MATPredict · mating-type report

FcircinatumNRRL25331

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 02:35 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 JAAQPE010000072MAT1-1 locus: genes from left to right on JAAQPE010000072, 62,491 to 76,579: 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).65 kb70 kb75 kb45.0 kb more to contig end →called locusCOX13: conserved flank, 62,491–63,253 (-), identity 59.3%, search hit onlyCOX13APN2: conserved flank, 63,769–65,786 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 66,513–67,263 (-), identity 83.3%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 66,537–66,809 (-), identity 32.967%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 67,658–69,013 (+), identity 83.6%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 69,467–70,782 (+), identity 89.0%, search hit onlyMAT1-1-1MAT1-2-7: core MAT gene, 69,787–70,005 (+), identity 30.38%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)SLA2: conserved flank, 72,997–76,579 (-), identity 75.4%, search hit onlySLA2
Gene order on JAAQPE010000072. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on JAAQPE010000072, 61,788 to 77,283FCIRC_2234 62,491-63,253 (-): cytochrome c oxidase subunit 6aFCIRC_2234FCIRC_2235 63,769-65,786 (+): AP endonuclease 2FCIRC_2235FCIRC_2236 66,513-67,263 (-): mating type 1-1-3FCIRC_2236FCIRC_2237 67,658-69,013 (+): mating type MAT1-1-2FCIRC_2237FCIRC_2238 69,467-70,782 (+): mating type MAT1-1-1FCIRC_2238FCIRC_2239 72,997-76,579 (-): cytoskeleton assembly control SLA2FCIRC_2239
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
JAAQPE010000072:62,491–76,579 · 14.1 kb
Own genes
JAAQPE010000072:62,491–76,579 · 14.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 8 gene hits
Nearest contig end
45.7 kb
Region (samtools)
JAAQPE010000072:62491-76579
Idiomorph scores
  • MAT1-1 679.0

Margin over the set-aside MAT1-2-1 hit: 50.3 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
MAT1-1-189.0MAT1-2-730.4100.0higher identity
MAT1-1-383.3MAT1-2-133.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome59.3cov 94.0%2.3e-54161 bits62,491–63,253 -–27337_vdls-17_MAT_MAT1-2FCIRC_2234
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%6.0e-218610 bits63,769–65,786 +–2903220_liq80xsp_MAT_combinedFCIRC_2235
MAT1-1-3core MAThit onlyDIAMOND, proteome83.3cov 89.5%1.6e-91259 bits66,513–67,263 -–5127_mo44_MAT_MAT1-1FCIRC_2236
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn33.0cov 20.0%2.5e-1366 bits66,537–66,809 -–40559_sas405_MAT_MAT1-2FCIRC_2236
MAT1-1-2core MAThit onlyDIAMOND, proteome83.6cov 98.3%4.1e-250679 bits67,658–69,013 +–5127_mo44_MAT_MAT1-1FCIRC_2237
MAT1-1-1core MAThit onlyDIAMOND, proteome89.0cov 97.4%1.1e-245665 bits69,467–70,782 +–5127_mo44_MAT_MAT1-1FCIRC_2238
MAT1-2-7core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn30.4cov 39.0%4.2e-0235 bits69,787–70,005 +–5158_cbs114723_MAT_unswitchedFCIRC_2238
SLA2conserved flankhit onlyDIAMOND, proteome75.4cov 99.4%< 1e-1801,350 bits72,997–76,579 -–27337_vdls-17_MAT_MAT1-2FCIRC_2239

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
MATJAAQPE010000201:50,075–76,888MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATJAAQPE010000539:15,843–18,007MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FcircinatumNRRL25331.genome.fasta
Assembly
1,223 contigs · 42.6 Mb · N50 96.2 kb
Genome SHA-256
b25fb19e8e2531c0379c7e3676e402263448412c03b56d04ce8afd83554034ab
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
2026-11-07T02:34:28Z
Run time
58 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