MATPredict · mating-type report

SparadoxusCBS432

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 02:04 UTC by MATPredict 0.8.1

Result

Mating-type loci

MATalphamedium confidenceMATalphamedium confidenceMATalphamedium confidence

Called loci 3

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP020244MATalpha locus: genes from left to right on CP020244, 42,785 to 44,210: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATALPHA1 (core MAT gene, plus strand).42.5 kb43.0 kb43.5 kb44.0 kb44.5 kb← 42.5 kb more to contig endcalled locusMATA2: core MAT gene, 42,785–43,417 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 42,785–43,417 (-), identity 100.0%, search hit onlyMATALPHA2MATALPHA1: core MAT gene, 43,683–44,210 (+), identity 90.3%, search hit onlyMATALPHA1
Gene order on CP020244. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP020244, 42,485 to 44,510SPAR_C00040 42,785-43,417 (-): Hmlalpha2SPAR_C00040SPAR_C00050 43,683-44,210 (+): Hmlalpha1SPAR_C00050
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
  • search hit only
Location
CP020244:42,785–44,210 · 1.4 kb
Cross-lineage class
MAT1-1
Own genes
CP020244:42,785–44,210 · 1.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 3 gene hits
Nearest contig end
42.8 kb
Region (samtools)
CP020244:42785-44210
Idiomorph scores
  • MATalpha 326.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.7e-84235 bits42,785–43,417 -–4932_s288c_MATsc_HMRaSPAR_C00040
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-149404 bits42,785–43,417 -–4932_s288c_MATsc_MATalphaSPAR_C00040
MATALPHA1core MAThit onlyDIAMOND, proteome90.3cov 100.0%1.1e-119326 bits43,683–44,210 +–4932_s288c_MATsc_MATalphaSPAR_C00050
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP020244MATalpha locus: genes from left to right on CP020244, 227,069 to 228,147: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATALPHA1 (core MAT gene, plus strand).227.0 kb227.5 kb228.0 kb129.2 kb more to contig end →called locusMATA2: core MAT gene, 227,069–227,701 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 227,069–227,701 (-), identity 100.0%, search hit onlyMATALPHA2MATALPHA1: core MAT gene, 227,803–228,147 (+), identity 85.0%, search hit onlyMATALPHA1
Gene order on CP020244. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP020244, 226,769 to 228,447SPAR_C00930 225,140-226,966 (-): Bud5SPAR_C00930SPAR_C00940 227,069-227,701 (-): Matalpha2SPAR_C00940SPAR_C00950 227,803-228,147 (+): Matalpha1SPAR_C00950
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
  • search hit only
Location
CP020244:227,069–228,147 · 1.1 kb
Cross-lineage class
MAT1-1
Own genes
CP020244:227,069–228,147 · 1.1 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 3 gene hits
Nearest contig end
129.5 kb
Region (samtools)
CP020244:227069-228147
Idiomorph scores
  • MATalpha 104.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.7e-84235 bits227,069–227,701 -–4932_s288c_MATsc_HMRaSPAR_C00940
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.2e-149404 bits227,069–227,701 -–4932_s288c_MATsc_MATalphaSPAR_C00940
MATALPHA1core MAThit onlyDIAMOND, proteome85.0cov 34.3%1.1e-33104 bits227,803–228,147 +–4932_s288c_MATsc_MATalphaSPAR_C00950
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP020244MATalpha locus: genes from left to right on CP020244, 321,159 to 322,477: MATA2 (core MAT gene, minus strand); MATALPHA2 (core MAT gene, minus strand); MATA1 (core MAT gene, plus strand); MATALPHA1 (core MAT gene, plus strand).321.0 kb321.5 kb322.0 kb322.5 kb34.9 kb more to contig end →called locusMATA2: core MAT gene, 321,159–321,518 (-), identity 100.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 321,159–321,518 (-), identity 100.0%, search hit onlyMATALPHA2MATA1: core MAT gene, 321,813–322,477 (+), identity 94.9%, search hit onlyMATA1 (lost to MATALPHA1)MATALPHA1: core MAT gene, 321,813–322,477 (+), identity 97.5%, search hit onlyMATALPHA1
Gene order on CP020244. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP020244, 320,859 to 322,777SPAR_C01400 321,159-321,518 (-): Hmra2SPAR_C01400SPAR_C01410 321,813-322,477 (+): Hmra1SPAR_C01410
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
  • search hit only
Location
CP020244:321,159–322,477 · 1.3 kb
Cross-lineage class
MAT1-1
Own genes
CP020244:321,159–322,477 · 1.3 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
3 of 4 gene hits
Nearest contig end
35.2 kb
Region (samtools)
CP020244:321159-322477
Idiomorph scores
  • MATalpha 89.7

