	F7E28AAD_000163	RHGG01000001.1	162	+	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_006139	RHGG01000038.1	8	-	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_000545	RHGG01000001.1	544	-	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_002590	RHGG01000009.1	129	-	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_004149	RHGG01000017.1	145	+	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_004248	RHGG01000018.1	90	-	Homeodomain			
+Taphrina_deformans_CBS_355.35	F7E28AAD_000825	RHGG01000002.1	265	+	Homeodomain	matPi	8.15e-18	49.2
+Taphrina_deformans_JCM22205	FA538064_006054	DF818788.1	15	-	HMG_box,HMG_box_2			
+Taphrina_deformans_JCM22205	FA538064_003556	DF818725.1	0	-	HMG_box,HMG_box_2			
+Taphrina_deformans_JCM22205	FA538064_000338	DF818697.1	139	+	HMG_box,HMG_box_2			
+Taphrina_deformans_JCM22205	FA538064_005961	DF818782.1	12	-	HMG_box,HMG_box_2	matMc	4.06e-172	100
+Taphrina_deformans_JCM22205	FA538064_003636	DF818726.1	0	+	HMG_box			
+Taphrina_deformans_JCM22205	FA538064_002732	DF818716.1	25	+	HMG_box,HMG_box_2			
+Taphrina_deformans_JCM22205	FA538064_000552	DF818698.1	143	-	HMG_box,HMG_box_2			
+Taphrina_deformans_JCM22205	FA538064_002479	DF818714.1	1	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_005126	DF818751.1	30	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_002043	DF818710.1	14	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_003617	DF818725.1	61	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_000997	DF818701.1	133	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_000469	DF818698.1	60	+	Homeodomain			
+Taphrina_deformans_JCM22205	FA538064_000294	DF818697.1	95	-	Homeodomain	matPi	6.02e-18	49.2
+Taphrina_deformans_PYCC_5710	F282FB4B_002506	HE965072.1	25	+	HMG_box,HMG_box_2			
+Taphrina_deformans_PYCC_5710	F282FB4B_003075	HE965085.1	26	+	HMG_box,HMG_box_2			
+Taphrina_deformans_PYCC_5710	F282FB4B_001289	HE965048.1	37	-	HMG_box,HMG_box_2			
+Taphrina_deformans_PYCC_5710	F282FB4B_005446	HE965192.1	4	-	HMG_box,HMG_box_2	matMc	4.06e-172	100
+Taphrina_deformans_PYCC_5710	F282FB4B_003830	HE965109.1	4	-	HMG_box			
+Taphrina_deformans_PYCC_5710	F282FB4B_002726	HE965077.1	10	-	HMG_box,HMG_box_2			
+Taphrina_deformans_PYCC_5710	F282FB4B_004255	HE965126.1	7	+	HMG_box,HMG_box_2			
+Taphrina_deformans_PYCC_5710	F282FB4B_000789	HE965041.1	1	+	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_003375	HE965094.1	23	+	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_000966	HE965043.1	35	-	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_004400	HE965132.1	8	-	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_004233	HE965125.1	7	-	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_001508	HE965052.1	23	+	Homeodomain			
+Taphrina_deformans_PYCC_5710	F282FB4B_000488	HE965036.1	85	-	Homeodomain	matPi	8.15e-18	49.2
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/unscanned_assembly_stats.tsv b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_assembly_stats.tsv
new file mode 100644
index 00000000..502ab556
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_assembly_stats.tsv
@@ -0,0 +1,58 @@
+phylum	species	asmid	Mb	contigs	N50
+Microsporidia	Mitosporidium daphniae	GCA_052576055.1_ASM5257605v1	5.8	10	864371
+Microsporidia	Spraguea lophii	GCA_001887945.1_ASM188794v1	5.6	143	99316
+Microsporidia	Spraguea lophii	GCA_001888035.1_ASM188803v1	5.6	158	98687
+Microsporidia	Spraguea lophii	GCA_001887975.1_ASM188797v1	5.6	158	97321
+Chytridiomycota	Globomyces pollinis-pini	GCA_025399215.1_Glopol1	21.4	983	51103
+Chytridiomycota	Globomyces sp. JEL0801	GCA_027595885.1_ASM2759588v1	15.3	800	45731
+Microsporidia	Vairimorpha sp. gmOTU17 SAN00002588	GCA_986194575.1_ilOchDupl1.microsporidian_1.1	0.5	12	41188
+Microsporidia	Mitosporidium daphniae	GCF_000760515.2_UGP1.1	5.3	273	34874
+(blank)	Pleurotus ostreatus-Saccharomyces cerevisiae fusant	GCA_024196135.1_ASM2419613v1	49.9	3160	26816
+Microsporidia	Metchnikovella incurvata	GCA_003600395.1_ASM360039v1	4.6	422	17624
+Microsporidia	Tubulinosema ratisbonensis	GCA_004000155.1_ASM400015v1	7.3	781	12578
+Sanchytriomycota	Amoeboradix gromovi	GCA_018985225.1_ASM1898522v1	4.2	549	10152
+Microsporidia	Vairimorpha ceranae BRL01	GCF_000182985.1_ASM18298v1	4.3	639	9467
+Microsporidia	Spraguea lophii	GCA_011076965.1_ASM1107696v1	5.5	847	9221
+Microsporidia	Spraguea lophii	GCA_011074935.1_ASM1107493v1	5.5	851	9066
+Sanchytriomycota	Sanchytrium tribonematis	GCA_018985235.1_ASM1898523v1	6.3	897	8976
+Microsporidia	Spraguea lophii	GCA_011076975.1_ASM1107697v1	5.6	864	8904
+Microsporidia	Spraguea lophii	GCA_011074965.1_ASM1107496v1	5.4	840	8888
+Microsporidia	Spraguea lophii	GCA_011074945.1_ASM1107494v1	5.4	844	8873
+Microsporidia	Spraguea lophii	GCA_011076955.1_ASM1107695v1	5.5	864	8853
+Microsporidia	Spraguea lophii	GCA_011074975.1_ASM1107497v1	5.5	863	8632
+Microsporidia	Pseudoloma neurophilia	GCA_001432165.1_ASM143216v1	4.3	654	8603
+(blank)	fungal sp.	GCA_023347065.1_ASM2334706v1	2.8	386	7866
+Glomeromycota	Gigaspora margarita	GCA_910592245.1_Gigaspora_margarita_120-4_pot_B_10_14	477.1	82485	7226
+Microsporidia	Spraguea lophii 42_110	GCA_000430065.1_Sprlop1.0	4.3	746	7226
+Microsporidia	Microsporidia sp. MB	GCA_050230985.1_KEMRI_ICIPE_ABN394	5.2	938	6673
+Microsporidia	Microsporidia sp. MB	GCA_049634765.1_KEMRI_ICIPE_Tes0708gam	6.1	1135	6204
+Microsporidia	Microsporidia sp. MB	GCA_032191455.1_ICIPE_MspMB_1.0	5.1	979	6059
+Chytridiomycota	Siphonaria sp. JEL0065	GCA_027596065.1_ASM2759606v1	3.7	681	6045
+Kickxellomycota	Coemansia sp. RSA 2524	GCA_027578135.1_UCR_CoemRSA2524_1.0	8.3	1593	5777
+Kickxellomycota	Coemansia sp. RSA 551	GCA_027577555.1_UCR_CoemRSA551_1.0	8.6	1625	5634
+Microsporidia	Microsporidia sp. MB	GCA_049634785.1_KEMRI_ICIPE_Tes094gam	5.7	1198	5422
+Kickxellomycota	Coemansia sp. RSA 921	GCA_027577315.1_UCR_CoemRSA921_1.0	8.5	1702	5237
+Microsporidia	Hepatospora eriocheir	GCA_002087875.1_ASM208787v1	3.2	691	5236
+Kickxellomycota	Coemansia sp. RSA 1287	GCA_027578735.1_UCR_CoemRSA1287_1.0	6.5	1347	5218
+Kickxellomycota	Coemansia aciculifera	GCA_027579955.1_UCR_CoacBCRC34181_1.0	9.0	1888	5126
+Kickxellomycota	Coemansia sp. RSA 475	GCA_027577635.1_UCR_CoemRSA475_1.0	8.8	1831	4882
+Kickxellomycota	Coemansia sp. RSA 530	GCA_027577795.1_UCR_CoemRSA530_1.0	8.1	1768	4577
+Kickxellomycota	Coemansia sp. RSA 1937	GCA_027578435.1_UCR_CoemRSA1937_1.0	7.5	1622	4561
+Kickxellomycota	Coemansia sp. RSA 788	GCA_027577475.1_UCR_CoemRSA788_1.0	8.4	1855	4510
+Microsporidia	Nosema rusticus	GCA_046563365.1_FR26_Nr_1	6.2	1452	4479
+Kickxellomycota	Coemansia sp. RSA 2052	GCA_027578455.1_UCR_CoemRSA2052_1.0	8.9	2097	4335
+Entomophthoromycota	Massospora cicadina	GCA_006912075.1_UMICH_Mcic_1	584.4	144784	4322
+Kickxellomycota	Coemansia sp. RSA 1836	GCA_027578595.1_UCR_CoemRSA1836_1.0	7.3	1795	4111
+Kickxellomycota	Coemansia sp. RSA 1694	GCA_027578655.1_UCR_CoemRSA1694_1.0	8.4	2055	3986
+Microsporidia	Dictyocoela roeselum	GCA_016255985.1_ASM1625598v1	1.4	383	3736
+Kickxellomycota	Coemansia sp. RSA 25	GCA_027478835.1_UCR_CoemRSA25_1.0	6.6	1749	3704
+Microsporidia	Areospora rohanae	GCA_056822185.1_ASM5682218v1	5.3	1428	3681
+Microsporidia	Anncaliia algerae	GCA_000313815.1_ASM31381v1	7.5	2245	3384
+Microsporidia	Alternosema astaquatica	GCA_030386735.1_Fv_Alternosema1	1.1	319	3337
+Microsporidia	Agmasoma carcini nom. nud.	GCA_029231695.1_Cm_Agmasoma_carcini_1	1.0	305	3167
+Entomophthoromycota	Massospora platypediae	GCA_006912095.1_Mplat_NP02_megahit	750.6	241057	3108
+Entomophthoromycota	Entomophthora muscae	GCA_900018355.1_Em_KVL-14-118	7.8	2615	2895
+Microsporidia	Hamiltosporidium tvaerminnensis	GCA_000180835.1_ASM18083v1	0.7	278	2517
+Neocallimastigomycota	Neocallimastix californiae	GCA_975848665.1_SNW_BASALT_bin1877_ASM_v1	0.3	101	2403
+Chytridiomycota	Chytridiomycetes sp.	GCA_023347045.1_ASM2334704v1	0.7	279	2396
+Chytridiomycota	Batrachochytrium dendrobatidis	GCA_982397245.1_T46-F	0	0	0
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/unscanned_by_locustag.tsv b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_by_locustag.tsv
new file mode 100644
index 00000000..4b208cbf
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_by_locustag.tsv
@@ -0,0 +1,62 @@
+phylum	species	locustag	annotation_folder	status
+Microsporidia	Agmasoma carcini nom. nud.	FAA64C3D		no_gene_models
+Microsporidia	Alternosema astaquatica	FE4DCDFD		no_gene_models
+Aphelidiomycota	Amoeboaphelidium protococcarum	FB2D10C7		no_gene_models
+Aphelidiomycota	Amoeboaphelidium protococcarum	F29201A4		no_gene_models
+Sanchytriomycota	Amoeboradix gromovi	F8E7AE41		no_gene_models
+Microsporidia	Anncaliia algerae	F5BF1495		no_gene_models
+Microsporidia	Areospora rohanae	F3962479		no_gene_models
+Chytridiomycota	Batrachochytrium dendrobatidis	F70639FB		no_gene_models
+Chytridiomycota	Chytridiomycetes sp.	FCAB5F5E		no_gene_models
+Kickxellomycota	Coemansia aciculifera	FF2BE7A9		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 1287	F4D8CC32		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 1694	FE598530		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 1836	FA6F2E5A		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 1937	F4069752		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 2052	F947FBFB		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 25	FF985C3D		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 2524	FBDE034A		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 475	FB00F276		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 530	FECE5CD9		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 551	F081097C		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 788	F1F0B3CA		no_gene_models
+Kickxellomycota	Coemansia sp. RSA 921	F98C7B1F		no_gene_models
+Microsporidia	Dictyocoela roeselum	F39DF118		no_gene_models
+Entomophthoromycota	Entomophthora muscae	F3E8F9AA		no_gene_models
+(blank)	fungal sp.	F0287966		no_gene_models
+Glomeromycota	Gigaspora margarita	F0C86779		no_gene_models
+Chytridiomycota	Globomyces pollinis-pini	FE908126		no_gene_models
+Chytridiomycota	Globomyces sp. JEL0801	FF51C85C		no_gene_models
+Microsporidia	Hamiltosporidium tvaerminnensis	FF23F37F		no_gene_models
+Microsporidia	Hepatospora eriocheir	FF43F814		no_gene_models
+Entomophthoromycota	Massospora cicadina	F5C00A22		no_gene_models
+Entomophthoromycota	Massospora platypediae	F5CD90C7		no_gene_models
+Microsporidia	Metchnikovella incurvata	F5E0AEA0		no_gene_models
+Microsporidia	Microsporidia sp. MB	FF4D0B6E		no_gene_models
+Microsporidia	Microsporidia sp. MB	FFC05C11		no_gene_models
+Microsporidia	Microsporidia sp. MB	FC2C59FA		no_gene_models
+Microsporidia	Microsporidia sp. MB	FD7D6C1A		no_gene_models
+Microsporidia	Mitosporidium daphniae	F3034FE2		no_gene_models
+Microsporidia	Mitosporidium daphniae	F55C60E6		no_gene_models
+Neocallimastigomycota	Neocallimastix californiae	FD9B054F		no_gene_models
+Microsporidia	Nosema rusticus	F9D18C52		no_gene_models
+(blank)	Pleurotus ostreatus-Saccharomyces cerevisiae fusant	FF473FF1		no_gene_models
+Microsporidia	Pseudoloma neurophilia	F2D727F8		no_gene_models
+Rozellomycota	Rozella allomycis CSF55	F17255EC		no_gene_models
+Sanchytriomycota	Sanchytrium tribonematis	FE0149E9		no_gene_models
+Chytridiomycota	Siphonaria sp. JEL0065	F91F9F0F		no_gene_models
+Microsporidia	Spraguea lophii 42_110	FF8037B5		no_gene_models
+Microsporidia	Spraguea lophii	F05892AA		no_gene_models
+Microsporidia	Spraguea lophii	F9C6BC09		no_gene_models
+Microsporidia	Spraguea lophii	FF654229		no_gene_models
+Microsporidia	Spraguea lophii	F31A03E9		no_gene_models
+Microsporidia	Spraguea lophii	F0DAB1F0		no_gene_models
+Microsporidia	Spraguea lophii	F59FA04C		no_gene_models
+Microsporidia	Spraguea lophii	F3C72C00		no_gene_models
+Microsporidia	Spraguea lophii	F9AE4EEB		no_gene_models
+Microsporidia	Spraguea lophii	F3E1BFAC		no_gene_models
+Microsporidia	Spraguea lophii	FEA8929C		no_gene_models
+Chytridiomycota	Synchytrium endobioticum	F811B56E		no_gene_models
+Microsporidia	Tubulinosema ratisbonensis	F2794F40		no_gene_models
+Microsporidia	Vairimorpha ceranae BRL01	F5F60078		no_gene_models
+Microsporidia	Vairimorpha sp. gmOTU17 SAN00002588	F1C7F2A0		no_gene_models
diff --git a/docs/notes/2026-11-14_mat-discovery-tables/unscanned_genomes_status.tsv b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_genomes_status.tsv
new file mode 100644
