MATPredict · mating-type report

FoxysporumFo5176

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 02:39 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on CM024366MAT1-1 locus: genes from left to right on CM024366, 3,155,400 to 3,172,692: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); MAT1-2-7 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand); MAT1-1-5 (core MAT gene, plus strand).3,155 kb3,160 kb3,165 kb3,170 kb917.2 kb more to contig end →called locusCOX13: conserved flank, 3,155,400–3,156,161 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 3,156,682–3,158,884 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 3,159,386–3,160,144 (-), identity 81.9%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 3,159,580–3,159,690 (-), identity 43.243%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 3,160,547–3,161,895 (+), identity 79.1%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 3,162,339–3,163,535 (+), identity 99.2%, search hit onlyMAT1-1-1MAT1-2-7: core MAT gene, 3,162,660–3,162,878 (+), identity 30.38%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)SLA2: conserved flank, 3,165,966–3,169,533 (-), identity 81.6%, search hit onlySLA2MAT1-1-5: core MAT gene, 3,172,561–3,172,692 (+), identity 37.5%, search hit onlyMAT1-1-5
Gene order on CM024366. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CM024366, 3,154,535 to 3,173,556HZS61_015698 3,155,400-3,156,161 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinHZS61_015698HZS61_015699 3,156,682-3,158,884 (+): DNA-(apurinic or apyrimidinic site) endonuclease 2HZS61_015699HZS61_015700 3,159,386-3,160,144 (-): HMG (high mobility group) box | domain-containing proteinHZS61_015700HZS61_015701 3,160,547-3,161,895 (+): Mating type protein 1-1-2 of unknown function | domain-containing proteinHZS61_015701HZS61_015702 3,162,339-3,163,535 (+): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinHZS61_015702HZS61_015703 3,164,296-3,164,554 (-): hypothetical proteinHZS61_015703HZS61_015704 3,165,966-3,169,533 (-): I/LWEQ domain | ANTH domain | domain-containing proteinHZS61_015704HZS61_015705 3,171,283-3,171,957 (-): Ribosomal protein L21e | domain-containing proteinHZS61_015705HZS61_015706 3,172,019-3,173,054 (+): S4 domain | Ribosomal protein S4/S9 N-terminal domain | domain-containing proteinHZS61_015706HZS61_015707 3,173,377-3,174,780 (-): Pre-mRNA splicing Prp18-interacting factor | domain-containing proteinHZS61_015707
FungiDB release 71 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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-2-7 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CM024366:3,155,400–3,172,692 · 17.3 kb
Own genes
CM024366:3,155,400–3,172,692 · 17.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 9 gene hits
Nearest contig end
918.1 kb
Region (samtools)
CM024366:3155400-3172692
Idiomorph scores
  • MAT1-1 712.0

Margin over the set-aside MAT1-2-1 hit: 38.7 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
MAT1-1-199.2MAT1-2-730.4100.0higher identity
MAT1-1-381.9MAT1-2-143.2100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits3,155,400–3,156,161 -–578113_sxlc146_MAT_MAT1-2HZS61_015698
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%8.0e-228640 bits3,156,682–3,158,884 +–2903220_liq80xsp_MAT_combinedHZS61_015699
MAT1-1-3core MAThit onlyDIAMOND, proteome81.9cov 88.9%5.1e-91258 bits3,159,386–3,160,144 -–5127_mo44_MAT_MAT1-1HZS61_015700
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn43.2cov 9.0%2.7e-0749 bits3,159,580–3,159,690 -–5180_44ba1_MAT_combinedHZS61_015700
MAT1-1-2core MAThit onlyDIAMOND, proteome79.1cov 98.3%1.5e-235642 bits3,160,547–3,161,895 +–5127_mo44_MAT_MAT1-1HZS61_015701
MAT1-1-1core MAThit onlyDIAMOND, proteome99.2cov 100.0%8.6e-265712 bits3,162,339–3,163,535 +–59765_880621a-1_MAT_MAT1-1HZS61_015702
MAT1-2-7core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn30.4cov 39.0%6.0e-0235 bits3,162,660–3,162,878 +–5158_cbs114723_MAT_unswitchedHZS61_015702
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,372 bits3,165,966–3,169,533 -–107463_unknown-1_MAT_MAT1-2HZS61_015704
MAT1-1-5core MAThit onlytblastn37.5cov 13.0%2.0e+0032 bits3,172,561–3,172,692 +–5180_44ba1_MAT_combinedHZS61_015706

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: too few of the family's genes found (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATCM024360:1,548,903–1,575,738MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATCM024364:1,534,634–1,541,584MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FoxysporumFo5176.genome.fasta
Assembly
19 contigs · 68.0 Mb · N50 4.1 Mb
Genome SHA-256
3e7a2e7716f3f6c784776bce7fb3765a315bb9ebe199c967c32bf948ef872533
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': 'genus', 'routing_taxid': 110618, '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 110618', 'routed_by': 'family taxid 110618 (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
2026-11-07T02:37:36Z
Run time
131 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