MATPredict · mating-type report

TstipitatusATCC10500

MAT locus above the FungiDB annotation (gene by gene)

organism not recorded

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 02:02 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-1medium confidenceMAT1-2medium confidence

Called loci 2

MAT1-1 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-1 locus on EQ962658MAT1-1 locus: genes from left to right on EQ962658, 1,029,674 to 1,044,421: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).1,030 kb1,035 kb1,040 kb1,045 kb← 1,028.9 kb more to contig endcalled locusCOX13: conserved flank, 1,029,674–1,030,530 (-), identity 76.1%, search hit onlyCOX13APN2: conserved flank, 1,030,636–1,032,833 (+), identity 90.9%, search hit onlyAPN2MAT1-1-4: core MAT gene, 1,035,072–1,035,512 (-), identity 23.81%, search hit onlyMAT1-1-4MAT1-1-1: core MAT gene, 1,036,386–1,037,483 (+), identity 46.5%, search hit onlyMAT1-1-1SLA2: conserved flank, 1,040,599–1,044,421 (-), identity 88.2%, search hit onlySLA2
Gene order on EQ962658. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on EQ962658, 1,028,938 to 1,045,158TSTA_100840 1,029,399-1,030,530 (-): cytochrome c oxidase subunit VIa, putativeTSTA_100840TSTA_100850 1,030,636-1,033,025 (+): DNA lyase Apn2TSTA_100850TSTA_100860 1,034,687-1,035,901 (-): hypothetical proteinTSTA_100860TSTA_100870 1,036,386-1,037,483 (+): Mating-type protein MAT-1, putativeTSTA_100870TSTA_100880 1,040,288-1,044,421 (-): cytoskeleton assembly control protein Sla2, putativeTSTA_100880TSTA_100890 1,044,903-1,048,107 (-): conserved hypothetical proteinTSTA_100890
FungiDB release 68 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • conserved flank
  • search hit only
Location
EQ962658:1,029,674–1,044,421 · 14.7 kb
Own genes
EQ962658:1,029,674–1,044,421 · 14.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.0 Mb
Region (samtools)
EQ962658:1029674-1044421
Idiomorph scores
  • MAT1-1 188.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome76.1cov 85.1%2.6e-61180 bits1,029,674–1,030,530 -–162425_fgsc-a4_MAT_combinedTSTA_100840
APN2conserved flankhit onlyDIAMOND, proteome90.9cov 36.7%2.1e-268744 bits1,030,636–1,032,833 +–2903220_liq80xsp_MAT_combinedTSTA_100850
MAT1-1-4core MAThit onlytblastn23.8cov 53.0%1.0e-0340 bits1,035,072–1,035,512 -–199306_rmscc1040_MAT_MAT1-1TSTA_100860
MAT1-1-1core MAThit onlyDIAMOND, proteome46.5cov 20.4%2.5e-59188 bits1,036,386–1,037,483 +–27337_nbrc6119_MAT_MAT1-1TSTA_100870
SLA2conserved flankhit onlyDIAMOND, proteome88.2cov 100.0%< 1e-1801,434 bits1,040,599–1,044,421 -–1301501_voucher-215_MAT_MAT1-1TSTA_100880

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on EQ962662MAT1-2 locus: genes from left to right on EQ962662, 154,049 to 159,997: APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, plus strand).154 kb155 kb156 kb157 kb158 kb159 kb160 kb87.6 kb more to contig end →called locusAPN2: conserved flank, 154,049–155,248 (+), identity 70.8%, search hit onlyAPN2MAT1-1-3: core MAT gene, 157,442–158,533 (-), identity 40.5%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 157,442–158,533 (-), identity 54.8%, search hit onlyMAT1-2-1MAT1-2-4: core MAT gene, 159,079–159,997 (+), identity 33.6%, search hit onlyMAT1-2-4
Gene order on EQ962662. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on EQ962662, 153,749 to 160,297TSTA_008520 154,049-155,248 (+): conserved hypothetical proteinTSTA_008520TSTA_008530 157,442-158,680 (-): mating type protein MAT1-2-1TSTA_008530TSTA_008540 159,079-160,752 (+): mating locus protein, putativeTSTA_008540
FungiDB release 68 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • conserved flank
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
EQ962662:154,049–159,997 · 5.9 kb
Own genes
EQ962662:154,049–159,997 · 5.9 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
3 of 4 gene hits
Nearest contig end
87.9 kb
Region (samtools)
EQ962662:154049-159997
Idiomorph scores
  • MAT1-2 159.0

Margin over the set-aside MAT1-1-3 hit: 14.3 identity points (the narrowest overlap resolution below).