index 00000000..c6f72a9e
--- /dev/null
+++ b/docs/notes/2026-11-14_mat-discovery-tables/unscanned_genomes_status.tsv
@@ -0,0 +1,66 @@
+phylum	annotation_folder	status
+Microsporidia	Agmasoma_carcini_nom._nud._v2	skipped:skipped_too_small
+Microsporidia	Alternosema_astaquatica_1	skipped:skipped_too_small
+Aphelidiomycota	Amoeboaphelidium_protococcarum_FD95	skipped:skipped_too_small
+Aphelidiomycota	Amoeboaphelidium_protococcarum_X5	skipped:skipped_too_small
+Sanchytriomycota	Amoeboradix_gromovi_X-113	skipped:skipped_too_small
+Microsporidia	Anncaliia_algerae_Undeen	skipped:skipped_too_small
+Microsporidia	Areospora_rohanae_ARG002	skipped:skipped_too_small
+Chytridiomycota	UNMAPPED:Batrachochytrium_dendrobatidis_	no_dir
+Chytridiomycota	UNMAPPED:Chytridiomycetes_sp._concoct_116	no_dir
+Kickxellomycota	Coemansia_aciculifera_BCRC_34181	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_1287_RSA_1287	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_1694_RSA_1694	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_1836_RSA_1836	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_1937_RSA_1937	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_2052_RSA_2052	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_25_RSA_25	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_2524_RSA_2524	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_475_RSA_475	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_530_RSA_530	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_551_RSA_551	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_788_RSA_788	skipped:skipped_too_small
+Kickxellomycota	Coemansia_sp._RSA_921_RSA_921	skipped:skipped_too_small
+Microsporidia	Dictyocoela_roeselum_Ou19	skipped:skipped_too_small
+Entomophthoromycota	UNMAPPED:Entomophthora_muscae_	no_dir
+	fungal_sp._concoct_113	skipped:skipped_too_small
+Glomeromycota	UNMAPPED:Gigaspora_margarita_120-4_pot_B_10-14	no_dir
+Chytridiomycota	Globomyces_pollinis-pini_Arg68	skipped:skipped_too_small
+Chytridiomycota	UNMAPPED:Globomyces_sp._JEL0801_JEL0801	no_dir
+Microsporidia	Hamiltosporidium_tvaerminnensis_OER-3-3	skipped:skipped_too_small
+Microsporidia	Hepatospora_eriocheir_canceri	skipped:skipped_too_small
+Chytridiomycota	Homolaphlyctis_polyrhiza_JEL142	annotated
+Entomophthoromycota	UNMAPPED:Massospora_cicadina_MICH_231384	no_dir
+Entomophthoromycota	Massospora_platypediae	dir_no_proteins
+Microsporidia	Metchnikovella_incurvata_LNA5	skipped:skipped_too_small
+Microsporidia	Microsporidia_sp._MB_AHL03	skipped:skipped_too_small
+Microsporidia	Microsporidia_sp._MB_BSAL01234	skipped:skipped_too_small
+Microsporidia	Microsporidia_sp._MB_BSALO12345	skipped:skipped_too_small
+Microsporidia	Microsporidia_sp._MB_BUSABN394_1.0	skipped:skipped_too_small
+Microsporidia	Mitosporidium_daphniae_CH-H	skipped:skipped_too_small
+Microsporidia	UNMAPPED:Mitosporidium_daphniae_UGP3	no_dir
+Neocallimastigomycota	Neocallimastix_californiae	skipped:skipped_too_small
+Microsporidia	Nosema_rusticus_FR26	skipped:skipped_too_small
+	UNMAPPED:Pleurotus_ostreatus-Saccharomyces_cerevisiae_fusant_D1-P	no_dir
+Microsporidia	Pseudoloma_neurophilia_MK1	skipped:skipped_too_small
+Glomeromycota	Rhizophagus_irregularis_DAOM_181602	annotated
+Glomeromycota	UNMAPPED:Rhizophagus_irregularis_DAOM_181602=DAOM_197198_DAOM_197198	no_dir
+Rozellomycota	Rozella_allomycis_CSF55	skipped:skipped_too_small
+Sanchytriomycota	Sanchytrium_tribonematis_X-128	skipped:skipped_too_small
+Chytridiomycota	UNMAPPED:Siphonaria_sp._JEL0065_JEL0065	no_dir
+Microsporidia	Spraguea_lophii_42_110	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_Celtic_Deep	dir_no_proteins
+Microsporidia	Spraguea_lophii_New_Brunswick_1	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Brunswick_4	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Brunswick_8	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Brunswick_9	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Jersey_JS61	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Jersey_RM18	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_New_Jersey_RW92	skipped:skipped_too_small
+Microsporidia	Spraguea_lophii_North_Atlantic	dir_no_proteins
+Microsporidia	Spraguea_lophii_RA12034	dir_no_proteins
+Chytridiomycota	Synchytrium_endobioticum_18_T1	skipped:skipped_too_small
+Microsporidia	Tubulinosema_ratisbonensis_Franzen	skipped:skipped_too_small
+Microsporidia	Vairimorpha_ceranae_BRL01	skipped:skipped_too_small
+Microsporidia	Vairimorpha_sp._gmOTU17_SAN00002588	skipped:skipped_too_small
+Microsporidia	Vavraia_culicis_floridensis	annotated
diff --git a/scripts/adjacent_pair_null.py b/scripts/adjacent_pair_null.py
new file mode 100644
index 00000000..cb7a0cf0
--- /dev/null
+++ b/scripts/adjacent_pair_null.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python3
+"""Chance expectation for adjacent HMG-box / homeodomain gene pairs per lineage.
+
+Read-only discovery tool. Input is stage-1 output of flank_first_scan.py (genes_all.tsv and candidates.tsv per genome).
+For each lineage (a list of genome names) and for each pair type (HMG+Homeo, 2xHomeo, 2xHMG) it counts the genomes that
+have a pair within --window genes on one contig, and compares that with random placement: in every genome the same
+number of HMG genes and homeodomain genes is drawn at random from all genes (--perms draws), the pair is looked for
+again, and the lineage count is summed. The reported p is the share of draws with a count at least as large as observed.
+A homeodomain family that is tandem-duplicated gives an excess here without being a mating-type locus, so the table also
+gives the share of observed pairs on the same strand.
+
+Usage: adjacent_pair_null.py --stage1 DIR --out OUT.tsv LIST[:LABEL] [LIST[:LABEL] ...]
+"""
+import argparse
+import collections
+import os
+import random
+
+
+def table(path):
+    return [l.rstrip("\n").split("\t") for l in open(path)][1:]
+
+
+def has_pair(a_items, b_items, window, same_class):
+    """a_items, b_items: lists of (contig, index). True when some a and b (different genes) lie within window."""
+    for c1, i1 in a_items:
+        for c2, i2 in b_items:
+            if c1 == c2 and 0 < abs(i1 - i2) <= window:
+                return True
+    return False
+
+
+def pair_strands(a_items, b_items, window):
+    """Return list of 'same'/'opposite' for observed pairs (a, b with a index < b index)."""
+    out = []
+    for c1, i1, s1 in a_items:
+        for c2, i2, s2 in b_items:
+            if c1 == c2 and 0 < i2 - i1 <= window:
+                out.append("same" if s1 == s2 else "opposite")
+    return out
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--stage1", required=True)
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--window", type=int, default=5)
+    ap.add_argument("--perms", type=int, default=500)
+    ap.add_argument("--seed", type=int, default=1)
+    ap.add_argument("lists", nargs="+")
+    a = ap.parse_args()
+    rng = random.Random(a.seed)
+    D = a.stage1
+    out = open(a.out, "w")
+    out.write("lineage\tpair_type\tgenomes\tobserved_genomes\texpected_mean\texpected_max\tp\tshare_same_strand\n")
+    for spec in a.lists:
+        path, _, label = spec.partition(":")
+        label = label or os.path.basename(path)
+        gs = [x.strip() for x in open(path) if x.strip()]
+        data = []
+        for g in gs:
+            gf, cf = f"{D}/{g}.genes_all.tsv", f"{D}/{g}.candidates.tsv"
+            if not (os.path.exists(gf) and os.path.exists(cf)):
+                continue
+            genes = table(gf)
+            st = {r[0]: (r[1], int(r[5]), r[4]) for r in genes}
+            hmg = [st[r[0]] for r in table(cf) if r[3] in ("HMG_box", "HMG_box_2") and r[0] in st]
+            hd = [st[r[0]] for r in table(cf) if r[3] == "Homeodomain" and r[0] in st]
+            data.append((hmg, hd, [(x[0], x[1]) for x in st.values()]))
+        for ptype, (ka, kb) in {"HMG+Homeo": ("hmg", "hd"), "2xHomeo": ("hd", "hd"), "2xHMG": ("hmg", "hmg")}.items():
+            obs, strands, exp = 0, [], [0] * a.perms
+            for hmg, hd, allg in data:
+                A, B = {"hmg": hmg, "hd": hd}[ka], {"hmg": hmg, "hd": hd}[kb]
+                if not A or not B or (ka == kb and len(A) < 2):
+                    continue
+                ai = [(x[0], x[1]) for x in A]
+                bi = [(x[0], x[1]) for x in B]
+                if has_pair(ai, bi, a.window, ka == kb):
+                    obs += 1
+                if ka == kb:
+                    strands += pair_strands(A, A, a.window)
+                else:
+                    strands += pair_strands(A, B, a.window) + pair_strands(B, A, a.window)
+                for p in range(a.perms):
+                    if ka == kb:
+                        s = rng.sample(allg, len(A))
+                        if has_pair(s, s, a.window, True):
+                            exp[p] += 1
+                    else:
+                        s = rng.sample(allg, len(A) + len(B))
+                        if has_pair(s[:len(A)], s[len(A):], a.window, False):
+                            exp[p] += 1
+            p_val = (sum(e >= obs for e in exp) + 1) / (a.perms + 1)
+            same = round(strands.count("same") / len(strands), 3) if strands else "NA"
+            out.write(f"{label}\t{ptype}\t{len(data)}\t{obs}\t{sum(exp) / a.perms:.1f}\t{max(exp)}\t{p_val:.4f}\t{same}\n")
+    out.close()
+    print(open(a.out).read())
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/augustus_gene_predict.slurm b/scripts/augustus_gene_predict.slurm
new file mode 100644
index 00000000..bc626c0a
--- /dev/null
+++ b/scripts/augustus_gene_predict.slurm
@@ -0,0 +1,33 @@
+#!/usr/bin/bash -l
+#SBATCH --job-name=aug-pred
+#SBATCH --partition=epyc
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=8gb
+#SBATCH --time=8:00:00
+#SBATCH --output=/bigdata/stajichlab/jstajich/projects/MATPredict/logs/aug_%A.log
+# Gene prediction with Augustus for assemblies that BFD skipped ("skipped_too_small"), so they can enter the flank-first scan.
+# Env: SRC (worktree with this script), LIST (TSV: ASMID<TAB>name), OUT (folder), SPECIES (Augustus model, default rhizopus_oryzae).
+# Output: $OUT/<name>/predict_results/<name>.proteins.fa.gz and <name>.gff3.gz (headers rewritten g1.t1 -> g1-T1 so
+# flank_first_scan.py maps protein to gene). The model is not trained on these lineages: gene models are approximate.
+set -uo pipefail
+: "${SRC:?}" "${LIST:?}" "${OUT:?}"
+SPECIES="${SPECIES:-rhizopus_oryzae}"
+LIB=/bigdata/stajichlab/shared/projects/BFD/Fungi_BFD_runs/input_clean_genomes
+# `module load augustus` prints a conda error in a batch shell; set the paths directly (checked on the login node 2026-11-14)
+AUG=/opt/linux/rocky/8.x/x86_64/pkgs/augustus/3.5.0/env
+export PATH="$AUG/bin:$PATH"
+export AUGUSTUS_CONFIG_PATH=/opt/linux/centos/8.x/x86_64/pkgs/augustus/3.5.0/env/config/
+W="${SCRATCH:?}/aug"; mkdir -p "$W"
+while IFS=$'\t' read -r asm name; do
+  [[ -z "$asm" ]] && continue
+  D="$OUT/$name/predict_results"; mkdir -p "$D"
+  [[ -s "$D/$name.gff3.gz" ]] && continue
+  zcat "$LIB/$asm.fa.gz" > "$W/$name.fa"
+  # one Augustus run per contig chunk would be faster; the genomes here are 11-24 Mb so one run is enough
+  augustus --species="$SPECIES" --gff3=on --protein=on --codingseq=off --softmasking=0 "$W/$name.fa" > "$W/$name.aug.gff3" 2> "$W/$name.aug.err" || { echo "FAIL $name"; tail -5 "$W/$name.aug.err"; continue; }
+  python3 "$SRC/scripts/augustus_proteins.py" "$W/$name.aug.gff3" "$D/$name.proteins.fa.gz"
+  awk -F'\t' '/^#/{next} $3=="gene"{print}' "$W/$name.aug.gff3" | gzip > "$D/$name.gff3.gz"
+  echo "$name genes=$(zcat "$D/$name.gff3.gz" | wc -l) proteins=$(zcat "$D/$name.proteins.fa.gz" | grep -c '>')"
+  rm -f "$W/$name".*
+done < "$LIST"
+echo done
diff --git a/scripts/augustus_proteins.py b/scripts/augustus_proteins.py
new file mode 100644
index 00000000..0c34eb67
--- /dev/null
+++ b/scripts/augustus_proteins.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+"""Write the proteins of an Augustus GFF3 (run with --protein=on) as FASTA, one per transcript.
+
+Augustus prints each protein in comment lines of its GFF3:
+  # start gene g1
+  ...
+  # protein sequence = [MKV...
+  # ...LLA]
+  # end gene g1
+The header is rewritten to <gene>-T<n> (g1.t1 -> g1-T1) so flank_first_scan.py maps a protein to its gene.
