Markers + reference

Oligostachyum

10 species · Poaceae · Poales

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Species 10
Genome length 140–140 kb
Candidate markers 258
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 556 0.0029 1.00 47.8 yes View details
trnG-UCC-trnT-GGU LSC 3347 0.0017 1.00 50.5 yes View details
trnC-GCA-rpoB LSC 1188 0.0015 0.99 55.4 yes View details
rbcL LSC 1434 0.0019 1.00 38.3 yes View details
rbcL-psaI LSC 1292 0.0042 1.00 49.8 yes View details
clpP LSC 651 0.0028 1.00 44.8 yes View details
petD LSC 1232 0.0008 1.00 44.6 yes View details
ndhF-rpl32 SSC 866 0.0028 1.00 48.9 yes View details
rpl32-trnL-UAG SSC 703 0.0032 1.00 48.6 yes View details
psaJ-rpl33 LSC 446 0.0031 1.00 51.7 yes View details
rps19-psbA LSC 139 0.0072 1.00 50.9 no View details
ndhC-trnV-UAC LSC 744 0.0011 1.00 47.9 yes View details
rps16 LSC 1087 0.0007 1.00 47.2 yes View details
trnD-GUC-psbM LSC 987 0.0012 1.00 47.1 yes View details
petN-trnC-GCA LSC 898 0.0013 1.00 46.9 yes View details
psbE-petL LSC 1228 0.0014 1.00 46.9 yes View details
psbD LSC 1062 0.0008 1.00 46.4 yes View details
trnN-GUU-rps15 IRb 1541 0.0006 1.00 46.2 yes 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2756–2763 1.000 73.7
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2755–2762 1.000 73.7
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2757–2764 1.000 69.7
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2756–2763 1.000 67.1
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2753–2760 1.000 67.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 67.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 66.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 66.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 65.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 65.1
rps16_p1 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGA 1241–1248 1.000 51.7
rps16_p2 rps16 TGGCACGACATAAATCCAGT TCAATTCCCTATACCACTTTGCA 1246–1253 1.000 49.0
rps16_p3 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGAA 1241–1248 1.000 49.0
rps16_p4 rps16 TGGCACGACATAAATCCAGT TTCCCTATACCACTTTGCAATGA 1242–1249 1.000 49.0
rps16_p5 rps16 TGGCACGACATAAATCCAGT CCCTATACCACTTTGCAATGA 1240–1247 1.000 47.6
psbD_p1 psbD AGTGATATGAGGTGCTCGGA GTCACGACCAGCTAAAACGA 1142 1.000 77.9
psbD_p2 psbD TGCTCGGAAATGGTTGAAGT GTCACGACCAGCTAAAACGA 1130 1.000 76.3
psbD_p3 psbD AGTGATATGAGGTGCTCGGA TCACGACCAGCTAAAACGAA 1141 1.000 75.6
psbD_p4 psbD TGCTCGGAAATGGTTGAAGT TCACGACCAGCTAAAACGAA 1129 1.000 74.0
psbD_p5 psbD GTGCTCGGAAATGGTTGAAG GTCACGACCAGCTAAAACGA 1131 1.000 73.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU GAAAACCCATAGCCAGGAGG AAGGAATTCGCGCTCTTCAT 403–409 1.000 81.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU CTTAAACGGAGAAGCGGACA AAGGAATTCGCGCTCTTCAT 756–762 1.000 80.5
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU TTAAACGGAGAAGCGGACAG AAGGAATTCGCGCTCTTCAT 755–761 1.000 80.5
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACTTAAACGGAGAAGCGGAC AAGGAATTCGCGCTCTTCAT 757–763 1.000 80.5
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU TCTGGTTAGTCGATCCTCCC AAGGAATTCGCGCTCTTCAT 699 0.900 75.8
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1072–1075 1.000 48.6
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1104–1107 1.000 47.2
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1073–1076 1.000 45.6
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1072–1075 1.000 45.6
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1073–1076 1.000 44.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Oligostachyum fujianense PP681670.1 139674 View on NCBI ↗
Oligostachyum heterophyllum PP681667.1 139681 View on NCBI ↗
Oligostachyum lanceolatum PP681651.1 139672 View on NCBI ↗
Oligostachyum lubricum PP681654.1 139676 View on NCBI ↗
Oligostachyum nuspiculum PP681649.1 139643 View on NCBI ↗
Oligostachyum oedogonatum PP681666.1 139659 View on NCBI ↗
Oligostachyum scabriflorum PP681645.1 139688 View on NCBI ↗
Oligostachyum shiuyingianum NC_024722.1 139647 View on NCBI ↗
Oligostachyum spongiosum PP681653.1 139709 View on NCBI ↗
Oligostachyum sulcatum NC_059752.1 139667 View on NCBI ↗