MATPredict · mating-type report

FoxysporumNRRL32931

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 02:06 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 JH717844.1MAT1-1 locus: genes from left to right on JH717844.1, 2,976,091 to 2,993,420: 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).2,980 kb2,985 kb2,990 kb1,121.5 kb more to contig end →called locusCOX13: conserved flank, 2,976,091–2,976,852 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 2,977,376–2,979,608 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 2,980,119–2,980,868 (-), identity 82.6%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 2,980,304–2,980,414 (-), identity 43.243%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 2,981,271–2,982,619 (+), identity 78.6%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 2,983,063–2,984,259 (+), identity 99.4%, search hit onlyMAT1-1-1MAT1-2-7: core MAT gene, 2,983,384–2,983,602 (+), identity 30.38%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)SLA2: conserved flank, 2,986,692–2,990,259 (-), identity 82.2%, search hit onlySLA2MAT1-1-5: core MAT gene, 2,993,289–2,993,420 (+), identity 37.5%, search hit onlyMAT1-1-5
Gene order on JH717844.1. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on JH717844.1, 2,975,224 to 2,994,287FOYG_10153 2,971,517-2,975,680 (-): anaphase-promoting complex subunit 5FOYG_10153FOYG_10154 2,975,775-2,976,929 (-): cytochrome c oxidase subunit 6aFOYG_10154FOYG_10155 2,977,066-2,979,797 (+): AP endonuclease 2FOYG_10155FOYG_10156 2,980,119-2,980,868 (-): hypothetical proteinFOYG_10156FOYG_10157 2,981,271-2,982,619 (+): hypothetical proteinFOYG_10157FOYG_10158 2,983,063-2,984,259 (+): mating-type protein MAT-1FOYG_10158FOYG_10159 2,984,649-2,985,393 (-): hypothetical proteinFOYG_10159FOYG_10160 2,986,122-2,990,590 (-): hypothetical proteinFOYG_10160FOYG_10161 2,991,747-2,993,906 (-): 50S ribosomal protein L21eFOYG_10161FOYG_10162 2,992,808-2,994,074 (+): 40S ribosomal protein S9FOYG_10162FOYG_10163 2,994,005-2,995,611 (-): pre-mRNA-splicing factor SLU7FOYG_10163
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
JH717844.1:2,976,091–2,993,420 · 17.3 kb
Own genes
JH717844.1:2,976,091–2,993,420 · 17.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 9 gene hits
Nearest contig end
1.1 Mb
Region (samtools)
JH717844.1:2976091-2993420
Idiomorph scores
  • MAT1-1 719.0

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
MAT1-1-199.4MAT1-2-730.4100.0higher 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 bits2,976,091–2,976,852 -–578113_sxlc146_MAT_MAT1-2FOYG_10154
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%1.5e-225634 bits2,977,376–2,979,608 +–2903220_liq80xsp_MAT_combinedFOYG_10155
MAT1-1-3core MAThit onlyDIAMOND, proteome82.6cov 88.9%6.5e-91257 bits2,980,119–2,980,868 -–5127_mo44_MAT_MAT1-1FOYG_10156
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn43.2cov 10.0%6.6e-0747 bits2,980,304–2,980,414 -–28548_06cwm-g22_MAT_combinedFOYG_10156
MAT1-1-2core MAThit onlyDIAMOND, proteome78.6cov 98.3%3.5e-234639 bits2,981,271–2,982,619 +–5127_mo44_MAT_MAT1-1FOYG_10157
MAT1-1-1core MAThit onlyDIAMOND, proteome99.4cov 100.0%1.6e-267719 bits2,983,063–2,984,259 +–59765_880621a-1_MAT_MAT1-1FOYG_10158
MAT1-2-7core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn30.4cov 39.0%8.5e-0234 bits2,983,384–2,983,602 +–5158_cbs114723_MAT_unswitchedFOYG_10158
SLA2conserved flankhit onlyDIAMOND, proteome82.2cov 100.0%< 1e-1801,373 bits2,986,692–2,990,259 -–107463_unknown-1_MAT_MAT1-2FOYG_10160
MAT1-1-5core MAThit onlytblastn37.5cov 13.0%1.4e+0032 bits2,993,289–2,993,420 +–5180_44ba1_MAT_combinedFOYG_10161 (opposite strand)
FOYG_10162

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
MATJH717839.1:3,763,392–3,765,561MAT1-2MAT1-2-11too few of the family's genes found
MATJH717842.1:4,572,137–4,573,728MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FoxysporumNRRL32931.genome.fasta
Assembly
168 contigs · 47.9 Mb · N50 4.5 Mb
Genome SHA-256
26f5b65ee3679561b045c0f3ecc2d5fcfc4a19a3314e66a0b5f2d7b504614746
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
2026-11-07T02:05:25Z
Run time
84 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