Score: bitscore of the best core-gene hit for each idiomorph.

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
MAT1-2-154.8MAT1-1-340.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
APN2conserved flankhit onlyDIAMOND, proteome70.8cov 10.0%5.0e-31109 bits154,049–155,248 +–746128_a1163_MAT_MAT1-1TSTA_008520
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.5cov 41.1%4.5e-1257 bits157,442–158,533 -–230073_uamh-1363_MAT_MAT1-1TSTA_008530
MAT1-2-1core MAThit onlyDIAMOND, proteome54.8cov 66.7%1.8e-48159 bits157,442–158,533 -–61372_suf959_MAT_MAT1-2TSTA_008530
MAT1-2-4core MAThit onlyDIAMOND, proteome33.6cov 97.6%8.9e-48152 bits159,079–159,997 +–746128_af293_MAT_MAT1-2TSTA_008540
SLA2expected, not found–
COX13expected, not found–

Withheld candidate loci 3

Places with some MAT-gene evidence that did not pass a quality gate. Most genomes have several. They are listed so a known locus can be checked against them, not because they are likely calls.

Reasons: too few of the family's genes found (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATEQ962652:4,677,544–4,684,364MAT1-2MAT1-2-1, CIMG_004071too few of the family's genes found
MATEQ962652:5,026,971–5,033,503MAT1-2MAT1-2-11too few of the family's genes found
MATEQ962661:848,886–865,344MAT1-2MAT1-2-1, MAT1-1-31too few of the family's genes found

Provenance

Genome file
TstipitatusATCC10500.genome.fasta
Assembly
821 contigs · 35.7 Mb · N50 4.4 Mb
Genome SHA-256
69eccf4593cfd468ef7957f04c879ce84917d35a405da397e501eebcd7703dad
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Ascomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'species', 'routing_taxid': 28568, 'routing_taxid_rank': 'family', 'flags': [], 'gmg_version': 'gmg 0.3.2 (66055154a)', 'index': 'bfd-reps-2026.10.5-s20000.gmgi', 'index_sha256': '0f319567f1cab17643e1daf7ffdc0e3b312bd43913e351568108d67a4a19702c', 'index_spec': 'bfd-reps-2026.10.5-s20000.gmgi', 'note': 'GmG called phylum Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 28568', 'routed_by': 'family taxid 28568 (lineage)'}, genetic_code=1, min_hits=2, require_core_role=True, max_polished_clusters_per_family=6, polish_strong_identity=50.0, polish_core_pair=True, partial_core_policy=off, homothallic_policy=off, confidence_cap_policy=off, cross_family_policy=off, fallback_after_withheld_policy=off, strong_single_gene_policy=off, scoped_roster_policy=off, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T02:01:52Z
Run time
61 s
Files
detection_report.yaml, detected_loci.gff3

Cite MATPredict as given in CITATION.cff at github.com/stajichlab/MATPredict. The reference records named in the gene tables are curated database entries; each record's metadata cites its source publication.

How to read this report

Idiomorph
The form of the mating-type locus a strain carries (for example MAT1-1 or MAT1-2, Plus or Minus). Basidiomycota HD and PR alleles are named after the reference they match.
High confidence
Every expected core MAT gene was found and modelled, with a conserved flanking gene where the family has one, on one contig.
Medium confidence
The core genes were found, but a gene could not be modelled, no conserved flank was found, or the locus is split (one step down).
Low confidence
A single isolated gene hit, or no core MAT gene.
Model status
Gene model: the reference protein was aligned to the genome to build the gene (exonerate, miniprot). Models differ: the two tools disagree on the structure; the alternate model is shown. Hit only: a search hit with no model, weaker evidence.
Identity
Percent amino-acid identity between the gene (or hit) and the closest reference protein.
Reference record
The curated database record whose protein matched best. Each record's metadata cites the publication or deposit it comes from.

Limits