MATPredict · mating-type report

MfructicolaCPMC6

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 02:56 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 RKRL01000009MAT1-2 locus: genes from left to right on RKRL01000009, 34,625 to 47,769: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-10 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).35 kb40 kb45 kb← 34.0 kb more to contig endcalled locusCOX13: conserved flank, 34,625–35,333 (-), identity 61.1%, search hit onlyCOX13APN2: conserved flank, 35,804–37,990 (+), identity 84.1%, search hit onlyAPN2MAT1-2-1: core MAT gene, 39,061–40,236 (-), identity 63.8%, search hit onlyMAT1-2-1MAT1-1-3: core MAT gene, 39,352–39,474 (-), identity 41.463%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-10: core MAT gene, 40,737–41,671 (+), identity 56.4%, search hit onlyMAT1-2-10MAT1-1-1: core MAT gene, 41,970–42,176 (+), identity 53.62%, the two modelling tools disagreeMAT1-1-1SLA2: conserved flank, 44,278–47,769 (-), identity 94.4%, search hit onlySLA2
Gene order on RKRL01000009. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on RKRL01000009, 33,968 to 48,426MFRU_009g00090 31,970-34,403 (+): Anaphase-promoting complex subunit 5 | domain-containing proteinMFRU_009g00090MFRU_009g00100 34,625-35,333 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinMFRU_009g00100MFRU_009g00110 35,804-37,990 (+): DNA-(apurinic or apyrimidinic site) endonuclease 2MFRU_009g00110MFRU_009g00120 38,807-40,665 (-): HMG (high mobility group) box | domain-containing proteinMFRU_009g00120MFRU_009g00130 40,737-41,671 (+): unspecified productMFRU_009g00130MFRU_009g00140 44,278-47,769 (-): ANTH domain | I/LWEQ domain | domain-containing proteinMFRU_009g00140MFRU_009g00150 48,342-51,414 (-): Pleckstrin homology domain | domain-containing proteinMFRU_009g00150
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
  • tools disagree
  • alternate model
  • search hit only
Location
RKRL01000009:34,625–47,769 · 13.1 kb
Own genes
RKRL01000009:34,625–47,769 · 13.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
34.6 kb
Region (samtools)
RKRL01000009:34625-47769
Idiomorph scores
  • MAT1-2 450.0
  • MAT1-1 70.5

Margin over the next idiomorph: 379.5

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
MAT1-2-163.8MAT1-1-341.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome61.1cov 97.7%2.6e-54160 bits34,625–35,333 -–578113_sxlc146_MAT_MAT1-2MFRU_009g00100
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%3.2e-255705 bits35,804–37,990 +–2903220_liq80xsp_MAT_combinedMFRU_009g00110
MAT1-2-1core MAThit onlyDIAMOND, proteome63.8cov 92.9%2.5e-161450 bits39,061–40,236 -–5180_44ba1_MAT_combinedMFRU_009g00120
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlytblastn41.5cov 23.0%1.1e-0842 bits39,352–39,474 -–5518_3639_MAT_combinedMFRU_009g00120
MAT1-2-10core MAThit onlyDIAMOND, proteome56.4cov 80.4%1.1e-86254 bits40,737–41,671 +–5180_44ba1_MAT_combinedMFRU_009g00130
MAT1-1-1core MATmodels differexonerateminiprot: 41,788–42,361, 33.5%1 internal stopdefective gene model53.6cov 19.5%2.7e-1670 bits41,970–42,176 +140559_sas56_MAT_MAT1-1none
SLA2conserved flankhit onlyDIAMOND, proteome94.4cov 100.0%< 1e-1801,379 bits44,278–47,769 -–28548_06cwm-g22_MAT_combinedMFRU_009g00140

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATRKRL01000004:229,216–231,873MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
MfructicolaCPMC6.genome.fasta
Assembly
99 contigs · 43.0 Mb · N50 988.5 kb
Genome SHA-256
8f441a62e14150ae1229f4a366984b22024c9da5a15743a40b795e5eec2e019e
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': 'species', 'routing_taxid': 28983, '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 28983', 'routed_by': 'family taxid 28983 (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
2026-11-07T02:54:37Z
Run time
90 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