MATPredict · mating-type report

FoxysporumFo472020

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 02:37 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on NC_072845MAT1-2 locus: genes from left to right on NC_072845, 1,240,123 to 1,255,433: MAT1-1-5 (core MAT gene, minus strand); SLA2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); COX13 (conserved flank, plus strand).1,240 kb1,245 kb1,250 kb1,255 kb← 1,239.4 kb more to contig endcalled locusMAT1-1-5: core MAT gene, 1,240,123–1,240,254 (-), identity 37.5%, search hit onlyMAT1-1-5SLA2: conserved flank, 1,243,280–1,246,848 (+), identity 81.6%, search hit onlySLA2MAT1-1-3: core MAT gene, 1,250,594–1,251,368 (+), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,250,594–1,251,368 (+), identity 99.2%, search hit onlyMAT1-2-1COX13: conserved flank, 1,254,672–1,255,433 (+), identity 69.8%, search hit onlyCOX13
Gene order on NC_072845. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on NC_072845, 1,239,357 to 1,256,198FOBCDRAFT_225390 1,237,934-1,239,472 (+): Pre-mRNA splicing Prp18-interacting factor-domain-containing proteinFOBCDRAFT_225390FOBCDRAFT_225392 1,239,544-1,240,589 (-): S4 domain | Ribosomal protein S4/S9 N-terminal domain | domain-containing proteinFOBCDRAFT_225392FOBCDRAFT_225393 1,240,590-1,241,774 (+): ribosomal protein L21e-domain-containing proteinFOBCDRAFT_225393FOBCDRAFT_225395 1,242,968-1,247,337 (+): ANTH domain-containing proteinFOBCDRAFT_225395FOBCDRAFT_137157 1,248,237-1,249,044 (-): mating type protein MAT1-2-3FOBCDRAFT_137157FOBCDRAFT_294451 1,250,594-1,251,448 (+): mating type 1-2-1 proteinFOBCDRAFT_294451FOBCDRAFT_225403 1,254,599-1,255,556 (+): cytochrome c oxidase, subunit VIaFOBCDRAFT_225403FOBCDRAFT_251164 1,256,026-1,258,811 (+): anaphase-promoting complex subunit 5-domain-containing proteinFOBCDRAFT_251164
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
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-1-5 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
NC_072845:1,240,123–1,255,433 · 15.3 kb
Own genes
NC_072845:1,240,123–1,255,433 · 15.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 5 gene hits
Nearest contig end
1.2 Mb
Region (samtools)
NC_072845:1240123-1255433
Idiomorph scores
  • MAT1-2 402.0
  • MAT1-1 31.6

Margin over the next idiomorph: 370.4

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
MAT1-2-199.2MAT1-1-340.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-5core MATother idiomorph, not countedhit onlytblastn37.5cov 13.0%1.5e+0032 bits1,240,123–1,240,254 -–5180_44ba1_MAT_combinedFOBCDRAFT_225392
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,372 bits1,243,280–1,246,848 +–107463_unknown-1_MAT_MAT1-2FOBCDRAFT_225395
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%1.3e-1360 bits1,250,594–1,251,368 +–230073_uamh-1363_MAT_MAT1-1FOBCDRAFT_294451
MAT1-2-1core MAThit onlyDIAMOND, proteome99.2cov 100.0%3.6e-147402 bits1,250,594–1,251,368 +–61372_suf959_MAT_MAT1-2FOBCDRAFT_294451
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits1,254,672–1,255,433 +–578113_sxlc146_MAT_MAT1-2FOBCDRAFT_225403
MAT1-1-1expected, not found–
APN2expected, not found–

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
MATNC_072840:4,680,861–4,707,687MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATNC_072841:3,816,273–3,818,442MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FoxysporumFo472020.genome.fasta
Assembly
12 contigs · 50.4 Mb · N50 4.5 Mb
Genome SHA-256
7efd68c54af3eec1d7a17a756890728d0f7291bf33d31783dfd65692c30fe894
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
2026-11-07T02:35:52Z
Run time
103 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