Margin over the set-aside MATA1 hit: 2.6 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
MATALPHA197.5MATA194.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATA2core MAThit onlyDIAMOND, proteome100.0cov 100.0%6.3e-85233 bits321,159–321,518 -–4932_s288c_MATsc_HMRaSPAR_C01400
MATALPHA2core MAThit onlyDIAMOND, proteome100.0cov 56.7%1.3e-83233 bits321,159–321,518 -–4932_s288c_MATsc_MATalphaSPAR_C01400
MATA1core MATlost to MATALPHA1, not countedhit onlyDIAMOND, proteome94.9cov 92.9%2.6e-77216 bits321,813–322,477 +–4932_s288c_MATsc_HMRaSPAR_C01410
MATALPHA1core MAThit onlyDIAMOND, proteome97.5cov 22.9%1.0e-2690 bits321,813–322,477 +–4932_s288c_MATsc_MATalphaSPAR_C01410
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 23

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: fewer than 2 genes could be modelled (23).

Show the 23 withheld loci

Withheld loci (23)

familylocationidiomorph genesmodelledreason
MATscCP020255:185,345–206,730undeterminedMATALPHA2, sla21fewer than 2 genes could be modelled
MATscCP020255:633,341–633,463MATaMATA10fewer than 2 genes could be modelled
MATscCP020255:661,409–661,585MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP020245:75,071–75,187MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP020245:272,686–272,946MATaMATA10fewer than 2 genes could be modelled
MATscCP020245:527,405–527,860MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP020245:1,211,327–1,211,464MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP020245:1,315,573–1,315,728undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020245:1,444,338–1,444,442undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020248:126,191–126,292undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020248:323,725–323,955undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020257:197,969–200,289undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP020257:240,259–240,393MATaMATA10fewer than 2 genes could be modelled
MATscCP020257:388,906–389,076undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020257:656,939–657,202undeterminedMATA20fewer than 2 genes could be modelled
MATscCP020249:485,278–485,382undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020256:228,437–228,625undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP020254:215,321–215,512MATaMATA10fewer than 2 genes could be modelled
MATscCP020243:442,017–444,191MATaMATA1, MATA20fewer than 2 genes could be modelled
MATscCP020252:446,518–446,613undeterminedMATA20fewer than 2 genes could be modelled
MATscCP020242:163,075–163,305undeterminedMATA20fewer than 2 genes could be modelled
MATscCP020251:502,221–502,343MATaMATA10fewer than 2 genes could be modelled
MATscCP020250:276,438–276,536MATalphaMATALPHA10fewer than 2 genes could be modelled

Provenance

Genome file
SparadoxusCBS432.genome.fasta
Assembly
17 contigs · 12.1 Mb · N50 903.0 kb
Genome SHA-256
ddcdafc7882ac8f0014182a2edd3a800bb75435ef92ca9758b831e5e95e2ad83
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': 4893, '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 4893', 'routed_by': 'family taxid 4893 (direct)'}, 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, supported_min_bitscore=33.0
Run started
2026-11-07T02:04:30Z
Run time
17 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