+Usage: augustus_proteins.py IN.gff3 OUT.faa[.gz]
+"""
+import gzip
+import re
+import sys
+
+
+def proteins(lines):
+    """Yield (transcript_id, sequence) for every protein block."""
+    gene, buf, on = None, [], False
+    for line in lines:
+        if line.startswith("# start gene "):
+            gene = line.split()[-1]
+        if "# protein sequence = [" in line:
+            on = True
+            buf = [line.split("[", 1)[1].strip()]
+        elif on:
+            buf.append(line[1:].strip())
+        if on and "]" in buf[-1]:
+            seq = "".join(buf).replace("]", "").replace(" ", "")
+            yield gene, seq
+            on, buf = False, []
+
+
+def main():
+    op = gzip.open if sys.argv[2].endswith(".gz") else open
+    n = 0
+    with op(sys.argv[2], "wt") as fo:
+        for gene, seq in proteins(open(sys.argv[1])):
+            fo.write(f">{gene}-T1\n{seq}\n")
+            n += 1
+    print(n, "proteins")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/flank_idiomorph_probe.py b/scripts/flank_idiomorph_probe.py
new file mode 100644
index 00000000..c0101d1f
--- /dev/null
+++ b/scripts/flank_idiomorph_probe.py
@@ -0,0 +1,170 @@
+#!/usr/bin/env python3
+"""Flank-first idiomorph probe for a small set of related genomes (for example the three Allomyces genomes).
+
+Read-only discovery tool. Needs stage-1 output of flank_first_scan.py (genes_all.tsv, candidates.tsv per genome) and
+the funannotate proteomes.
+
+For every HMG_box / Homeodomain candidate gene X in genome A and every other genome B:
+  1. reciprocal best hits (diamond blastp, E <= --evalue) between all genes of A and B;
+  2. take the genes within --flank genes of X (not X); keep those with a reciprocal best hit in B;
+  3. synteny: >= --min-flank of them lie within --span genes of each other on one contig of B (the largest such group);
+  4. class of X for B:
+       conserved     X has a reciprocal best hit inside the syntenic region
+       other_domain  the region holds an HMG/Homeodomain candidate that is not the reciprocal best hit of X
+                     (a divergent or replaced gene: idiomorph-like)
+       absent        syntenic region found, no HMG/Homeodomain gene in it (X missing in B: idiomorph-like or gene loss)
+       no_synteny    fewer than --min-flank flank genes map as one block (not testable)
+The class is a lead, not a call. Gene loss, assembly gaps and annotation errors give the same result.
+
+Usage: flank_idiomorph_probe.py --stage1 DIR --out OUT --genomes G1 G2 [G3 ...]
+Output: OUT/baseline.tsv (random non-candidate genes through the same test: conserved / not_conserved / no_synteny), OUT/probe.tsv (genome_A, gene, domain, genome_B, class, flank_mapped, region_contig, region_span), OUT/summary.tsv
+"""
+import argparse
+import collections
+import gzip
+import os
+import random
+import subprocess
+import sys
+
+ANN = "/bigdata/stajichlab/shared/projects/BFD/Fungi_BFD_runs/genome_annotation"
+
+
+def table(path):
+    rows = [l.rstrip("\n").split("\t") for l in open(path)]
+    return rows[1:]
+
+
+def read_genes(stage1, g):
+    """-> (genes_in_order: list of (gene, contig, idx), idx_of: gene->(contig, idx))"""
+    rows = table(f"{stage1}/{g}.genes_all.tsv")
+    genes = [(r[0], r[1], int(r[5])) for r in rows]
+    return genes, {r[0]: (r[1], int(r[5])) for r in rows}
+
+
+def read_candidates(stage1, g):
+    return {r[0]: r[3] for r in table(f"{stage1}/{g}.candidates.tsv") if r[3] in ("HMG_box", "HMG_box_2", "Homeodomain")}
+
+
+def rbh(a, b, tmp, evalue, threads):
+    """Reciprocal best hits between proteomes a and b (fasta paths, gz ok) -> dict gene_a -> gene_b."""
+    def prep(path, tag):
+        out = os.path.join(tmp, tag + ".faa")
+        op = gzip.open if path.endswith(".gz") else open
+        with op(path, "rt") as fi, open(out, "w") as fo:
+            for line in fi:
+                if line.startswith(">"):
+                    name = line[1:].split()[0]
+                    name = name.rsplit("-T", 1)[0] if "-T" in name else name
+                    fo.write(f">{name}\n")
+                else:
+                    fo.write(line)
+        return out
+    fa, fb = prep(a, "A"), prep(b, "B")
+    best = {}
+    for q, s, tag in ((fa, fb, "ab"), (fb, fa, "ba")):
+        subprocess.run(["diamond", "makedb", "--in", s, "-d", os.path.join(tmp, "db_" + tag), "--quiet"], check=True)
+        out = os.path.join(tmp, tag + ".tsv")
+        subprocess.run(["diamond", "blastp", "-q", q, "-d", os.path.join(tmp, "db_" + tag), "-o", out, "--quiet",
+                        "--max-target-seqs", "1", "-e", str(evalue), "--threads", str(threads),
+                        "--outfmt", "6", "qseqid", "sseqid", "bitscore"], check=True)
+        best[tag] = {}
+        for line in open(out):
+            f = line.split("\t")
+            best[tag].setdefault(f[0], f[1])
+    return {x: y for x, y in best["ab"].items() if best["ba"].get(y) == x}
+
+
+def classify_gene(x, flank_genes, orth, idx_b, cand_b, min_flank, span):
+    """Return (class, n_flank_mapped, contig, region_span). Pure function, used by the tests.
+    x: gene id; flank_genes: genes near x in A; orth: A->B reciprocal best hits;
+    idx_b: gene->(contig, idx) in B; cand_b: set of HMG/Homeodomain genes in B."""
+    pos = [idx_b[orth[f]] for f in flank_genes if f in orth and orth[f] in idx_b]
+    by = collections.defaultdict(list)
+    for c, i in pos:
+        by[c].append(i)
+    best = (0, None, None, None)
+    for c, v in by.items():
+        v.sort()
+        lo = 0
+        for hi in range(len(v)):
+            while v[hi] - v[lo] > span:
+                lo += 1
+            n = hi - lo + 1
+            if n > best[0]:
+                best = (n, c, v[lo], v[hi])
+    n, c, lo, hi = best
+    if n < min_flank:
+        return "no_synteny", len(pos), "", ""
+    inside = [g for g in cand_b if idx_b[g][0] == c and lo - 2 <= idx_b[g][1] <= hi + 2]
+    if x in orth and orth[x] in idx_b and idx_b[orth[x]][0] == c and lo - 2 <= idx_b[orth[x]][1] <= hi + 2:
+        return "conserved", len(pos), c, f"{lo}-{hi}"
+    if inside:
+        return "other_domain", len(pos), c, f"{lo}-{hi}"
+    return "absent", len(pos), c, f"{lo}-{hi}"
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--stage1", required=True)
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--genomes", nargs="+", required=True)
+    ap.add_argument("--flank", type=int, default=5)
+    ap.add_argument("--min-flank", type=int, default=3)
+    ap.add_argument("--span", type=int, default=25)
+    ap.add_argument("--evalue", type=float, default=1e-5)
+    ap.add_argument("--threads", type=int, default=4)
+    ap.add_argument("--ann", default=ANN, help="folder holding <genome>/predict_results/<genome>.proteins.fa.gz")
+    ap.add_argument("--baseline", type=int, default=500, help="random non-candidate genes per genome pair for the baseline")
+    ap.add_argument("--seed", type=int, default=1)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    os.makedirs(a.out, exist_ok=True)
+    G = {g: read_genes(a.stage1, g) for g in a.genomes}
+    C = {g: read_candidates(a.stage1, g) for g in a.genomes}
+    rows, base = [], []
+    rng = random.Random(a.seed)
+    for ga in a.genomes:
+        for gb in a.genomes:
+            if ga == gb:
+                continue
+            tmp = os.path.join(a.tmp, f"fip_{os.getpid()}_{a.genomes.index(ga)}_{a.genomes.index(gb)}")
+            os.makedirs(tmp, exist_ok=True)
+            orth = rbh(f"{a.ann}/{ga}/predict_results/{ga}.proteins.fa.gz", f"{a.ann}/{gb}/predict_results/{gb}.proteins.fa.gz",
+                       tmp, a.evalue, a.threads)
+            genes_a, idx_a = G[ga]
+            by_contig = collections.defaultdict(dict)
+            for g, c, i in genes_a:
+                by_contig[c][i] = g
+            idx_b = G[gb][1]
+            for x, dom in C[ga].items():
+                c, i = idx_a[x]
+                fl = [by_contig[c][j] for j in range(i - a.flank, i + a.flank + 1) if j != i and j in by_contig[c]]
+                cls, n, rc, sp = classify_gene(x, fl, orth, idx_b, set(C[gb]), a.min_flank, a.span)
+                rows.append((ga, x, dom, gb, cls, n, rc, sp))
+            others = [g for g, _c, _i in genes_a if g not in C[ga]]
+            for x in rng.sample(others, min(a.baseline, len(others))):
+                c, i = idx_a[x]
+                fl = [by_contig[c][j] for j in range(i - a.flank, i + a.flank + 1) if j != i and j in by_contig[c]]
+                cls, n, rc, sp = classify_gene(x, fl, orth, idx_b, set(), a.min_flank, a.span)
+                base.append((ga, gb, "conserved" if cls == "conserved" else "not_conserved" if cls == "absent" else cls))
+    with open(os.path.join(a.out, "probe.tsv"), "w") as fo:
+        fo.write("genome_A\tgene\tdomain\tgenome_B\tclass\tflank_mapped\tregion_contig\tregion_span\n")
+        for r in rows:
+            fo.write("\t".join(map(str, r)) + "\n")
+    cnt = collections.Counter((r[0], r[3], r[4]) for r in rows)
+    with open(os.path.join(a.out, "summary.tsv"), "w") as fo:
+        fo.write("genome_A\tgenome_B\tclass\tgenes\n")
+        for k, v in sorted(cnt.items()):
+            fo.write("\t".join(map(str, k)) + f"\t{v}\n")
+    bc = collections.Counter(base)
+    with open(os.path.join(a.out, "baseline.tsv"), "w") as fo:
+        fo.write("genome_A\tgenome_B\tclass\tgenes\n")
+        for k, v in sorted(bc.items()):
+            fo.write("\t".join(map(str, k)) + f"\t{v}\n")
+    print(open(os.path.join(a.out, "summary.tsv")).read())
+    print(open(os.path.join(a.out, "baseline.tsv")).read())
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/infer_strandedness.py b/scripts/infer_strandedness.py
new file mode 100644
index 00000000..e6d30f34
--- /dev/null
+++ b/scripts/infer_strandedness.py
@@ -0,0 +1,91 @@
+#!/usr/bin/env python3
+"""Infer library strandedness from a BAM and a GFF3, and report read orientation over named regions.
+
+Read-only analysis (needs samtools on PATH). For up to --n annotated genes of at least --min-len bp (and not overlapping another
+gene), count properly paired reads by the orientation of read 1 relative to the gene strand:
+  same     read 1 on the gene strand  (forward-stranded library, 'fr-secondstrand')
+  opposite read 1 on the opposite strand (reverse-stranded library, dUTP, 'fr-firststrand')
+A library is called stranded when one orientation holds >= --threshold of the reads; otherwise unstranded.
+For each region (name:contig:start:end) the same count is reported as read-1 forward / reverse counts and, if the library is
+stranded, the implied transcript strand.
+Usage: infer_strandedness.py --bam X.bam --gff3 X.gff3 [--region name:contig:start:end ...]
+"""
+import argparse
+import gzip
+import subprocess
+
+
+def classify(same, opposite, threshold=0.85):
+    """-> 'forward-stranded', 'reverse-stranded' or 'unstranded' from read counts relative to gene strand."""
+    tot = same + opposite
+    if tot == 0:
+        return "no_reads"
+    if same / tot >= threshold:
+        return "forward-stranded"
+    if opposite / tot >= threshold:
+        return "reverse-stranded"
+    return "unstranded"
+
+
+def implied_strand(r1_fwd, r1_rev, library):
+    """Transcript strand implied by read-1 orientation in a stranded library."""
+    if library == "forward-stranded":
+        return "+" if r1_fwd > r1_rev else "-"
+    if library == "reverse-stranded":
+        return "-" if r1_fwd > r1_rev else "+"
+    return "unknown"
+
+
+def reads_r1(bam, region):
+    """(r1_forward, r1_reverse) among primary, mapped, properly paired reads in a region."""
+    out = subprocess.run(["samtools", "view", "-f", "66", "-F", "3852", bam, region], capture_output=True, text=True).stdout
+    fw = rv = 0
+    for line in out.splitlines():
+        flag = int(line.split("\t", 2)[1])
+        if flag & 64:
+            if flag & 16:
+                rv += 1
+            else:
+                fw += 1
+    return fw, rv
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--bam", required=True)
+    ap.add_argument("--gff3", required=True)
+    ap.add_argument("--region", action="append", default=[])
+    ap.add_argument("--n", type=int, default=400)
+    ap.add_argument("--min-len", type=int, default=1000)
+    ap.add_argument("--threshold", type=float, default=0.85)
+    a = ap.parse_args()
+    genes = []
+    op = gzip.open if a.gff3.endswith(".gz") else open
+    with op(a.gff3, "rt") as fh:
+        for line in fh:
+            f = line.rstrip("\n").split("\t")
+            if len(f) > 8 and f[2] == "gene":
+                genes.append((f[0], int(f[3]), int(f[4]), f[6]))
+    genes.sort()
+    keep = []
+    for i, g in enumerate(genes):
+        prev_end = genes[i - 1][2] if i and genes[i - 1][0] == g[0] else -1
+        next_start = genes[i + 1][1] if i + 1 < len(genes) and genes[i + 1][0] == g[0] else 10 ** 12
+        if g[2] - g[1] + 1 >= a.min_len and g[1] > prev_end and g[2] < next_start:
+            keep.append(g)
+    step = max(1, len(keep) // a.n)
+    same = opp = 0
+    for c, s, e, st in keep[::step][:a.n]:
+        fw, rv = reads_r1(a.bam, f"{c}:{s}-{e}")
+        same += fw if st == "+" else rv
+        opp += rv if st == "+" else fw
+    lib = classify(same, opp, a.threshold)
+    print(f"genes used {len(keep[::step][:a.n])}; read1 same-strand {same}, opposite {opp}; share same {same / max(1, same + opp):.3f}; library: {lib}")
+    for r in a.region:
+        name, c, s, e = r.split(":")
+        fw, rv = reads_r1(a.bam, f"{c}:{s}-{e}")
+        print(f"{name}\tread1_forward {fw}\tread1_reverse {rv}\timplied_strand {implied_strand(fw, rv, lib)}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/locus_expression.py b/scripts/locus_expression.py
new file mode 100644
index 00000000..7051d2a4
--- /dev/null
+++ b/scripts/locus_expression.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+"""Expression of named loci relative to all annotated genes, from `samtools bedcov` output.
