MATPredict · mating-type report

CdeneoformansXL280

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 02:15 UTC by MATPredict 0.8.1

Result

Mating type

alphahigh confidence

Called loci 1

alpha MAT family · Basidiomycota

high confidence
Gene order of the alpha locus on CM008076alpha locus: genes from left to right on CM008076, 1,518,701 to 1,640,730: PAN6 (conserved flank, minus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, minus strand); RPL39 (core MAT gene, plus strand); STE3 (core MAT gene, plus strand); SXI1 (core MAT gene, minus strand); FAO1 (conserved flank, minus strand).1,520 kb1,540 kb1,560 kb1,580 kb1,600 kb1,620 kb1,640 kb136.2 kb more to contig end →called locusPAN6: conserved flank, 1,518,701–1,520,365 (-), identity 100.0%, the two modelling tools disagreePAN6MFa: core MAT gene, 1,534,687–1,534,800 (-), identity 54.762%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 1,534,687–1,534,800 (-), identity 100.0%, gene modelMFalphaRPL39: core MAT gene, 1,540,627–1,540,882 (+), identity 92.0%, the two modelling tools disagreeRPL39STE3: core MAT gene, 1,577,450–1,578,767 (+), identity 100.0%, gene modelSTE3SXI1: core MAT gene, 1,637,243–1,638,600 (-), identity 100.0%, gene modelSXI1FAO1: conserved flank, 1,639,372–1,640,730 (-), identity 100.0%, gene modelFAO1
Gene order on CM008076. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
Location
CM008076:1,518,701–1,640,730 · 122.0 kb
Own genes
CM008076:1,518,701–1,640,730 · 122.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
142.3 kb
Region (samtools)
CM008076:1518701-1640730
Idiomorph scores
  • alpha 538.0

Margin over the set-aside MFa hit: 45.2 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
MFalpha100.0MFa54.8100.0higher identity
MFalpha100.0MFa54.8100.0higher identity
MFalpha100.0MFa54.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
PAN6conserved flankmodels differexonerateminiprot: 1,518,698–1,520,365, 95.8%100.0cov 100.0%< 1e-180474 bits1,518,701–1,520,365 -740410_jec20_MAT_a
MFacore MATlost to MFalpha, not countedhit onlytblastn54.8cov 100.0%4.3e-0743 bits1,534,687–1,534,800 -–40410_jec20_MAT_a
MFalphacore MATgene modelexonerate100.0cov 100.0%2.1e-2080 bits1,534,687–1,534,800 -140410_jec21_MAT_alpha
RPL39core MATmodels differexonerateminiprot: 1,540,627–1,540,885, 92.2%1 internal stopdefective gene model92.0cov 100.0%1.2e-1667 bits1,540,627–1,540,882 +240410_jec20_MAT_a
STE3core MATgene modelexonerate100.0cov 100.0%< 1e-180285 bits1,577,450–1,578,767 +440410_jec21_MAT_alpha
SXI1core MATgene modelexonerate100.0cov 100.0%4.4e-174538 bits1,637,243–1,638,600 -340410_jec21_MAT_alpha
FAO1conserved flankgene modelexonerate100.0cov 100.0%4.3e-112357 bits1,639,372–1,640,730 -640410_jec21_MAT_alpha
NOG2not searchable: no reference protein in the database
UAP1not searchable: no reference protein in the database

Withheld candidate loci 2

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: fewer than 2 genes could be modelled (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATCM008080:390,392–461,312alphaSTE3, SXI10fewer than 2 genes could be modelled
MATAWPH01000003:491,250–504,586alphaSTE3, SXI10fewer than 2 genes could be modelled

Provenance

Genome file
CdeneoformansXL280.genome.fasta
Assembly
37 contigs · 19.0 Mb · N50 1.1 Mb
Genome SHA-256
ec6daf2997f2139f837fc7fda743b9b82ae24d28d121605b5d0d3e95b3f6fc43
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'species', 'routing_taxid': 1884633, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1884633', 'routed_by': 'family taxid 1884633 (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, supported_min_bitscore=33.0
Run started
2026-11-07T02:14:48Z
Run time
24 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