Markers + reference

Gnetum

3 species · Gnetaceae · Gnetales

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Species 3
Genome length 115–115 kb
Candidate markers 245
Primer pairs 60

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 245 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbD-trnT-GGU LSC 584 0.0251 1.00 59.5 yes View details
trnT-GGU-trnK-UUU LSC 836 0.0865 1.00 82.5 yes View details
trnH-GUG-trnI-CAU IRa 278 0.0216 1.00 53.4 yes View details
ycf4 LSC 567 0.0024 1.00 59.8 yes View details
rpl16 LSC 1182 0.0011 1.00 59.5 yes View details
psbB-ORF223 LSC 574 0.0061 0.96 57.8 yes View details
ycf1 SSC 6978 0.0032 1.00 54.6 yes View details
ycf1-trnP-GGG SSC 280 0.0000 0.99 53.6 yes View details
ycf2 IRb 6558 0.0005 1.00 52.8 yes View details
trnA-UGC IRb 35 0.0190 1.00 52.1 yes View details
trnA-UGC IRa 35 0.0190 1.00 52.1 yes View details
ycf2 IRa 6558 0.0003 1.00 40.2 no View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbD-trnT-GGU_p1 psbD-trnT-GGU GTCACAAAGGTTGTCCCTGT CGCCAGGAATGAGAAACGTA 954–956 1.000 82.1
psbD-trnT-GGU_p2 psbD-trnT-GGU GTCACAAAGGTTGTCCCTGT TACGCCAGGAATGAGAAACG 956–958 1.000 82.1
psbD-trnT-GGU_p3 psbD-trnT-GGU ACTAGCTAAGCCGTGGGTAT CGCCAGGAATGAGAAACGTA 982–984 1.000 81.8
psbD-trnT-GGU_p4 psbD-trnT-GGU ACAGAGAAGAGCAGCACCTA CGCCAGGAATGAGAAACGTA 1420–1422 1.000 81.5
psbD-trnT-GGU_p5 psbD-trnT-GGU ACAGAGAAGAGCAGCACCTA TACGCCAGGAATGAGAAACG 1422–1424 1.000 81.5
trnT-GGU-trnK-UUU_p1 trnT-GGU-trnK-UUU TACCGCTGAGTTAAAAGGGC AGCCGAGTACTCTACCATTGA 883–889 1.000 79.7
trnT-GGU-trnK-UUU_p2 trnT-GGU-trnK-UUU TACCGCTGAGTTAAAAGGGC GCCGAGTACTCTACCATTGAG 882–888 1.000 76.9
trnT-GGU-trnK-UUU_p3 trnT-GGU-trnK-UUU TACCGCTGAGTTAAAAGGGC GCCGAGTACTCTACCATTGA 882–888 1.000 75.5
trnT-GGU-trnK-UUU_p4 trnT-GGU-trnK-UUU TACCGCTGAGTTAAAAGGGC AGCCGAGTACTCTACCATTG 883–889 1.000 75.4
trnT-GGU-trnK-UUU_p5 trnT-GGU-trnK-UUU TACCGCTGAGTTAAAAGGGC AAGCCGAGTACTCTACCATTG 884–890 1.000 73.4
trnK-UUU_p1 trnK-UUU ACATCGACTGGGTTTAGTGT AAATAGACGCCTTGCCCAAA 2987–2991 0.667 54.1
trnK-UUU_p2 trnK-UUU ACATCGACTGGGTTTAGTGT AATAGACGCCTTGCCCAAAA 2986–2990 0.667 54.1
trnK-UUU_p3 trnK-UUU ACATCGACTGGGTTTAGTGT AGACGCCTTGCCCAAAAATA 2983–2987 0.667 54.1
trnK-UUU_p4 trnK-UUU ACATCGACTGGGTTTAGTGT ATAGACGCCTTGCCCAAAAA 2985–2989 0.667 54.1
trnK-UUU_p5 trnK-UUU ACATCGACTGGGTTTAGTGT TAGACGCCTTGCCCAAAAAT 2984–2988 0.667 54.1
ycf2_p1 ycf2 CTCCTTTTCGGTTTTTGTCGA GGAAGGCCGGTTCATTGTAT 345 1.000 64.2
ycf2_p2 ycf2 CTCCTTTTCGGTTTTTGTCGA TAAGGAAGGCCGGTTCATTG 348 1.000 63.6
ycf2_p3 ycf2 CTCCTTTTCGGTTTTTGTCGA TCCAATTTAAGGAAGGCCGG 355 1.000 63.5
ycf2_p4 ycf2 TCGGTTTTTGTCGATTGAAACC GGAAGGCCGGTTCATTGTAT 338 1.000 63.5
ycf2_p5 ycf2 CTCCTTTTCGGTTTTTGTCGA CCAATTTAAGGAAGGCCGGT 354 1.000 63.4
trnA-UGC_p1 trnA-UGC TGGAGAGCACAGTACGATGA AAATCCTAGATTCCCGGCCT 206 1.000 77.6
trnA-UGC_p2 trnA-UGC TGGAGAGCACAGTACGATGA AATCCTAGATTCCCGGCCTT 205 1.000 77.6
trnA-UGC_p3 trnA-UGC TGGTAGAATCACTCGGGGAG AAATCCTAGATTCCCGGCCT 136 1.000 77.4
trnA-UGC_p4 trnA-UGC TGGTAGAATCACTCGGGGAG AATCCTAGATTCCCGGCCTT 135 1.000 77.4
trnA-UGC_p5 trnA-UGC TCGTTGGCCTCTATGGTAGA AATCCTAGATTCCCGGCCTT 148 1.000 75.5
ycf1_p1 ycf1 TAAACCCGAAAAGGAACCCG TGCGGCTTCTCTCTGTTTTT 899–971 1.000 79.8
ycf1_p2 ycf1 TAAACCCGAAAAGGAACCCG AAACTTGTATTTTGCGCCGG 514–586 1.000 79.7
ycf1_p3 ycf1 TAAACCCGAAAAGGAACCCG GCCGGATAAACCCCAATTCT 499–571 1.000 79.6
ycf1_p4 ycf1 TAAACCCGAAAAGGAACCCG TCCGCCTTTGTTAGAAGTCG 949–1021 1.000 79.4
ycf1_p5 ycf1 TAAACCCGAAAAGGAACCCG GCTTGGCTTTCCTCTTCCTT 1054–1126 1.000 79.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Gnetum luofuense NC_050277.1 114795 View on NCBI ↗
Gnetum parvifolium NC_011942.1 114914 View on NCBI ↗
Gnetum pendulum KX385197.1 114917 View on NCBI ↗