+
+Read-only analysis. Inputs
+  --gff3      BFD GFF3 (gene features)
+  --bedcov    output of `samtools bedcov REGIONS.bed BAM` (chrom start end name sum_of_depth) for every gene and every locus region
+  --loci      TSV name<TAB>chrom<TAB>start<TAB>end (1-based inclusive) of the extra regions that were added to the BED, plus
+              --genes ids of annotated genes to report
+Output (stdout and --out): for each reported locus: length, mean depth, depth percentile among all annotated genes with length >= 300 bp,
+and the share of annotated genes with mean depth >= 1.
+Mean depth is not TPM: it is not corrected for library size; compare within one library only.
+"""
+import argparse
+
+
+def parse_bedcov(path):
+    """-> {name: (length, mean_depth)} with BED half-open coordinates."""
+    out = {}
+    for line in open(path):
+        f = line.rstrip("\n").split("\t")
+        if len(f) < 5:
+            continue
+        s, e = int(f[1]), int(f[2])
+        out[f[3]] = (e - s, float(f[4]) / max(1, e - s))
+    return out
+
+
+def percentile_of(value, values):
+    """Share of values strictly below `value`."""
+    return sum(v < value for v in values) / len(values) if values else float("nan")
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--bedcov", required=True)
+    ap.add_argument("--report", nargs="+", required=True, help="names in the bedcov file to report")
+    ap.add_argument("--gene-prefix", default="", help="names that start with this prefix are annotated genes (the background)")
+    ap.add_argument("--min-len", type=int, default=300)
+    ap.add_argument("--out")
+    a = ap.parse_args()
+    cov = parse_bedcov(a.bedcov)
+    bg = [d for n, (l, d) in cov.items() if n.startswith(a.gene_prefix) and l >= a.min_len and n not in a.report]
+    lines = ["name\tlength\tmean_depth\tpercentile_among_genes\tgenes_with_depth_ge_1"]
+    for n in a.report:
+        if n not in cov:
+            lines.append(f"{n}\tNA\tNA\tNA\tNA")
+            continue
+        l, d = cov[n]
+        lines.append(f"{n}\t{l}\t{d:.2f}\t{percentile_of(d, bg):.3f}\t{sum(x >= 1 for x in bg) / len(bg):.3f}")
+    text = "\n".join(lines) + "\n"
+    print(text)
+    if a.out:
+        open(a.out, "w").write(text)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/locus_transcripts.py b/scripts/locus_transcripts.py
new file mode 100644
index 00000000..9b7ccb0d
--- /dev/null
+++ b/scripts/locus_transcripts.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python3
+"""Transcripts that overlap a locus, with exon structure, strand and Pfam hits on every ORF of the spliced sequence.
+
+Read-only analysis of a StringTie assembly (GTF) and the spliced transcript FASTA from `gffread -w`.
+For every transcript on --contig that overlaps [--lo, --hi]: number of exons, span, strand, spliced length, the longest ORF,
+and the Pfam domains (HMG_box, HMG_box_2, Homeodomain; GA cutoff) found on any ORF of >= --min-aa residues in the six frames of
+the spliced sequence, with the frame (negative = reverse of the transcript as written).
+Limit: with unstranded RNA-seq StringTie takes the strand from splice-site motifs, so a homeodomain ORF in a negative frame of a
+'+' transcript (or the reverse) is on the strand opposite to the assembled transcript.
+Usage: locus_transcripts.py --gtf X.gtf --tx X.tx.fa --contig C --lo N --hi N --hmm HMM
+"""
+import argparse
+import os
+import re
+import subprocess
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+from region_pfam_check import orfs  # noqa: E402
+
+
+def read_fasta(path):
+    d, h = {}, None
+    for line in open(path):
+        if line[0] == ">":
+            h = line[1:].split()[0]
+            d[h] = []
+        else:
+            d[h].append(line.strip())
+    return {k: "".join(v) for k, v in d.items()}
+
+
+def read_gtf_transcripts(path, contig):
+    """-> {transcript_id: {'strand': s, 'exons': [(start, end)]}} for one contig."""
+    recs = {}
+    for line in open(path):
+        f = line.split("\t")
+        if len(f) < 9 or f[0] != contig:
+            continue
+        m = re.search(r'transcript_id "([^"]+)"', f[8])
+        if not m:
+            continue
+        r = recs.setdefault(m.group(1), {"strand": f[6], "exons": []})
+        if f[2] == "exon":
+            r["exons"].append((int(f[3]), int(f[4])))
+    return recs
+
+
+def overlaps(exons, lo, hi):
+    ex = sorted(exons)
+    return bool(ex) and ex[-1][1] >= lo and ex[0][0] <= hi
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--gtf", required=True)
+    ap.add_argument("--tx", required=True)
+    ap.add_argument("--contig", required=True)
+    ap.add_argument("--lo", type=int, required=True)
+    ap.add_argument("--hi", type=int, required=True)
+    ap.add_argument("--hmm", required=True)
+    ap.add_argument("--min-aa", type=int, default=30)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    tx = read_fasta(a.tx)
+    print("transcript\tstrand\texons\tspan\ttx_len\tlongest_orf_aa\tpfam_hits(aa,frame,domain,evalue)")
+    for tid, r in read_gtf_transcripts(a.gtf, a.contig).items():
+        if not overlaps(r["exons"], a.lo, a.hi) or tid not in tx:
+            continue
+        ex = sorted(r["exons"])
+        os_ = orfs(tx[tid], a.min_aa)
+        faa = os.path.join(a.tmp, "lt.faa")
+        with open(faa, "w") as fh:
+            for i, o in enumerate(os_):
+                fh.write(f">o{i}\n{o[3]}\n")
+        tbl = os.path.join(a.tmp, "lt.tbl")
+        subprocess.run(["hmmsearch", "--cut_ga", "--domtblout", tbl, "-o", "/dev/null", a.hmm, faa], check=True)
+        hits = []
+        for line in open(tbl):
+            if line[0] != "#":
+                f = line.split()
+                o = os_[int(f[0][1:])]
+                hits.append((len(o[3]), o[0], f[3], f[6]))
+        longest = max((len(o[3]) for o in os_), default=0)
+        print(f"{tid}\t{r['strand']}\t{len(ex)}\t{ex[0][0]}-{ex[-1][1]}\t{len(tx[tid])}\t{longest}\t{hits or 'none'}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/matpi_hmg_adjacency.py b/scripts/matpi_hmg_adjacency.py
new file mode 100644
index 00000000..c7cb8118
--- /dev/null
+++ b/scripts/matpi_hmg_adjacency.py
@@ -0,0 +1,127 @@
+#!/usr/bin/env python3
+"""How often does an HMG-box gene lie near a matPi-like (homeodomain) region on the same contig?
+
+Read-only discovery tool. Combines
+  - matpi_hits.tsv from matpi_tblastn.py (genome-level homeodomain-like regions, annotated or not), and
+  - scan_genes.tsv from pm_lead_followup.py scan (all genes with an HMG_box / HMG_box_2 Pfam hit),
+with gene coordinates from the BFD GFF3. For every HMG gene it finds the nearest region on the same contig.
+Output (--out): adjacency_pairs.tsv (genome, hmg_gene, contig, region_rank, region_identity, distance_bp) for pairs within
+--max-dist, and adjacency_summary.tsv (genome, hmg_genes, hmg_genes_near_region, regions_tested).
+The summary gives the background rate: in a genome with several HMG genes and several homeodomain regions, how often a pair
+falls within --max-dist by chance on one contig. Assembly fragmentation hides pairs, so a missing pair is not evidence of
+absence.
+With --perms N the same number of HMG genes is placed at random gene positions N times in every genome; adjacency_null.tsv gives the
+observed number of genomes with an HMG gene within --null-dist of a region, the expected number and p (share of draws >= observed).
+Usage: matpi_hmg_adjacency.py --hits matpi_hits.tsv --genes SCAN_GENES.tsv [SCAN_GENES.tsv ...] --genomes GENOMES.tsv --out OUT
+"""
+import argparse
+import csv
+import gzip
+import os
+import random
+import sys
+
+
+def opener(p):
+    return gzip.open(p, "rt") if p.endswith(".gz") else open(p)
+
+
+def read_gene_coords(gff, wanted):
+    out = {}
+    with opener(gff) as fh:
+        for line in fh:
+            if line.startswith("#"):
+                continue
+            f = line.rstrip("\n").split("\t")
+            if len(f) > 8 and f[2] == "gene":
+                gid = f[8].split("ID=")[1].split(";")[0]
+                if gid in wanted:
+                    out[gid] = (f[0], int(f[3]), int(f[4]))
+    return out
+
+
+def read_all_genes(gff):
+    out = []
+    with opener(gff) as fh:
+        for line in fh:
+            if line.startswith("#"):
+                continue
+            f = line.rstrip("\n").split("\t")
+            if len(f) > 8 and f[2] == "gene":
+                out.append((f[0], int(f[3]), int(f[4])))
+    return out
+
+
+def gap(a0, a1, b0, b1):
+    return max(0, max(a0, b0) - min(a1, b1))
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--hits", required=True)
+    ap.add_argument("--genes", nargs="+", required=True)
+    ap.add_argument("--genomes", required=True, help="TSV name, fasta, gff3, matMc gene")
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--max-dist", type=int, default=50000)
+    ap.add_argument("--perms", type=int, default=2000, help="random placements of the HMG genes for the null (0 = skip)")
+    ap.add_argument("--null-dist", type=int, default=20000, help="distance used for the permutation test")
+    ap.add_argument("--seed", type=int, default=1)
+    a = ap.parse_args()
+    os.makedirs(a.out, exist_ok=True)
+    gff = {l.split("\t")[0]: l.split("\t")[2] for l in open(a.genomes)}
+    hits = {}
+    for r in csv.DictReader(open(a.hits), delimiter="\t"):
+        hits.setdefault(r["genome"], []).append(r)
+    hmg = {}
+    for p in a.genes:
+        for r in csv.DictReader(open(p), delimiter="\t"):
+            if "HMG" in r["domain"]:
+                hmg.setdefault(r["genome"], set()).add(r["gene"])
+    fp = open(os.path.join(a.out, "adjacency_pairs.tsv"), "w")
+    fs = open(os.path.join(a.out, "adjacency_summary.tsv"), "w")
+    fp.write("genome\thmg_gene\tcontig\tregion_rank\tregion_identity\tdistance_bp\n")
+    fs.write("genome\thmg_genes\thmg_genes_near_region\tregions_tested\n")
+    for g, regs in hits.items():
+        coords = read_gene_coords(gff[g], hmg.get(g, set()))
+        near = set()
+        for gene, (c, s, e) in coords.items():
+            for r in regs:
+                if r["contig"] != c:
+                    continue
+                d = gap(s, e, int(r["start"]), int(r["end"]))
+                if d <= a.max_dist:
+                    near.add(gene)
+                    fp.write(f"{g}\t{gene}\t{c}\t{r['rank']}\t{r['best_identity']}\t{d}\n")
+        fs.write(f"{g}\t{len(coords)}\t{len(near)}\t{len(regs)}\n")
+    fp.close()
+    fs.close()
+    if a.perms:
+        rng = random.Random(a.seed)
+        obs, exp = 0, [0] * a.perms
+        used = 0
+        for g, regs in hits.items():
+            allg = read_all_genes(gff[g])
+            k = len(hmg.get(g, ()))
+            if not k or not allg:
+                continue
+            used += 1
+            by = {}
+            for r in regs:
+                by.setdefault(r["contig"], []).append((int(r["start"]), int(r["end"])))
+            def near(genes):
+                return any(c in by and any(gap(s0, e0, x0, x1) <= a.null_dist for x0, x1 in by[c]) for c, s0, e0 in genes)
+            coords = read_gene_coords(gff[g], hmg.get(g, set()))
+            obs += near(list(coords.values()))
+            for i in range(a.perms):
+                exp[i] += near(rng.sample(allg, k))
+        p_val = (sum(e >= obs for e in exp) + 1) / (a.perms + 1)
+        with open(os.path.join(a.out, "adjacency_null.tsv"), "w") as fn:
+            fn.write("max_dist_bp\tgenomes\tobserved_genomes\texpected_mean\texpected_max\tp\n")
+            fn.write(f"{a.null_dist}\t{used}\t{obs}\t{sum(exp) / a.perms:.2f}\t{max(exp)}\t{p_val:.4f}\n")
+        print(open(os.path.join(a.out, "adjacency_null.tsv")).read())
+    print(open(os.path.join(a.out, "adjacency_summary.tsv")).read())
+    print(open(os.path.join(a.out, "adjacency_pairs.tsv")).read())
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/matpi_tblastn.py b/scripts/matpi_tblastn.py
new file mode 100644
index 00000000..09bf6879
--- /dev/null
+++ b/scripts/matpi_tblastn.py
@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+"""Genome-level search for matPi (homeodomain) regions and their distance to the matMc-like gene.
+
+Read-only discovery tool. The curated T. deformans matPi is a 181 aa partial protein whose homeodomain region lies in
+unannotated sequence, so an annotation-based search (pm_lead_followup.py scan) cannot find it. This script searches the
+assembly itself.
+
+For each genome (TSV: name, genome fasta, BFD gff3, matMc gene id or '-'):
+  1. tblastn of the matPi query set (FASTA) against the genome (E <= --evalue, no SEG filter);
+  2. per contig, hits closer than --merge bp are merged; the best regions by summed bitscore are kept;
+  3. the matMc gene's coordinates come from the GFF3; for each matPi region on the matMc contig the distance is given.
+Output (--out): matpi_hits.tsv (genome, rank, contig, start, end, best_identity, best_evalue, bitscore, on_matMc_contig,
+distance_to_matMc_bp, overlapping_gene).
+"""
+import argparse
+import collections
+import gzip
+import os
+import subprocess
+import sys
+
+
+def opener(p):
+    return gzip.open(p, "rt") if p.endswith(".gz") else open(p)
+
+
+def merge_hits(hits, merge):
+    """hits: list of (contig, start, end, pident, evalue, bits) -> merged regions sorted by total bitscore.
+    Returns list of dict(contig, start, end, ident, evalue, bits)."""
+    by = collections.defaultdict(list)
+    for c, s, e, p, ev, b in hits:
+        by[c].append((min(s, e), max(s, e), p, ev, b))
+    regions = []
+    for c, v in by.items():
+        v.sort()
+        cur = None
+        for s, e, p, ev, b in v:
+            if cur and s - cur["end"] <= merge:
+                cur["end"] = max(cur["end"], e)
+                cur["ident"] = max(cur["ident"], p)
+                cur["evalue"] = min(cur["evalue"], ev)
+                cur["bits"] += b
+            else:
+                if cur:
+                    regions.append(cur)
+                cur = {"contig": c, "start": s, "end": e, "ident": p, "evalue": ev, "bits": b}
+        if cur:
+            regions.append(cur)
+    return sorted(regions, key=lambda r: -r["bits"])
+
+
+def distance(a_start, a_end, b_start, b_end):
+    """Gap in bp between two intervals; 0 when they overlap."""
