MATPredict · mating-type report

Foxysporum4287

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

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on CM000596.1MAT1-1 locus: genes from left to right on CM000596.1, 3,019,772 to 3,037,015: 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).3,020 kb3,025 kb3,030 kb3,035 kb946.5 kb more to contig end →called locusCOX13: conserved flank, 3,019,772–3,020,533 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 3,021,054–3,023,286 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 3,023,797–3,024,546 (-), identity 82.6%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 3,023,982–3,024,092 (-), identity 43.243%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 3,024,949–3,026,297 (+), identity 78.9%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 3,026,741–3,027,937 (+), identity 100.0%, search hit onlyMAT1-1-1MAT1-2-7: core MAT gene, 3,027,062–3,027,280 (+), identity 30.38%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)SLA2: conserved flank, 3,030,745–3,031,230 (-), identity 92.0%, search hit onlySLA2MAT1-1-5: core MAT gene, 3,036,884–3,037,015 (+), identity 37.5%, search hit onlyMAT1-1-5
Gene order on CM000596.1. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CM000596.1, 3,018,909 to 3,037,877FOXG_03612 3,015,198-3,019,361 (-): anaphase-promoting complex subunit 5FOXG_03612FOXG_03613 3,019,456-3,020,626 (-): cytochrome c oxidase subunit 6aFOXG_03613FOXG_03614 3,020,744-3,023,475 (+): AP endonuclease 2FOXG_03614FOXG_17746 3,023,797-3,024,546 (-): hypothetical proteinFOXG_17746FOXG_03615 3,024,949-3,026,297 (+): hypothetical proteinFOXG_03615FOXG_03616 3,026,741-3,027,937 (+): mating-type protein MAT-1FOXG_03616FOXG_18599 3,028,328-3,029,073 (-): hypothetical proteinFOXG_18599FOXG_03617 3,030,745-3,031,230 (-): hypothetical proteinFOXG_03617FOXG_03618 3,031,467-3,033,850 (-): hypothetical proteinFOXG_03618FOXG_03619 3,035,342-3,037,501 (-): 50S ribosomal protein L21eFOXG_03619FOXG_03620 3,036,403-3,037,669 (+): 40S ribosomal protein S9FOXG_03620FOXG_03621 3,037,600-3,039,206 (-): pre-mRNA-splicing factor SLU7FOXG_03621
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
  • MAT1-2-1 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
CM000596.1:3,019,772–3,037,015 · 17.2 kb
Own genes
CM000596.1:3,019,772–3,037,015 · 17.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 9 gene hits
Nearest contig end
947.4 kb
Region (samtools)
CM000596.1:3019772-3037015
Idiomorph scores
  • MAT1-1 722.0

Margin over the set-aside MAT1-2-1 hit: 39.4 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
MAT1-1-1100.0MAT1-2-730.4100.0higher identity
MAT1-1-382.6MAT1-2-143.2100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits3,019,772–3,020,533 -–578113_sxlc146_MAT_MAT1-2FOXG_03613
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%1.2e-227640 bits3,021,054–3,023,286 +–2903220_liq80xsp_MAT_combinedFOXG_03614
MAT1-1-3core MAThit onlyDIAMOND, proteome82.6cov 88.9%6.5e-91257 bits3,023,797–3,024,546 -–5127_mo44_MAT_MAT1-1FOXG_17746
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn43.2cov 10.0%8.5e-0747 bits3,023,982–3,024,092 -–28548_06cwm-g22_MAT_combinedFOXG_17746
MAT1-1-2core MAThit onlyDIAMOND, proteome78.9cov 98.3%1.7e-234639 bits3,024,949–3,026,297 +–5127_mo44_MAT_MAT1-1FOXG_03615
MAT1-1-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%9.4e-269722 bits3,026,741–3,027,937 +–59765_880621a-1_MAT_MAT1-1FOXG_03616
MAT1-2-7core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn30.4cov 39.0%9.4e-0234 bits3,027,062–3,027,280 +–5158_cbs114723_MAT_unswitchedFOXG_03616
SLA2conserved flankhit onlyDIAMOND, proteome92.0cov 15.5%1.5e-268762 bits3,030,745–3,031,230 -–5158_cbs114723_MAT_unswitchedFOXG_03617
MAT1-1-5core MAThit onlytblastn37.5cov 13.0%1.8e+0032 bits3,036,884–3,037,015 +–5180_44ba1_MAT_combinedFOXG_03619 (opposite strand)
FOXG_03620

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
MATCM000589.1:1,632,558–1,634,149MAT1-2MAT1-2-11too few of the family's genes found
MATCM000592.1:1,473,529–1,475,698MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
Foxysporum4287.genome.fasta
Assembly
88 contigs · 61.5 Mb · N50 4.6 Mb
Genome SHA-256
13a8588ff1867e273766629a912c44570bfd3a6447debde704a1d2baa3fb6714
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
2026-11-07T02:00:21Z
Run time
102 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