Markers + reference

Achyranthes

3 species · Amaranthaceae · Caryophyllales

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Species 3
Genome length 151–152 kb
Candidate markers 254
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC LSC 834 0.0024 1.00 60.3 yes View details
psbM-trnD LSC 1053 0.0019 1.00 47.5 yes View details
psaA LSC 2253 0.0009 1.00 57.7 yes View details
trnT-trnL LSC 672 0.0030 1.00 60.8 yes View details
trnF-ndhJ LSC 711 0.0019 1.00 49.4 yes View details
ndhC LSC 363 0.0018 1.00 29.1 yes View details
trnT-atpE LSC 176 0.0076 1.00 44.8 yes View details
trnN-ndhF IRb 1766 0.0008 1.00 44.3 yes View details
ndhI-ndhA SSC 1579 0.0008 1.00 49.2 yes View details
ndhH-ycf1 SSC 670 0.0020 1.00 33.1 yes View details
psbZ-trnM LSC 665 0.0020 1.00 64.8 yes View details
atpF LSC 1343 0.0010 1.00 61.8 yes View details
rpoA LSC 1011 0.0020 1.00 60.0 yes View details
petN-psbM LSC 1177 0.0017 1.00 59.8 yes View details
psbD LSC 1062 0.0013 1.00 59.6 yes View details
psaA-ycf3 LSC 807 0.0000 1.00 59.0 yes View details
matK LSC 1512 0.0018 1.00 58.2 yes View details
ndhK-ndhC LSC 50 0.0267 1.00 57.0 yes View details
psbL-psbF LSC 27 0.0247 1.00 55.7 yes View details
rpoC2 LSC 4110 0.0006 1.00 54.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK_p1 trnK TGCCCGTGTCAACCAATATC ACTTTGTTTCGATGTTTTGCT 2746–2749 1.000 47.5
trnK_p2 trnK CCCGTGTCAACCAATATCCA ACTTTGTTTCGATGTTTTGCT 2744–2747 1.000 46.2
trnK_p3 trnK ATATGCCCGTGTCAACCAAT ACTTTGTTTCGATGTTTTGCT 2749–2752 1.000 46.0
trnK_p4 trnK ATGCCCGTGTCAACCAATAT ACTTTGTTTCGATGTTTTGCT 2747–2750 1.000 46.0
trnK_p5 trnK TGCCCGTGTCAACCAATATC AACTTTGTTTCGATGTTTTGCT 2747–2750 1.000 45.6
matK_p1 matK TACTCAATGGCTTCAACCCC CCTTGTTTTGACTGTATCGCA 1708–1710 1.000 58.8
matK_p2 matK TACTCAATGGCTTCAACCCC ACCTTGTTTTGACTGTATCGC 1709–1711 1.000 58.8
matK_p3 matK TACTCAATGGCTTCAACCCC CCTTGTTTTGACTGTATCGCAC 1708–1710 1.000 58.6
matK_p4 matK CTCAATGGCTTCAACCCCTA CCTTGTTTTGACTGTATCGCA 1706–1708 1.000 56.4
matK_p5 matK CTCAATGGCTTCAACCCCTA ACCTTGTTTTGACTGTATCGC 1707–1709 1.000 56.4
atpF_p1 atpF TCGTCTGCTCGAATGGTTAC GCAAAGAAGTCAAATAATACAACGG 1444–1497 1.000 42.7
atpF_p2 atpF GTCTGCTCGAATGGTTACCA GCAAAGAAGTCAAATAATACAACGG 1442–1495 1.000 42.7
atpF_p3 atpF TTTCGTCTGCTCGAATGGTT GCAAAGAAGTCAAATAATACAACGG 1446–1499 1.000 42.6
atpF_p4 atpF ATTTCGTCTGCTCGAATGGT GCAAAGAAGTCAAATAATACAACGG 1447–1500 1.000 42.6
atpF_p5 atpF TTTCGTCTGCTCGAATGGTT AGAAGTAGCAAAGAAGTCAA 1453–1506 1.000 42.6
rpoC2_p1 rpoC2 ACGTACGAACAGTTCCTTGG AGCCACTCGAGAAATTTCGG 320 1.000 77.2
rpoC2_p2 rpoC2 CGTACGAACAGTTCCTTGGT AGCCACTCGAGAAATTTCGG 319 1.000 77.2
rpoC2_p3 rpoC2 ACGTACGAACAGTTCCTTGG GCCACTCGAGAAATTTCGGA 319 1.000 77.1
rpoC2_p4 rpoC2 CGTACGAACAGTTCCTTGGT GCCACTCGAGAAATTTCGGA 318 1.000 77.1
rpoC2_p5 rpoC2 CCCAACAACGTACGAACAGT AGCCACTCGAGAAATTTCGG 327 1.000 74.9
rpoB-trnC_p1 rpoB-trnC AAGCCCCGATCAATGAATCT CGGATTTGAACTGGGGAACA 987 1.000 71.2
rpoB-trnC_p2 rpoB-trnC GTTCTTCTCTTAAGCCCCGA CGGATTTGAACTGGGGAACA 998 1.000 71.1
rpoB-trnC_p3 rpoB-trnC AGTTCTTCTCTTAAGCCCCG CGGATTTGAACTGGGGAACA 999 1.000 71.0
rpoB-trnC_p4 rpoB-trnC CTTCATTTCCATCCCGTAGCA CGGATTTGAACTGGGGAACA 917 1.000 70.8
rpoB-trnC_p5 rpoB-trnC TTCATTTCCATCCCGTAGCA CGGATTTGAACTGGGGAACA 916 1.000 70.8
petN-psbM_p1 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAACGGTCAGCCAAAATGA 1285 1.000 65.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGCCAAAATGA 1223 1.000 64.9
petN-psbM_p3 petN-psbM ATTGTAAGTCTCGCTTGGGC AAACGGTCAGCCAAAATGAT 1284 1.000 63.8
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC AACGGTCAGCCAAAATGATT 1283 1.000 63.8
petN-psbM_p5 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAAACGGTCAGCCAAAATGA 1286 1.000 63.6

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
Achyranthes aspera NC_050063.1 151486 View on NCBI ↗
Achyranthes bidentata NC_050062.1 151284 View on NCBI ↗
Achyranthes longifolia NC_050061.1 151520 View on NCBI ↗