+    return max(0, max(a_start, b_start) - min(a_end, b_end))
+
+
+def gene_coords(gff, gene_id):
+    if gene_id in ("", "-"):
+        return None
+    with opener(gff) as fh:
+        for line in fh:
+            if line.startswith("#"):
+                continue
+            f = line.rstrip("\n").split("\t")
+            if len(f) > 8 and f[2] == "gene" and f"ID={gene_id};" in f[8] + ";":
+                return f[0], int(f[3]), int(f[4])
+    return None
+
+
+def genes_on(gff, contig):
+    out = []
+    with opener(gff) as fh:
+        for line in fh:
+            if line.startswith("#"):
+                continue
+            f = line.rstrip("\n").split("\t")
+            if len(f) > 8 and f[2] == "gene" and f[0] == contig:
+                out.append((int(f[3]), int(f[4]), f[8].split("ID=")[1].split(";")[0]))
+    return out
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--genomes", required=True)
+    ap.add_argument("--queries", required=True)
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--evalue", type=float, default=1e-5)
+    ap.add_argument("--merge", type=int, default=2000)
+    ap.add_argument("--top", type=int, default=3)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    os.makedirs(a.out, exist_ok=True)
+    fo = open(os.path.join(a.out, "matpi_hits.tsv"), "w")
+    fo.write("genome\trank\tcontig\tstart\tend\tbest_identity\tbest_evalue\tbitscore\ton_matMc_contig\tdistance_to_matMc_bp\toverlapping_gene\n")
+    for line in open(a.genomes):
+        name, fa, gff, mc = line.rstrip("\n").split("\t")
+        db = os.path.join(a.tmp, "tb_" + name)
+        genome = os.path.join(a.tmp, name + ".fa")
+        subprocess.run(f"zcat -f {fa} > {genome}", shell=True, check=True)
+        subprocess.run(["makeblastdb", "-in", genome, "-dbtype", "nucl", "-out", db, "-logfile", "/dev/null"], check=True)
+        out = os.path.join(a.tmp, name + ".tb")
+        subprocess.run(["tblastn", "-query", a.queries, "-db", db, "-seg", "no", "-evalue", str(a.evalue), "-out", out,
+                        "-outfmt", "6 sseqid sstart send pident evalue bitscore"], check=True)
+        hits = []
+        for l in open(out):
+            c, s, e, p, ev, b = l.split("\t")
+            hits.append((c, int(s), int(e), float(p), float(ev), float(b)))
+        regions = merge_hits(hits, a.merge)[:a.top]
+        mcc = gene_coords(gff, mc)
+        for i, r in enumerate(regions, 1):
+            on = "NA"
+            dist = "NA"
+            if mcc:
+                on = "yes" if r["contig"] == mcc[0] else "no"
+                if on == "yes":
+                    dist = distance(r["start"], r["end"], mcc[1], mcc[2])
+            gl = [g[2] for g in genes_on(gff, r["contig"]) if g[1] >= r["start"] and g[0] <= r["end"]]
+            fo.write(f"{name}\t{i}\t{r['contig']}\t{r['start']}\t{r['end']}\t{r['ident']}\t{r['evalue']}\t{r['bits']}\t{on}\t{dist}\t{','.join(gl) or '-'}\n")
+        for f in (genome, out):
+            os.remove(f)
+    fo.close()
+    print(open(os.path.join(a.out, "matpi_hits.tsv")).read())
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/pm_lead_followup.py b/scripts/pm_lead_followup.py
new file mode 100644
index 00000000..689980e8
--- /dev/null
+++ b/scripts/pm_lead_followup.py
@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+"""Structural follow-up of PM-family detector leads, and a rescan of genomes with no call.
+
+Read-only discovery tool. It does not change the detector.
+
+lead   : for every `PM` locus in detection_report.yaml files, take the gene_evidence entries for matMc / matPi
+         (contig, start, end, strand), find the predicted gene (BFD funannotate GFF3) that overlaps each, test that
+         protein with Pfam HMG_box / HMG_box_2 / Homeodomain (hmmsearch, GA cutoff), and write the gene order of
+         the locus +/- --flank genes with strands. Output: lead_genes.tsv, lead_summary.tsv.
+scan   : for genomes with no PM call, run hmmsearch (HMG_box, HMG_box_2, Homeodomain) over the proteome and diamond blastp
+         against the curated PM proteins (matMc, matPi, matMi) and the curated S. pombe mat1 proteins. Output: scan_genes.tsv,
+         scan_pairs.tsv (candidate genes within --near genes on one contig).
+Usage: pm_lead_followup.py lead --runs RUNS_DIR --genomes LIST --out OUT --hmm HMM
+       pm_lead_followup.py scan --genomes LIST --out OUT --hmm HMM --controls FAA
+Pfam and diamond are needed on PATH (module hmmer/3.4, diamond).
+"""
+import argparse
+import collections
+import gzip
+import os
+import re
+import subprocess
+import sys
+
+ANN = "/bigdata/stajichlab/shared/projects/BFD/Fungi_BFD_runs/genome_annotation"
+DOMAINS = ("HMG_box", "HMG_box_2", "Homeodomain")
+
+
+def opener(p):
+    return gzip.open(p, "rt") if p.endswith(".gz") else open(p)
+
+
+def read_gff_genes(gff):
+    """-> {contig: [(start, end, strand, gene_id)]} sorted by start."""
+    out = collections.defaultdict(list)
+    with opener(gff) as fh:
+        for line in fh:
+            if line.startswith("#"):
+                continue
+            f = line.rstrip("\n").split("\t")
+            if len(f) < 9 or f[2] != "gene":
+                continue
+            m = re.search(r"ID=([^;]+)", f[8])
+            out[f[0]].append((int(f[3]), int(f[4]), f[6], m.group(1) if m else ""))
+    for v in out.values():
+        v.sort()
+    return out
+
+
+def overlapping_gene(genes, contig, s, e):
+    """Gene with the largest overlap with [s, e] on contig -> (index, gene tuple) or (None, None)."""
+    best, bi = 0, None
+    for i, g in enumerate(genes.get(contig, [])):
+        ov = min(e, g[1]) - max(s, g[0]) + 1
+        if ov > best:
+            best, bi = ov, i
+    return (bi, genes[contig][bi]) if bi is not None else (None, None)
+
+
+def hmm_domains(proteome, hmm, tmp, tag):
+    """{protein_id: [(domain, evalue)]} from hmmsearch --cut_ga."""
+    tbl = os.path.join(tmp, tag + ".tbl")
+    faa = os.path.join(tmp, tag + ".faa")
+    subprocess.run(f"zcat -f {proteome} > {faa}", shell=True, check=True)
+    # hmmsearch cannot rewind a pipe when the HMM file holds several models, so search a plain file
+    subprocess.run(["hmmsearch", "--cut_ga", "--cpu", "2", "--domtblout", tbl, "-o", "/dev/null", hmm, faa], check=True)
+    out = collections.defaultdict(list)
+    for line in open(tbl):
+        if line[0] == "#":
+            continue
+        f = line.split()
+        out[re.sub(r"-T\d+$", "", f[0])].append((f[3], float(f[6])))
+    return out
+
+
+def layout_row(rows_idx, genes_c, hits, flank):
+    """Gene order text for the genes spanning the evidence indices +/- flank."""
+    lo, hi = max(0, min(rows_idx) - flank), min(len(genes_c) - 1, max(rows_idx) + flank)
+    out = []
+    for i in range(lo, hi + 1):
+        g = genes_c[i]
+        dom = ",".join(sorted({d for d, _ in hits.get(g[3], []) if d in DOMAINS}))
+        out.append((i, g[3], g[2], g[0], g[1], dom))
+    return out
+
+
+def do_lead(a):
+    import yaml
+    os.makedirs(a.out, exist_ok=True)
+    tmp = os.environ.get("SCRATCH", "/tmp")
+    fo = open(os.path.join(a.out, "lead_genes.tsv"), "w")
+    fs = open(os.path.join(a.out, "lead_summary.tsv"), "w")
+    fo.write("genome\tlocus\tgene_index\tgene\tstrand\tstart\tend\tdomain\tevidence\n")
+    fs.write("genome\tcontig\tmatMc_gene\tmatMc_domain\tmatPi_gene\tmatPi_domain\tgenes_between\tstrand_relation\n")
+    for line in open(a.genomes):
+        asm, _, name = line.rstrip("\n").partition("\t")
+        rep = os.path.join(a.runs, asm, "detection_report.yaml")
+        if not os.path.exists(rep):
+            continue
+        d = yaml.safe_load(open(rep))
+        pm = [x for x in (d.get("detected") or []) if x["family"].endswith(":PM")]
+        if not pm:
+            continue
+        P = f"{ANN}/{name}/predict_results"
+        genes = read_gff_genes(f"{P}/{name}.gff3.gz")
+        hits = hmm_domains(f"{P}/{name}.proteins.fa.gz", a.hmm, tmp, "lead")
+        for li, locus in enumerate(pm):
+            contig = locus["contig"]
+            ev, idx = {}, []
+            for e in locus["gene_evidence"]:
+                if e["gene"] in ("matMc", "matPi", "matMi"):
+                    i, g = overlapping_gene(genes, contig, e["start"], e["end"])
+                    if g:
+                        ev[e["gene"]] = (i, g, f"{e['identity']}% id, {e['coverage']}% cov")
+                        idx.append(i)
+            if not idx:
+                continue
+            for r in layout_row(idx, genes[contig], hits, a.flank):
+                tag = ";".join(f"{k}:{v[2]}" for k, v in ev.items() if v[0] == r[0])
+                fo.write(f"{name}\t{contig}#{li}\t{r[0]}\t{r[1]}\t{r[2]}\t{r[3]}\t{r[4]}\t{r[5]}\t{tag}\n")
+
+            def dom(k):
+                return ",".join(sorted({x for x, _ in hits.get(ev[k][1][3], []) if x in DOMAINS})) if k in ev else "NA"
+            mc, pi = ev.get("matMc"), ev.get("matPi")
+            btw = rel = "NA"
+            if mc and pi and mc[0] != pi[0]:
+                btw = abs(mc[0] - pi[0]) - 1
+                left, right = (mc, pi) if mc[0] < pi[0] else (pi, mc)
+                rel = {"+-": "convergent", "-+": "divergent"}.get(left[1][2] + right[1][2], "same")
+            elif mc and pi:
+                btw, rel = "same gene", "fused"
+            fs.write(f"{name}\t{contig}\t{mc[1][3] if mc else 'NA'}\t{dom('matMc')}\t{pi[1][3] if pi else 'NA'}\t{dom('matPi')}\t{btw}\t{rel}\n")
+    fo.close(); fs.close()
+    print(open(os.path.join(a.out, "lead_summary.tsv")).read())
+
+
+def do_scan(a):
+    os.makedirs(a.out, exist_ok=True)
+    tmp = os.environ.get("SCRATCH", "/tmp")
+    subprocess.run(["diamond", "makedb", "--in", a.controls, "-d", os.path.join(tmp, "ctl"), "--quiet"], check=True)
+    fg = open(os.path.join(a.out, "scan_genes.tsv"), "w")
+    fp = open(os.path.join(a.out, "scan_pairs.tsv"), "w")
+    fg.write("genome\tgene\tcontig\tindex\tstrand\tdomain\tbest_control\tcontrol_evalue\tcontrol_identity\n")
+    fp.write("genome\tgene_a\tgene_b\tcontig\tgenes_between\tstrand_relation\tdomains\n")
+    for line in open(a.genomes):
+        name = line.strip().split("\t")[-1]
+        if not name:
+            continue
+        P = f"{ANN}/{name}/predict_results"
+        genes = read_gff_genes(f"{P}/{name}.gff3.gz")
+        order = {}
+        for c, v in genes.items():
+            for i, g in enumerate(v):
+                order[g[3]] = (c, i, g[2])
+        hits = hmm_domains(f"{P}/{name}.proteins.fa.gz", a.hmm, tmp, "scan")
+        out = os.path.join(tmp, "dm.tsv")
+        subprocess.run(f"zcat -f {P}/{name}.proteins.fa.gz | diamond blastp -d {os.path.join(tmp, 'ctl')} -o {out} --quiet "
+                       f"--max-target-seqs 1 -e 1e-3 --outfmt 6 qseqid sseqid evalue pident --threads 2 -q /dev/stdin",
+                       shell=True, check=True)
+        best = {}
+        for l in open(out):
+            f = l.split("\t")
+            best.setdefault(re.sub(r"-T\d+$", "", f[0]), (f[1].split("|")[-1] if "name=" not in f[1] else re.search(r"name=([^|]+)", f[1]).group(1), f[2], f[3].strip()))
+        cand = []
+        for g, hs in hits.items():
+            dm = ",".join(sorted({d for d, _ in hs if d in DOMAINS}))
+            if dm and g in order:
+                b = best.get(g, ("", "", ""))
+                c, i, s = order[g]
+                cand.append((c, i, s, g, dm))
+                fg.write(f"{name}\t{g}\t{c}\t{i}\t{s}\t{dm}\t{b[0]}\t{b[1]}\t{b[2]}\n")
+        for g in best:
+            if g in order and g not in {x[3] for x in cand}:
+                c, i, s = order[g]
+                fg.write(f"{name}\t{g}\t{c}\t{i}\t{s}\t\t{best[g][0]}\t{best[g][1]}\t{best[g][2]}\n")
+        cand.sort()
+        for x, y in zip(cand, cand[1:]):
+            if x[0] == y[0] and y[1] - x[1] <= a.near:
+                rel = {"+-": "convergent", "-+": "divergent"}.get(x[2] + y[2], "same")
+                fp.write(f"{name}\t{x[3]}\t{y[3]}\t{x[0]}\t{y[1] - x[1] - 1}\t{rel}\t{x[4]}|{y[4]}\n")
+    fg.close(); fp.close()
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("cmd", choices=["lead", "scan"])
+    ap.add_argument("--runs")
+    ap.add_argument("--genomes", required=True, help="TSV: ASMID<TAB>annotation folder name")
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--hmm", required=True)
+    ap.add_argument("--controls")
+    ap.add_argument("--flank", type=int, default=5)
+    ap.add_argument("--near", type=int, default=5)
+    a = ap.parse_args()
+    do_lead(a) if a.cmd == "lead" else do_scan(a)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/pm_locus_models.py b/scripts/pm_locus_models.py
new file mode 100644
index 00000000..c11f3545
--- /dev/null
+++ b/scripts/pm_locus_models.py
@@ -0,0 +1,155 @@
+#!/usr/bin/env python3
+"""Gene models and cross-genome orthology for HMG + homeodomain pairs (the PM-like locus).
