Markers + reference

Achnatherum

3 species · Poaceae · Poales

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Species 3
Genome length 138–138 kb
Candidate markers 275
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 1644 0.0062 0.99 52.5 yes View details
petN-trnC-GCA LSC 927 0.0058 1.00 53.0 yes View details
rbcL LSC 1431 0.0061 1.00 48.3 yes View details
petA-psbJ LSC 816 0.0123 1.00 62.7 yes View details
rpl33-rps18 LSC 272 0.0000 0.99 41.5 yes View details
rpl20-rps12 LSC 697 0.0086 1.00 53.0 yes View details
ndhH IRb 132 0.0000 1.00 19.2 no View details
ndhF SSC 2220 0.0068 1.00 47.5 yes View details
rpl32-trnL-UAG SSC 722 0.0140 0.99 61.3 yes View details
ccsA SSC 969 0.0076 1.00 56.7 yes View details
ndhH SSC 1182 0.0073 1.00 53.1 yes View details
ndhC-trnV-UAC LSC 875 0.0034 1.00 63.1 yes View details
rpoB-rpoC1 LSC 37 0.0360 1.00 63.0 yes View details
atpI-atpH LSC 531 0.0063 1.00 61.7 yes View details
trnC-GCA-rpoB LSC 1158 0.0035 1.00 61.1 yes View details
ndhH-ndhF SSC 38 0.0351 1.00 61.0 yes View details
psaC-ndhE SSC 480 0.0069 1.00 60.7 yes View details
trnG-GCC-trnM-CAU LSC 500 0.0042 0.96 60.3 yes View details
atpF LSC 1382 0.0029 1.00 60.3 yes View details
petD LSC 1233 0.0022 1.00 60.1 yes View details
trnN-GUU-rps15 IRb 1531 0.0022 1.00 60.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU GTCGACCCAAGCGGATATAC GTTTCCAGTACTCCAGAGCG 682–703 1.000 82.3
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU GCGAGCGTAGTTCAATGGTA GTTTCCAGTACTCCAGAGCG 642–663 1.000 82.3
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU TAGCGAGCGTAGTTCAATGG GTTTCCAGTACTCCAGAGCG 644–665 1.000 81.3
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU TATCCTGTAGCGAGCGTAGT GTTTCCAGTACTCCAGAGCG 651–672 1.000 80.9
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU CTGTAGCGAGCGTAGTTCAA GTTTCCAGTACTCCAGAGCG 647–668 1.000 80.9
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1781–1796 1.000 50.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGACTTACGTCTTACCACGC 1784–1799 1.000 49.7
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1783–1798 1.000 49.7
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1782–1797 1.000 48.8
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCACGCT 1780–1795 1.000 48.4
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 976–977 1.000 71.0
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 978–979 1.000 70.6
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CAGTTCAAATCTGGGTGCCG 977–978 1.000 67.6
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGGGGACTGCAAATCCTTTA 1001–1002 1.000 66.7
petN-trnC-GCA_p5 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTATCCCCAGT 994–995 1.000 65.4
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1241–1247 1.000 77.3
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1306–1312 1.000 76.9
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1305–1311 1.000 76.8
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1307–1313 1.000 76.8
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG GTTCTTCTGCCAAGCCTTGA 1304–1310 1.000 76.8
rpoB-rpoC1_p1 rpoB-rpoC1 CGTGCGAGAACTACGATCTT CGCCAACGACTTCTCCATTA 231 1.000 79.3
rpoB-rpoC1_p2 rpoB-rpoC1 CGTGCGAGAACTACGATCTT TTTTGTTAGCCCAAGCCCTT 204 1.000 78.6
rpoB-rpoC1_p3 rpoB-rpoC1 CGTGCGAGAACTACGATCTT TTTTTGTTAGCCCAAGCCCT 205 1.000 78.6
rpoB-rpoC1_p4 rpoB-rpoC1 CTCGTGCGAGAACTACGATC CGCCAACGACTTCTCCATTA 233 1.000 78.5
rpoB-rpoC1_p5 rpoB-rpoC1 CGTGCGAGAACTACGATCTT GTTTTTGTTAGCCCAAGCCC 206 1.000 78.1
atpI-atpH_p1 atpI-atpH TTTTGCAACATTAGCCGCAG GCAATAACAGAAGCAGCAGC 621–628 1.000 79.6
atpI-atpH_p2 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGCAATAACAGAAGCAGC 624–631 1.000 79.6
atpI-atpH_p3 atpI-atpH TTTTGCAACATTAGCCGCAG AAGCAGCAGCAATTAGTGGA 611–618 1.000 78.8
atpI-atpH_p4 atpI-atpH TTTTGCAACATTAGCCGCAG GCCAATCCAGCAGCAATAAC 633–640 1.000 78.7
atpI-atpH_p5 atpI-atpH TTTTGCAACATTAGCCGCAG CCTTCTACAGCTTGTCCTGC 699–706 1.000 78.1

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
Achnatherum calamagrostis PP316502.1 137670 View on NCBI ↗
Achnatherum inebrians MW423581.1 137714 View on NCBI ↗
Achnatherum pekinense NC_058870.1 137837 View on NCBI ↗