Markers + reference

Hymenidium

21 species · Apiaceae · Apiales

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Species 21
Genome length 145–172 kb
Candidate markers 272
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 394 0.1090 0.83 73.1 yes View details
trnK-UUU-rps16 LSC 888 0.0690 0.98 80.4 yes View details
rps16-trnQ-UUG LSC 1332 0.0739 0.98 83.1 yes View details
trnE-UUC-trnT-GGU LSC 893 0.0831 0.88 80.3 yes View details
ndhC-trnV-UAC LSC 732 0.0818 0.96 84.5 yes View details
ycf1 IRb 1899 0.0151 1.00 61.3 no View details
ndhF-rpl32 SSC 920 0.0735 0.95 82.4 yes View details
rpl32-trnL-UAG SSC 962 0.0830 0.93 81.1 yes View details
rps15-ycf1 SSC 413 0.0769 0.97 79.7 yes View details
ycf1 SSC 5439 0.0352 1.00 71.2 yes View details
trnT-UGU-trnL-UAA LSC 806 0.0595 0.97 88.0 yes View details
pafI-trnS-GGA LSC 708 0.0455 0.97 84.6 yes View details
trnS-GCU-trnG-UCC LSC 537 0.0627 0.98 84.3 yes View details
trnT-GGU-psbD LSC 1285 0.0531 0.99 84.1 yes View details
petA-psbJ LSC 916 0.0574 0.98 83.7 yes View details
trnC-GCA-petN LSC 707 0.0409 0.97 83.0 yes View details
atpH-atpI LSC 1156 0.0489 0.98 82.7 yes View details
petN-psbM LSC 746 0.0534 0.93 81.8 yes View details
psbM-trnD-GUC LSC 695 0.0493 0.99 81.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTCCATCTACAAATGGGT 199–444 1.000 76.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTCCATCTACAAATGGGT 213–458 1.000 76.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTCCATCTACAAATGGGT 212–457 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTCCATCTACAAATGGGT 214–459 1.000 76.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AAGCTCCATCTACAAATGGGT 200–445 1.000 74.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 918–1300 0.857 85.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 917–1299 0.857 85.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAGTGTATCGCGGGGAATC 1732–1766 0.238 53.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGTGTATCGCGGGGAATC 1731–1765 0.238 53.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAGTGTATCGCGGGGAATC 1680–1714 0.238 53.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CTTACAGCAGCTTGCCAAAC 1343–2319 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATTCCCCGCGATACACTTT CTTACAGCAGCTTGCCAAAC 2234–2334 0.238 54.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATTCCCCGCGATACACTTT TTTGCCCTGGAATTGACCAA 1779–1872 0.238 54.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATTCCCCGCGATACACTTT CCCAGCTATCCAACGAAGAC 2380–2460 0.143 50.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CCCAGCTATCCAACGAAGAC 2193–2272 0.143 49.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 585–818 1.000 60.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 580–813 1.000 59.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACGAATCACACTTTTACCACT 586–819 1.000 58.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AACGAATCACACTTTTACCACT 581–814 1.000 57.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT ACGAATCACACTTTTACCACT 581–814 1.000 57.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTCTAATTGGTCAGGAGCGC 1213–1646 1.000 91.5
atpH-atpI_p2 atpH-atpI CTCGCGATACCTTCTACAGC TTCTAATTGGTCAGGAGCGC 1303–1736 0.952 89.6
atpH-atpI_p3 atpH-atpI CTTGGACTACGAACGGGAAG TTCTAATTGGTCAGGAGCGC 1620–2053 0.714 79.8
atpH-atpI_p4 atpH-atpI CTTGGACTACGAACGGGAAG CTAATTGGTCAGGAGCGCTT 1618–2051 0.714 79.8
atpH-atpI_p5 atpH-atpI CTTGGACTACGAACGGGAAG TGCTTTGGCTTTACTCACGT 1527–1960 0.667 77.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 636–773 1.000 90.1
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 654–791 0.952 86.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 635–772 1.000 84.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 644–781 1.000 84.1
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC AGCCCAAGCGAGACTTACTA 631–768 1.000 84.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Hymenidium amabile NC_071796.1 155882 View on NCBI ↗
Hymenidium apiolens NC_060757.1 146554 View on NCBI ↗
Hymenidium benthamii NC_071799.1 155425 View on NCBI ↗
Hymenidium davidii OP425141.1 155656 View on NCBI ↗
Hymenidium decurrens OP425130.1 155503 View on NCBI ↗
Hymenidium delavayi NC_049052.1 155623 View on NCBI ↗
Hymenidium dentatum NC_060750.1 146806 View on NCBI ↗
Hymenidium giraldii OP425120.1 171866 View on NCBI ↗
Hymenidium hedinii NC_071803.1 156155 View on NCBI ↗
Hymenidium heracleifolium OP425135.1 155580 View on NCBI ↗
Hymenidium hookeri NC_071804.1 145404 View on NCBI ↗
Hymenidium ladyginii OP425118.1 155695 View on NCBI ↗
Hymenidium lhasanum NC_083197.1 155985 View on NCBI ↗
Hymenidium linearilobum NC_060751.1 155592 View on NCBI ↗
Hymenidium pachycaule OP425122.1 156293 View on NCBI ↗
Hymenidium pulszkyi PQ551058.1 157227 View on NCBI ↗
Hymenidium rivulorum NC_060753.1 146815 View on NCBI ↗
Hymenidium tsekuense NC_071809.1 155231 View on NCBI ↗
Hymenidium virgatum NC_083205.1 161314 View on NCBI ↗
Hymenidium wilsonii NC_071811.1 155950 View on NCBI ↗
Hymenidium yunnanense OP680994.1 155631 View on NCBI ↗