+
+Read-only discovery tool.
+
+models : for each locus (TSV: name, genome fasta, contig, hd_start, hd_end), run exonerate protein2genome with the curated
+         matPi proteins in a window around the homeodomain-like region, keep the best-scoring model, build the CDS from the
+         exonerate `cds` features, translate it and run Pfam (HMG_box, HMG_box_2, Homeodomain, GA cutoff).
+         Output: models.tsv (name, contig, strand, cds_start, cds_end, exons, aa_len, score, query, domains) and models.faa.
+orthology : from a FASTA of protein sets (id = genome|role|gene, role in HMG, HD, HMG_locus, HD_locus), diamond all-vs-all;
+         for each locus protein and each other genome, the best hit among that genome's proteins of the same domain class and
+         whether it is that genome's locus protein (reciprocal best hit).
+Usage: pm_locus_models.py models --loci LOCI.tsv --queries Q.faa --hmm HMM --out OUT
+       pm_locus_models.py orthology --proteins ALL.faa --out OUT
+"""
+import argparse
+import collections
+import os
+import subprocess
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+from region_pfam_check import read_fasta_region, revcomp, translate  # noqa: E402
+
+
+def parse_exonerate_gff(text):
+    """-> list of models; model = dict(score, query, strand, cds=[(start,end)], contig). Coordinates 1-based on the window."""
+    models, cur = [], None
+    for line in text.splitlines():
+        if line.startswith("# --- START OF GFF DUMP"):
+            cur = {"cds": [], "score": 0, "query": "", "strand": "+", "contig": ""}
+        elif line.startswith("# --- END OF GFF DUMP"):
+            if cur and cur["cds"]:
+                models.append(cur)
+            cur = None
+        elif cur is not None and not line.startswith("#"):
+            f = line.split("\t")
+            if len(f) < 9:
+                continue
+            if f[2] == "gene":
+                cur["score"] = float(f[5]) if f[5] != "." else 0
+                cur["strand"] = f[6]
+                cur["contig"] = f[0]
+                for kv in f[8].split(";"):
+                    kv = kv.strip()
+                    if kv.startswith("sequence "):
+                        cur["query"] = kv.split(" ", 1)[1]
+            elif f[2] == "cds":
+                cur["cds"].append((int(f[3]), int(f[4])))
+    return models
+
+
+def cds_protein(window_seq, cds, strand):
+    """Translate the concatenated CDS exons of a model. cds: list of (start,end) 1-based on window_seq."""
+    parts = [window_seq[s - 1:e] for s, e in sorted(cds)]
+    dna = "".join(parts)
+    if strand == "-":
+        dna = revcomp(dna)
+    prot = translate(dna)
+    return prot.rstrip("*")
+
+
+def do_models(a):
+    os.makedirs(a.out, exist_ok=True)
+    fo = open(os.path.join(a.out, "models.tsv"), "w")
+    fa = open(os.path.join(a.out, "models.faa"), "w")
+    fo.write("name\tcontig\tstrand\tcds_start\tcds_end\texons\taa_len\tscore\tquery\tdomains\n")
+    for line in open(a.loci):
+        name, fasta, contig, s, e = line.rstrip("\n").split("\t")
+        ws, we = max(1, int(s) - a.pad), int(e) + a.pad
+        seq = read_fasta_region(fasta, contig, ws, we)
+        win = os.path.join(a.tmp, "win.fa")
+        open(win, "w").write(f">{contig}\n{seq}\n")
+        out = subprocess.run(["exonerate", "--model", "protein2genome", "--query", a.queries, "--target", win,
+                              "--showtargetgff", "yes", "--showalignment", "no", "--showvulgar", "no", "--bestn", "1",
+                              "--percent", str(a.percent), "--exhaustive", "no"], capture_output=True, text=True).stdout
+        models = sorted(parse_exonerate_gff(out), key=lambda m: -m["score"])
+        if not models:
+            fo.write(f"{name}\t{contig}\t\t\t\t\t\t\t\tno_model\n")
+            continue
+        m = models[0]
+        prot = cds_protein(seq, m["cds"], m["strand"])
+        faa = os.path.join(a.tmp, "m.faa")
+        open(faa, "w").write(f">m\n{prot}\n")
+        tbl = os.path.join(a.tmp, "m.tbl")
+        subprocess.run(["hmmsearch", "--cut_ga", "--domtblout", tbl, "-o", "/dev/null", a.hmm, faa], check=True)
+        dom = sorted({l.split()[3] for l in open(tbl) if l[0] != "#"})
+        starts = ws - 1 + min(x for x, _ in m["cds"])
+        ends = ws - 1 + max(y for _, y in m["cds"])
+        fo.write(f"{name}\t{contig}\t{m['strand']}\t{starts}\t{ends}\t{len(m['cds'])}\t{len(prot)}\t{m['score']}\t{m['query']}\t{','.join(dom) or 'none'}\n")
+        fa.write(f">{name}\n{prot}\n")
+    fo.close()
+    fa.close()
+    print(open(os.path.join(a.out, "models.tsv")).read())
+
+
+def do_orthology(a):
+    os.makedirs(a.out, exist_ok=True)
+    seqs, cur = {}, None
+    for line in open(a.proteins):
+        if line[0] == ">":
+            cur = line[1:].strip().split()[0]
+            seqs[cur] = []
+        else:
+            seqs[cur].append(line.strip())
+    meta = {k: k.split("|") for k in seqs}  # genome, role, gene
+    db = os.path.join(a.tmp, "orth")
+    subprocess.run(["diamond", "makedb", "--in", a.proteins, "-d", db, "--quiet"], check=True)
+    tsv = os.path.join(a.tmp, "orth.tsv")
+    subprocess.run(["diamond", "blastp", "-q", a.proteins, "-d", db, "-o", tsv, "--ultra-sensitive", "-e", "1e-3", "--max-target-seqs", "500",
+                    "--outfmt", "6", "qseqid", "sseqid", "pident", "length", "evalue", "bitscore", "--quiet"], check=True)
+    hits = collections.defaultdict(list)
+    for l in open(tsv):
+        q, s, p, n, ev, b = l.rstrip("\n").split("\t")
+        hits[q].append((float(b), s, float(p), int(n)))
+    cls = {"HMG_locus": "HMG", "HD_locus": "HD", "HMG": "HMG", "HD": "HD"}
+    fo = open(os.path.join(a.out, "orthology.tsv"), "w")
+    fo.write("locus_protein\tother_genome\tbest_hit\thit_is_locus_protein\tidentity\taligned_aa\treciprocal\n")
+    best = {}
+    for q in seqs:
+        for other in {m[0] for m in meta.values()}:
+            cand = [(b, s, p, n) for b, s, p, n in hits[q] if meta[s][0] == other and cls[meta[s][1]] == cls[meta[q][1]] and s != q]
+            best[(q, other)] = max(cand) if cand else None
+    for q, (g, role, gene) in meta.items():
+        if not role.endswith("_locus"):
+            continue
+        for other in sorted({m[0] for m in meta.values()} - {g}):
+            b = best[(q, other)]
+            if not b:
+                fo.write(f"{q}\t{other}\tnone\t\t\t\t\n")
+                continue
+            s = b[1]
+            back = best[(s, g)]
+            fo.write(f"{q}\t{other}\t{s}\t{meta[s][1].endswith('_locus')}\t{b[2]}\t{b[3]}\t{bool(back and back[1] == q)}\n")
+    fo.close()
+    print(open(os.path.join(a.out, "orthology.tsv")).read())
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("cmd", choices=["models", "orthology"])
+    ap.add_argument("--loci")
+    ap.add_argument("--queries")
+    ap.add_argument("--hmm")
+    ap.add_argument("--proteins")
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--pad", type=int, default=2500)
+    ap.add_argument("--percent", type=int, default=10)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    do_models(a) if a.cmd == "models" else do_orthology(a)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/region_pfam_check.py b/scripts/region_pfam_check.py
new file mode 100644
index 00000000..6399d77f
--- /dev/null
+++ b/scripts/region_pfam_check.py
@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+"""Six-frame translation of genome regions and a Pfam check (HMG_box, HMG_box_2, Homeodomain).
+
+Read-only discovery tool. Used for regions that a tblastn hit points to but that carry no gene model, to ask whether the
+region encodes a homeodomain or HMG-box domain.
+
+Input  --regions TSV: name, genome fasta, contig, start, end (1-based, inclusive)
+       --hmm     HMM file with the Pfam models (GA cutoffs)
+Method: the region is widened by --pad bp each side; all six frames are translated; stop-free stretches of at least
+        --min-aa residues are kept as ORFs (a spliced gene can be split over several ORFs; no intron model is used);
+        hmmsearch --cut_ga on the ORFs.
+Output --out: region_pfam.tsv (name, region, orf_frame, orf_start, orf_end, aa_len, domain, evalue); orf_start/orf_end are
+        1-based and inclusive on the forward strand of the contig
+"""
+import argparse
+import os
+import subprocess
+import sys
+
+BASES = "TCAG"
+AA = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
+CODON = {a + b + c: AA[16 * i + 4 * j + k] for i, a in enumerate(BASES) for j, b in enumerate(BASES) for k, c in enumerate(BASES)}
+COMP = str.maketrans("ACGTacgtN", "TGCAtgcaN")
+
+
+def revcomp(s):
+    return s.translate(COMP)[::-1]
+
+
+def translate(seq):
+    return "".join(CODON.get(seq[i:i + 3].upper(), "X") for i in range(0, len(seq) - 2, 3))
+
+
+def orfs(seq, min_aa):
+    """Stop-free stretches of >= min_aa residues in the six frames. Returns (frame, start0, end0, aa).
+    Coordinates are 0-based on the forward strand of `seq`; frames 1-3 forward, -1..-3 reverse."""
+    out = []
+    n = len(seq)
+    for strand, s in ((1, seq), (-1, revcomp(seq))):
+        for f in range(3):
+            prot = translate(s[f:])
+            pos = 0
+            for chunk in prot.split("*"):
+                if len(chunk) >= min_aa:
+                    a0 = f + pos * 3
+                    a1 = a0 + len(chunk) * 3
+                    if strand == 1:
+                        out.append((f + 1, a0, a1, chunk))
+                    else:
+                        out.append((-(f + 1), n - a1, n - a0, chunk))
+                pos += len(chunk) + 1
+    return out
+
+
+def read_fasta_region(fa, contig, start, end):
+    """Sequence of contig[start-1:end] from a (plain or gz) FASTA, streamed."""
+    import gzip
+    op = gzip.open if fa.endswith(".gz") else open
+    buf, on = [], False
+    with op(fa, "rt") as fh:
+        for line in fh:
+            if line.startswith(">"):
+                if on:
+                    break
+                on = line[1:].split()[0] == contig
+            elif on:
+                buf.append(line.strip())
+    return "".join(buf)[start - 1:end]
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--regions", required=True)
+    ap.add_argument("--hmm", required=True)
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--pad", type=int, default=600)
+    ap.add_argument("--min-aa", type=int, default=40)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    os.makedirs(a.out, exist_ok=True)
+    fo = open(os.path.join(a.out, "region_pfam.tsv"), "w")
+    fo.write("name\tregion\torf_frame\torf_start\torf_end\taa_len\tdomain\tevalue\n")
+    for line in open(a.regions):
+        name, fa, contig, s, e = line.rstrip("\n").split("\t")
+        s, e = max(1, int(s) - a.pad), int(e) + a.pad
+        seq = read_fasta_region(fa, contig, s, e)
+        faa = os.path.join(a.tmp, "orfs.faa")
+        meta = {}
+        with open(faa, "w") as fh:
+            for i, (fr, o0, o1, prot) in enumerate(orfs(seq, a.min_aa)):
+                fh.write(f">o{i}\n{prot}\n")
+                meta[f"o{i}"] = (fr, s + o0, s + o1 - 1, len(prot))  # 1-based, inclusive
+        tbl = os.path.join(a.tmp, "orfs.tbl")
+        subprocess.run(["hmmsearch", "--cut_ga", "--domtblout", tbl, "-o", "/dev/null", a.hmm, faa], check=True)
+        hits = {}
+        for l in open(tbl):
+            if l[0] != "#":
+                f = l.split()
+                hits.setdefault(f[0], []).append((f[3], f[6]))
+        region = f"{contig}:{s}-{e}"
+        if not hits:
+            fo.write(f"{name}\t{region}\t\t\t\t\tnone\t\n")
+        for oid, hs in hits.items():
+            fr, o0, o1, n = meta[oid]
+            for dom, ev in hs:
+                fo.write(f"{name}\t{region}\t{fr}\t{o0}\t{o1}\t{n}\t{dom}\t{ev}\n")
+    fo.close()
+    print(open(os.path.join(a.out, "region_pfam.tsv")).read())
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/rnaseq_locus_expression.slurm b/scripts/rnaseq_locus_expression.slurm
new file mode 100644
index 00000000..563d217e
--- /dev/null
+++ b/scripts/rnaseq_locus_expression.slurm
@@ -0,0 +1,37 @@
+#!/usr/bin/bash -l
+#SBATCH --job-name=rna-locus
+#SBATCH --partition=epyc
+#SBATCH --cpus-per-task=4
+#SBATCH --mem=24gb
+#SBATCH --time=6:00:00
+#SBATCH --output=/bigdata/stajichlab/jstajich/projects/MATPredict/logs/rnalocus_%A_%a.log
+# Map public RNA-seq to a genome and measure depth over annotated genes and over named loci.
+# Env: SRC (worktree), OUT (folder), RUN (SRA accession; .sra already fetched under $OUT/sra/$RUN), ENA_COUNT (read pairs),
+#      NAME (label), FASTA, GFF3, LOCI (TSV: name chrom start end, 1-based inclusive; extra regions to report), REPORT (space-separated
+#      names to report: gene ids and loci names).
+# Steps: fasterq-dump, read-count check against ENA (fail on mismatch), hisat2, samtools bedcov, locus_expression.py.
+set -uo pipefail
+: "${SRC:?}" "${OUT:?}" "${RUN:?}" "${ENA_COUNT:?}" "${NAME:?}" "${FASTA:?}" "${GFF3:?}" "${LOCI:?}" "${REPORT:?}"
+module load sratoolkit/3.2.0 hisat2/2.2.1 samtools/1.22.1
+W="${SCRATCH:?}/rna_$NAME"; mkdir -p "$W" "$OUT/$NAME"
+cd "$W"
+fasterq-dump "$OUT/sra/$RUN/$RUN.sra" --split-files -e ${SLURM_CPUS_PER_TASK:-4} -O "$W" -t "$W" > fd.log 2>&1 || { echo "fasterq-dump failed"; tail -3 fd.log; exit 1; }
+n1=$(( $(wc -l < "${RUN}_1.fastq") / 4 )); n2=$(( $(wc -l < "${RUN}_2.fastq") / 4 ))
+echo "reads: mate1=$n1 mate2=$n2 ena=$ENA_COUNT"
+if [[ "$n1" != "$ENA_COUNT" || "$n2" != "$ENA_COUNT" ]]; then echo "READ COUNT MISMATCH"; exit 1; fi
+zcat -f "$FASTA" > genome.fa
+hisat2-build -p ${SLURM_CPUS_PER_TASK:-4} genome.fa idx > hb.log 2>&1
+hisat2 -p ${SLURM_CPUS_PER_TASK:-4} --dta --max-intronlen 5000 -x idx -1 "${RUN}_1.fastq" -2 "${RUN}_2.fastq" 2> "$OUT/$NAME/hisat2.log" | samtools sort -@ ${SLURM_CPUS_PER_TASK:-4} -o "$NAME.bam" -
+samtools index "$NAME.bam"
+# BED of all genes (0-based start) plus the named loci
+zcat -f "$GFF3" | awk -F'\t' '$3=="gene"{split($9,a,";"); id=a[1]; sub("ID=","",id); print $1"\t"$4-1"\t"$5"\t"id}' > regions.bed
+awk -F'\t' '{print $2"\t"$3-1"\t"$4"\t"$1}' "$LOCI" >> regions.bed
+samtools bedcov regions.bed "$NAME.bam" > bedcov.tsv
+python3 "$SRC/scripts/locus_expression.py" --bedcov bedcov.tsv --report $REPORT --gene-prefix "${GENE_PREFIX:-}" --out "$OUT/$NAME/locus_expression.tsv"
+# spliced reads over each named locus (CIGAR with N)
+while IFS=$'\t' read -r lname chrom s e; do
+  tot=$(samtools view -c "$NAME.bam" "$chrom:$s-$e"); sp=$(samtools view "$NAME.bam" "$chrom:$s-$e" | awk '$6 ~ /N/' | wc -l)
+  echo -e "$lname\treads_overlapping=$tot\tspliced_reads=$sp" | tee -a "$OUT/$NAME/spliced.tsv"
+done < "$LOCI"
+cp "$NAME.bam" "$NAME.bam.bai" "$OUT/$NAME/" 2>/dev/null
+echo done
diff --git a/scripts/unannotated_genome_search.py b/scripts/unannotated_genome_search.py
new file mode 100644
index 00000000..2106322c
--- /dev/null
+++ b/scripts/unannotated_genome_search.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python3
+"""Annotation-free search for HMG-box and homeodomain regions in assemblies without gene models.
+
+Read-only discovery tool. For genomes that BFD did not annotate (fragmentary assemblies), a gene-order scan is not possible. This script
+searches the assembly directly with tblastn and reports, per genome, the regions that match HMG-class and homeodomain-class controls and
+the contigs that carry both within --pair-dist bp.
+
+Queries (FASTA headers): the class comes from the header. Two header styles are understood:
+  curated '>id|gene|class' (class sexM, sexP -> HMG; matMc, mat1-Mc, matMi... -> HMG; matPi, mat1-Pc, mat1-Pi, matPc -> HD)
+  free text containing 'hd1' or 'hd2' -> HD
+Other classes (flank genes) are ignored.
+Per genome (TSV: name, fasta): tblastn (E <= --evalue, SEG off); hits of one class on one contig closer than --merge bp are merged into
+a region; a pair is an HMG region and an HD region on one contig with a gap <= --pair-dist bp.
+Output (--out): regions.tsv (genome, class, contig, start, end, identity, evalue, bitscore) and summary.tsv (genome, contigs, bp,
+hmg_regions, hd_regions, pairs, contigs_with_pair, longest_pair_contig_bp).
+Limit: tblastn with controls from Mucoromycota and Taphrinomycotina finds HMG and homeodomain genes of any family; a pair in a short contig
+is weak evidence (contigs are shorter than the pair distance), and no pair is not evidence of absence.
+"""
+import argparse
+import collections
+import gzip
+import os
+import re
+import subprocess
+import sys
+
+HMG = {"sexM", "sexP", "matMc", "mat1-Mc", "matMi", "mat1-Mi", "matMc|"}
+HD = {"matPi", "mat1-Pc", "mat1-Pi", "matPc", "HD1", "HD2"}
+
+
+def query_class(header):
+    """'HMG', 'HD' or None from a FASTA header (without '>')."""
+    h = header.strip()
+    low = h.lower()
+    if "|" in h:
+        tail = h.split("|")[-1].split()[0]
+        if "name=" in h:
+            for tok in h.split("|"):
+                if tok.startswith("name="):
+                    tail = tok[5:]
+        if tail in HMG:
+            return "HMG"
+        if tail in HD:
+            return "HD"
+        return None
+    if "hd1" in low or "hd2" in low:
+        return "HD"
+    return None
+
+
+def merge(hits, gap):
+    """hits: (contig, start, end, ident, evalue, bits) -> merged regions sorted by contig and start."""
+    by = collections.defaultdict(list)
+    for c, s, e, p, ev, b in hits:
+        by[c].append((min(s, e), max(s, e), p, ev, b))
+    out = []
+    for c, v in by.items():
+        v.sort()
+        cur = None
+        for s, e, p, ev, b in v:
+            if cur and s - cur[2] <= gap:
+                cur[2] = max(cur[2], e)
+                cur[3] = max(cur[3], p)
+                cur[4] = min(cur[4], ev)
+                cur[5] += b
+            else:
+                if cur:
+                    out.append(tuple(cur))
+                cur = [c, s, e, p, ev, b]
+        if cur:
+            out.append(tuple(cur))
+    return sorted(out)
+
+
+def pairs(hmg, hd, dist):
+    """(hmg_region, hd_region) with both on one contig and a gap <= dist."""
+    out = []
+    for a in hmg:
+        for b in hd:
+            if a[0] == b[0] and max(0, max(a[1], b[1]) - min(a[2], b[2])) <= dist:
+                out.append((a, b))
+    return out
+
+
+def main():
+    ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--genomes", required=True)
+    ap.add_argument("--queries", nargs="+", required=True, help="FASTA files; classes from headers")
+    ap.add_argument("--out", required=True)
+    ap.add_argument("--evalue", type=float, default=1e-5)
+    ap.add_argument("--merge", type=int, default=2000)
+    ap.add_argument("--pair-dist", type=int, default=20000)
+    ap.add_argument("--tmp", default=os.environ.get("SCRATCH", "/tmp"))
+    a = ap.parse_args()
+    os.makedirs(a.out, exist_ok=True)
+    qfa = {"HMG": os.path.join(a.tmp, "q_hmg.faa"), "HD": os.path.join(a.tmp, "q_hd.faa")}
+    handles = {k: open(v, "w") for k, v in qfa.items()}
+    counts = collections.Counter()
+    for path in a.queries:
+        cur, buf = None, []
+        for line in open(path):
+            if line[0] == ">":
+                if cur:
+                    handles[cur].write("".join(buf))
+                    counts[cur] += 1
+                cls = query_class(line[1:])
+                cur, buf = cls, ([line] if cls else [])
+            elif cur:
+                buf.append(line)
+        if cur:
+            handles[cur].write("".join(buf))
+            counts[cur] += 1
+    for h in handles.values():
+        h.close()
+    print("queries:", dict(counts))
+    fr = open(os.path.join(a.out, "regions.tsv"), "w")
+    fs = open(os.path.join(a.out, "summary.tsv"), "w")
+    fr.write("genome\tclass\tcontig\tstart\tend\tidentity\tevalue\tbitscore\n")
+    fs.write("genome\tcontigs\tbp\thmg_regions\thd_regions\tpairs\tcontigs_with_pair\tlongest_pair_contig_bp\n")
+    for line in open(a.genomes):
+        name, fasta = line.rstrip("\n").split("\t")[:2]
+        safe = re.sub(r"[^A-Za-z0-9_.-]", "_", name)  # the label may hold '|' or spaces; file names must be shell-safe
+        genome = os.path.join(a.tmp, safe + ".fa")
+        subprocess.run(["bash", "-c", f"zcat -f \"$0\" > \"$1\"", fasta, genome], check=True)
+        db = os.path.join(a.tmp, "db_" + safe)
+        subprocess.run(["makeblastdb", "-in", genome, "-dbtype", "nucl", "-out", db, "-logfile", "/dev/null"], check=True)
+        lens, cur = {}, None
+        for l in open(genome):
+            if l[0] == ">":
+                cur = l[1:].split()[0]
+                lens[cur] = 0
+            else:
+                lens[cur] += len(l.strip())
+        regs = {}
+        for cls in ("HMG", "HD"):
+            out = os.path.join(a.tmp, safe + "." + cls + ".tb")
+            subprocess.run(["tblastn", "-query", qfa[cls], "-db", db, "-seg", "no", "-evalue", str(a.evalue), "-out", out,
+                            "-outfmt", "6 sseqid sstart send pident evalue bitscore"], check=True)
+            hits = []
+            for l in open(out):
+                c, s, e, p, ev, b = l.split("\t")
+                hits.append((c, int(s), int(e), float(p), float(ev), float(b)))
+            regs[cls] = merge(hits, a.merge)
+            for r in regs[cls]:
+                fr.write(f"{name}\t{cls}\t{r[0]}\t{r[1]}\t{r[2]}\t{r[3]}\t{r[4]}\t{r[5]}\n")
+            os.remove(out)
+        pr = pairs(regs["HMG"], regs["HD"], a.pair_dist)
+        pc = {p[0][0] for p in pr}
+        longest = max((lens[c] for c in pc), default=0)
+        fs.write(f"{name}\t{len(lens)}\t{sum(lens.values())}\t{len(regs['HMG'])}\t{len(regs['HD'])}\t{len(pr)}\t{len(pc)}\t{longest}\n")
+        os.remove(genome)
+    fr.close()
+    fs.close()
+    print(open(os.path.join(a.out, "summary.tsv")).read())
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/tests/test_adjacent_pair_null.py b/tests/test_adjacent_pair_null.py
new file mode 100644
index 00000000..48a6766e
--- /dev/null
+++ b/tests/test_adjacent_pair_null.py
@@ -0,0 +1,49 @@
+"""Tests for scripts/adjacent_pair_null.py (pair helpers and the p-value logic on a toy lineage)."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+spec = importlib.util.spec_from_file_location("adjacent_pair_null", SCRIPTS / "adjacent_pair_null.py")
+apn = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(apn)
+
+
+def test_has_pair_window_and_contig():
+    assert apn.has_pair([("c1", 10)], [("c1", 13)], 5, False)
+    assert not apn.has_pair([("c1", 10)], [("c1", 17)], 5, False)
+    assert not apn.has_pair([("c1", 10)], [("c2", 11)], 5, False)
+
+
+def test_has_pair_same_gene_is_not_a_pair():
+    assert not apn.has_pair([("c1", 10)], [("c1", 10)], 5, True)
+    assert apn.has_pair([("c1", 10), ("c1", 12)], [("c1", 10), ("c1", 12)], 5, True)
+
+
+def test_pair_strands():
+    a = [("c1", 10, "+")]
+    b = [("c1", 12, "+"), ("c1", 14, "-"), ("c1", 30, "+")]
+    assert apn.pair_strands(a, b, 5) == ["same", "opposite"]
+
+
+def _write(tmp_path, name, genes, cands):
+    with open(tmp_path / f"{name}.genes_all.tsv", "w") as fo:
+        fo.write("gene\tcontig\tstart\tend\tstrand\tindex\n")
+        for i, g in enumerate(genes):
+            fo.write(f"{g}\tc1\t{i * 10}\t{i * 10 + 5}\t+\t{i}\n")
+    with open(tmp_path / f"{name}.candidates.tsv", "w") as fo:
+        fo.write("gene\tcontig\tindex\tpfam\tpfam_evalue\tcontrol_class\tcontrol_id\tcontrol_evalue\n")
+        for g, d in cands.items():
+            fo.write(f"{g}\tc1\t0\t{d}\t1e-10\t\t\t\n")
+
+
+def test_main_counts_observed_pair(tmp_path, monkeypatch, capsys):
+    genes = [f"g{i}" for i in range(200)]
+    _write(tmp_path, "G1", genes, {"g10": "HMG_box", "g12": "Homeodomain"})
+    (tmp_path / "list.txt").write_text("G1\n")
+    out = tmp_path / "out.tsv"
+    monkeypatch.setattr("sys.argv", ["x", "--stage1", str(tmp_path), "--out", str(out), "--perms", "50", str(tmp_path / "list.txt") + ":L"])
+    apn.main()
+    rows = {l.split("\t")[1]: l.split("\t") for l in out.read_text().splitlines()[1:]}
+    assert rows["HMG+Homeo"][3] == "1"  # observed genomes
+    assert float(rows["HMG+Homeo"][4]) < 0.5  # a random pair in 200 genes is rare
+    assert rows["2xHomeo"][3] == "0"
diff --git a/tests/test_flank_idiomorph_probe.py b/tests/test_flank_idiomorph_probe.py
new file mode 100644
index 00000000..b5657294
--- /dev/null
+++ b/tests/test_flank_idiomorph_probe.py
@@ -0,0 +1,41 @@
+"""Tests for scripts/flank_idiomorph_probe.py (classify_gene)."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+spec = importlib.util.spec_from_file_location("flank_idiomorph_probe", SCRIPTS / "flank_idiomorph_probe.py")
+fip = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(fip)
+
+# genome B: contig c1 genes b0..b29 at index 0..29
+IDX_B = {f"b{i}": ("c1", i) for i in range(30)}
+FLANK = [f"a{i}" for i in range(1, 6)]
+ORTH = {f"a{i}": f"b{10 + i}" for i in range(1, 6)}  # flank maps to b11..b15
+
+
+def test_conserved_when_x_has_ortholog_in_region():
+    orth = dict(ORTH, x="b12x")
+    idx = dict(IDX_B, b12x=("c1", 12))
+    assert fip.classify_gene("x", FLANK, orth, idx, set(), 3, 25)[0] == "conserved"
+
+
+def test_absent_when_region_has_no_domain_gene():
+    assert fip.classify_gene("x", FLANK, ORTH, IDX_B, set(), 3, 25)[:2] == ("absent", 5)
+
+
+def test_other_domain_when_region_has_unrelated_domain_gene():
+    assert fip.classify_gene("x", FLANK, ORTH, IDX_B, {"b13"}, 3, 25)[0] == "other_domain"
+
+
+def test_domain_gene_far_from_region_does_not_count():
+    assert fip.classify_gene("x", FLANK, ORTH, IDX_B, {"b29"}, 3, 25)[0] == "absent"
+
+
+def test_no_synteny_with_too_few_flank_hits():
+    orth = {"a1": "b11", "a2": "b12"}
+    assert fip.classify_gene("x", FLANK, orth, IDX_B, set(), 3, 25)[0] == "no_synteny"
+
+
+def test_flank_genes_split_over_contigs_are_not_one_block():
+    idx = {f"b{i}": ("c1" if i < 12 else "c2", i) for i in range(30)}
+    assert fip.classify_gene("x", FLANK, ORTH, idx, set(), 5, 25)[0] == "no_synteny"
diff --git a/tests/test_locus_expression.py b/tests/test_locus_expression.py
new file mode 100644
index 00000000..2a08d63a
--- /dev/null
+++ b/tests/test_locus_expression.py
@@ -0,0 +1,47 @@
+"""Tests for scripts/locus_expression.py."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+spec = importlib.util.spec_from_file_location("locus_expression", SCRIPTS / "locus_expression.py")
+le = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(le)
+
+
+def test_parse_bedcov_mean_depth(tmp_path):
+    p = tmp_path / "b.tsv"
+    p.write_text("c1\t0\t1000\tg1\t5000\nc1\t2000\t2500\tg2\t0\n")
+    assert le.parse_bedcov(str(p)) == {"g1": (1000, 5.0), "g2": (500, 0.0)}
+
+
+def test_percentile_of():
+    assert le.percentile_of(5.0, [1.0, 2.0, 5.0, 9.0]) == 0.5
+    assert le.percentile_of(0.0, [1.0, 2.0]) == 0.0
+
+
+def test_locus_transcripts_helpers(tmp_path):
+    spec2 = importlib.util.spec_from_file_location("locus_transcripts", SCRIPTS / "locus_transcripts.py")
+    lt = importlib.util.module_from_spec(spec2)
+    spec2.loader.exec_module(lt)
+    gtf = tmp_path / "x.gtf"
+    gtf.write_text('c1\tStringTie\ttranscript\t100\t500\t.\t-\t.\ttranscript_id "t1"; gene_id "g1";\n'
+                   'c1\tStringTie\texon\t100\t200\t.\t-\t.\ttranscript_id "t1"; gene_id "g1";\n'
+                   'c1\tStringTie\texon\t400\t500\t.\t-\t.\ttranscript_id "t1"; gene_id "g1";\n'
+                   'c2\tStringTie\texon\t1\t50\t.\t+\t.\ttranscript_id "t2"; gene_id "g2";\n')
+    r = lt.read_gtf_transcripts(str(gtf), "c1")
+    assert list(r) == ["t1"] and r["t1"]["strand"] == "-" and r["t1"]["exons"] == [(100, 200), (400, 500)]
+    assert lt.overlaps(r["t1"]["exons"], 450, 600)
+    assert not lt.overlaps(r["t1"]["exons"], 600, 700)
+
+
+def test_strandedness_helpers():
+    spec3 = importlib.util.spec_from_file_location("infer_strandedness", SCRIPTS / "infer_strandedness.py")
+    st = importlib.util.module_from_spec(spec3)
+    spec3.loader.exec_module(st)
+    assert st.classify(900, 100) == "forward-stranded"
+    assert st.classify(80, 920) == "reverse-stranded"
+    assert st.classify(520, 480) == "unstranded"
+    assert st.classify(0, 0) == "no_reads"
+    assert st.implied_strand(90, 10, "forward-stranded") == "+"
+    assert st.implied_strand(90, 10, "reverse-stranded") == "-"
+    assert st.implied_strand(90, 10, "unstranded") == "unknown"
diff --git a/tests/test_pm_lead_followup.py b/tests/test_pm_lead_followup.py
new file mode 100644
index 00000000..9bf506f0
--- /dev/null
+++ b/tests/test_pm_lead_followup.py
@@ -0,0 +1,49 @@
+"""Tests for scripts/pm_lead_followup.py (gene lookup and layout helpers)."""
+import gzip
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+spec = importlib.util.spec_from_file_location("pm_lead_followup", SCRIPTS / "pm_lead_followup.py")
+pm = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(pm)
+
+GENES = {"c1": [(100, 200, "+", "g1"), (300, 400, "-", "g2"), (500, 600, "+", "g3")]}
+
+
+def test_overlapping_gene_picks_largest_overlap():
+    assert pm.overlapping_gene(GENES, "c1", 350, 520)[1][3] == "g2"  # 50 bp on g2, 21 bp on g3
+    assert pm.overlapping_gene(GENES, "c1", 510, 700)[1][3] == "g3"
+
+
+def test_overlapping_gene_none_when_no_overlap_or_contig():
+    assert pm.overlapping_gene(GENES, "c1", 210, 290) == (None, None)
+    assert pm.overlapping_gene(GENES, "c9", 100, 200) == (None, None)
+
+
+def test_read_gff_genes_sorted_and_gene_rows_only(tmp_path):
+    p = tmp_path / "x.gff3.gz"
+    with gzip.open(p, "wt") as fo:
+        fo.write("##gff-version 3\n")
+        fo.write("c1\tf\tgene\t300\t400\t.\t-\t.\tID=g2;Name=b\n")
+        fo.write("c1\tf\tmRNA\t300\t400\t.\t-\t.\tID=g2-T1\n")
+        fo.write("c1\tf\tgene\t100\t200\t.\t+\t.\tID=g1\n")
+    assert pm.read_gff_genes(str(p))["c1"] == [(100, 200, "+", "g1"), (300, 400, "-", "g2")]
+
+
+def test_layout_row_flank_and_domains():
+    hits = {"g2": [("HMG_box", 1e-9), ("Other", 1e-9)]}
+    rows = pm.layout_row([1], GENES["c1"], hits, 1)
+    assert [r[1] for r in rows] == ["g1", "g2", "g3"]
+    assert rows[1][5] == "HMG_box"
+    assert pm.layout_row([0], GENES["c1"], {}, 5)[0][0] == 0  # clipped at contig start
+
+
+def test_augustus_proteins_blocks(tmp_path):
+    spec2 = importlib.util.spec_from_file_location("augustus_proteins", SCRIPTS / "augustus_proteins.py")
+    ap = importlib.util.module_from_spec(spec2)
+    spec2.loader.exec_module(ap)
+    lines = ["# start gene g1\n", "c1\tAUGUSTUS\tgene\t1\t90\t.\t+\t.\tID=g1\n",
+             "# protein sequence = [MKVL\n", "# AAGG]\n", "# end gene g1\n",
+             "# start gene g2\n", "# protein sequence = [MSS]\n", "# end gene g2\n"]
+    assert list(ap.proteins(lines)) == [("g1", "MKVLAAGG"), ("g2", "MSS")]
diff --git a/tests/test_pm_locus_models.py b/tests/test_pm_locus_models.py
new file mode 100644
index 00000000..09054e79
--- /dev/null
+++ b/tests/test_pm_locus_models.py
@@ -0,0 +1,45 @@
+"""Tests for scripts/pm_locus_models.py (exonerate GFF parsing and CDS translation)."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+import sys
+sys.path.insert(0, str(SCRIPTS))
+spec = importlib.util.spec_from_file_location("pm_locus_models", SCRIPTS / "pm_locus_models.py")
+pl = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(pl)
+
+GFF = """Command line: [exonerate ...]
+# --- START OF GFF DUMP ---
+#
+w\texonerate:protein2genome:local\tgene\t11\t40\t394\t+\t.\tgene_id 0 ; sequence q1 ; gene_orientation +
+w\texonerate:protein2genome:local\tcds\t11\t19\t.\t+\t.\t
+w\texonerate:protein2genome:local\tcds\t31\t40\t.\t+\t.\t
+# --- END OF GFF DUMP ---
+# --- START OF GFF DUMP ---
+w\texonerate:protein2genome:local\tgene\t1\t9\t100\t-\t.\tgene_id 0 ; sequence q2 ; gene_orientation -
+w\texonerate:protein2genome:local\tcds\t1\t9\t.\t-\t.\t
+# --- END OF GFF DUMP ---
+"""
+
+
+def test_parse_exonerate_gff_models():
+    m = pl.parse_exonerate_gff(GFF)
+    assert len(m) == 2
+    assert m[0]["score"] == 394.0 and m[0]["query"] == "q1" and m[0]["strand"] == "+"
+    assert m[0]["cds"] == [(11, 19), (31, 40)]
+    assert m[1]["strand"] == "-" and m[1]["cds"] == [(1, 9)]
+
+
+def test_cds_protein_spliced_plus_strand():
+    # exon 1 = ATGGCCAAA (window bases 11-19), an intron, exon 2 = TAA (bases 31-33): M A K stop
+    window = "N" * 10 + "ATGGCCAAA" + "GT" + "A" * 9 + "TAA" + "GGGCCCT"
+    assert window[30:33] == "TAA"
+    assert pl.cds_protein(window, [(11, 19), (31, 33)], "+") == "MAK"  # the trailing stop is removed
+
+
+def test_cds_protein_minus_strand():
+    from region_pfam_check import revcomp
+    dna = "ATGGCCAAA"
+    window = "CC" + revcomp(dna) + "GG"
+    assert pl.cds_protein(window, [(3, 11)], "-") == "MAK"
diff --git a/tests/test_region_pfam_check.py b/tests/test_region_pfam_check.py
new file mode 100644
index 00000000..cbf0cbd7
--- /dev/null
+++ b/tests/test_region_pfam_check.py
@@ -0,0 +1,59 @@
+"""Tests for scripts/region_pfam_check.py (translation and ORF helpers) and scripts/matpi_tblastn.py (merge, distance)."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+
+
+def _load(name):
+    spec = importlib.util.spec_from_file_location(name, SCRIPTS / f"{name}.py")
+    mod = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(mod)
+    return mod
+
+
+rp = _load("region_pfam_check")
+mt = _load("matpi_tblastn")
+
+
+def test_translate_and_revcomp():
+    assert rp.translate("ATGGCCTAA") == "MA*"
+    assert rp.revcomp("AACG") == "CGTT"
+
+
+def test_orfs_forward_and_reverse_coordinates():
+    prot = "M" + "A" * 49  # 50 aa
+    dna = "ATG" + "GCC" * 49
+    seq = "TT" + dna + "TAA" + "CC"
+    fw = [o for o in rp.orfs(seq, 40) if o[0] > 0]
+    assert any(len(o[3]) >= 50 and o[3].startswith("MAAA") for o in fw)
+    rc = rp.revcomp(seq)
+    rv = [o for o in rp.orfs(rc, 40) if o[0] < 0]
+    hit = [o for o in rv if len(o[3]) >= 50 and o[3].startswith("MAAA")][0]
+    # the ORF spans the same 150 bases of the reverse-complemented input: start0 .. end0 inside the sequence
+    assert 0 <= hit[1] < hit[2] <= len(rc)
+    assert hit[2] - hit[1] >= 150
+
+
+def test_orfs_min_length_filter():
+    assert rp.orfs("ATGGCCTAA", 40) == []
+
+
+def test_merge_hits_and_distance():
+    hits = [("c1", 100, 300, 50.0, 1e-10, 80.0), ("c1", 1000, 1200, 60.0, 1e-20, 90.0), ("c1", 9000, 9100, 40.0, 1e-5, 30.0),
+            ("c2", 500, 400, 45.0, 1e-8, 70.0)]
+    regs = mt.merge_hits(hits, 2000)
+    assert [(r["contig"], r["start"], r["end"]) for r in regs] == [("c1", 100, 1200), ("c2", 400, 500), ("c1", 9000, 9100)]
+    assert regs[0]["ident"] == 60.0 and regs[0]["bits"] == 170.0
+    assert mt.distance(100, 200, 500, 600) == 300
+    assert mt.distance(100, 700, 500, 600) == 0
+
+
+def test_orf_coordinates_roundtrip_reverse_strand():
+    """The (start, end) of a reverse-strand ORF, 1-based inclusive, re-translates to the same protein."""
+    dna = "ATG" + "GCC" * 49 + "TAA"
+    seq = "TT" + rp.revcomp(dna) + "CC"  # the ORF is on the reverse strand
+    hit = [o for o in rp.orfs(seq, 40) if o[0] < 0 and o[3].startswith("MAAA")][0]
+    start1, end1 = 1 + hit[1], hit[2]  # 0-based half-open -> 1-based inclusive
+    assert end1 - start1 + 1 == 3 * len(hit[3])
+    assert rp.translate(rp.revcomp(seq[start1 - 1:end1])) == hit[3]
diff --git a/tests/test_unannotated_genome_search.py b/tests/test_unannotated_genome_search.py
new file mode 100644
index 00000000..413199e3
--- /dev/null
+++ b/tests/test_unannotated_genome_search.py
@@ -0,0 +1,35 @@
+"""Tests for scripts/unannotated_genome_search.py (query classes, region merging, pairing)."""
+import importlib.util
+import pathlib
+
+SCRIPTS = pathlib.Path(__file__).resolve().parents[1] / "scripts"
+spec = importlib.util.spec_from_file_location("unannotated_genome_search", SCRIPTS / "unannotated_genome_search.py")
+ug = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(ug)
+
+
+def test_query_class_header_styles():
+    assert ug.query_class("3231046_uomd23-19_MAT_Plus|gene1|sexP") == "HMG"
+    assert ug.query_class("4837_nrrl1555_MAT_Minus|gene1|sexM") == "HMG"
+    assert ug.query_class("5011_unknown-1_PM_combined|gene_index=1|name=matMc|role=core_MAT") == "HMG"
+    assert ug.query_class("5011_unknown-1_PM_combined|gene_index=0|name=matPi|role=core_MAT") == "HD"
+    assert ug.query_class("4896_972h_mat1_M|gene_index=2|name=mat1-Pc|role=core_MAT") == "HD"
+    assert ug.query_class("AMN92711.1 hd1-like protein [Rhizophagus irregularis]") == "HD"
+    assert ug.query_class("AMM63126.1 HD2 AMF mating type protein") == "HD"
+    assert ug.query_class("3108396_ai-2023a_MAT_Plus|gene1|tptA") is None
+    assert ug.query_class("AMM63120.1 choline transporter-like protein") is None
+
+
+def test_merge_regions():
+    hits = [("c1", 100, 300, 50.0, 1e-9, 60.0), ("c1", 1500, 1800, 60.0, 1e-20, 90.0), ("c1", 9000, 9100, 40.0, 1e-6, 30.0),
+            ("c2", 500, 400, 45.0, 1e-8, 70.0)]
+    reg = ug.merge(hits, 2000)
+    assert [(r[0], r[1], r[2]) for r in reg] == [("c1", 100, 1800), ("c1", 9000, 9100), ("c2", 400, 500)]
+    assert reg[0][3] == 60.0 and reg[0][5] == 150.0
+
+
+def test_pairs_distance_and_contig():
+    hmg = [("c1", 100, 300, 50.0, 1e-9, 60.0), ("c2", 100, 300, 50.0, 1e-9, 60.0)]
+    hd = [("c1", 15000, 15500, 40.0, 1e-9, 50.0), ("c1", 90000, 90100, 40.0, 1e-9, 50.0), ("c3", 100, 200, 40.0, 1e-9, 50.0)]
+    assert ug.pairs(hmg, hd, 20000) == [(hmg[0], hd[0])]
+    assert ug.pairs(hmg, hd, 100) == []