Markers + reference

Trachydium

8 species · Apiaceae · Apiales

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Species 8
Genome length 146–168 kb
Candidate markers 276
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1365 0.0472 0.95 74.3 yes View details
ndhC-trnV-UAC LSC 760 0.0765 0.89 78.4 yes View details
ndhF-rpl32 SSC 1151 0.0509 0.95 78.8 yes View details
rpl32-trnL-UAG SSC 674 0.0779 0.96 83.3 yes View details
ndhG-ndhI SSC 487 0.0770 0.77 68.9 yes View details
rpl14-trnH-GUG LSC 4370 0.4311 0.00 56.4 no View details
trnS-GCU-trnG-UCC LSC 559 0.0385 0.97 80.4 yes View details
trnW-CCA-trnP-UGG LSC 147 0.0556 1.00 79.1 yes View details
trnT-UGU-trnL-UAA LSC 751 0.0370 0.98 78.4 yes View details
trnE-UUC-trnT-GGU LSC 940 0.0502 0.96 78.3 yes View details
trnK-UUU-rps16 LSC 872 0.0470 1.00 77.8 yes View details
ycf3-trnS-GGA LSC 849 0.0362 1.00 77.2 yes View details
petN-psbM LSC 712 0.0433 0.99 76.4 yes View details
petA-psbJ LSC 951 0.0399 0.97 76.4 yes View details
trnC-GCA-petN LSC 696 0.0434 0.94 75.8 yes View details
trnL-UAA-trnF-GAA LSC 360 0.0410 1.00 75.7 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAGTGTATCGCGGGGAATC 1740–1778 0.750 75.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGTGTATCGCGGGGAATC 1739–1777 0.750 75.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TCTATCCCAATGAGCCGTCT 1193–1232 0.750 74.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 1192–1231 0.750 74.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAGTGTATCGCGGGGAATC 1688–1701 0.625 69.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CTTACAGCAGCTTGCCAAAC 1342–2332 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATTCCCCGCGATACACTTT CTTACAGCAGCTTGCCAAAC 1587–2354 0.750 75.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATTCCCCGCGATACACTTT CCCAGCTATCCAACGAAGAC 1725–2492 0.750 75.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATTCCCCGCGATACACTTT TTTGCCCTGGAATTGACCAA 1128–1895 0.750 75.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCTACCCGAGCTCCATCAT CCCAGCTATCCAACGAAGAC 1538–2305 0.750 75.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 618–804 1.000 63.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 667–853 1.000 62.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 619–805 1.000 61.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 668–854 1.000 60.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 604–790 1.000 60.4
trnC-GCA-petN_p1 trnC-GCA-petN CGATATGGCCGAGTGGTAAG GGCTTCGTGTCGATCAATCT 1299–1757 1.000 90.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GGCTTCGTGTCGATCAATCT 1259–1717 1.000 90.8
trnC-GCA-petN_p3 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 680–792 1.000 90.3
trnC-GCA-petN_p4 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AACATGTTGCAGAACGGTCT 894–922 0.750 76.0
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AACATGTTGCAGAACGGTCT 854–882 0.750 76.0
petN-psbM_p1 petN-psbM TGGCTGAGTCTTGAATTCCG AGTATCCCCTTCTGACTCCG 1676–2132 0.875 83.0
petN-psbM_p2 petN-psbM GGCTGAGTCTTGAATTCCGT AGTATCCCCTTCTGACTCCG 1675–2131 0.875 83.0
petN-psbM_p3 petN-psbM TGGCTGAGTCTTGAATTCCG TATTCAATTCGCGACGACGA 1527–1870 0.875 83.0
petN-psbM_p4 petN-psbM AGTCCCTTTTTGACTCTGCG AGTATCCCCTTCTGACTCCG 1313–1753 0.875 82.3
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTATCCCCTTCTGACTCCG 1215–1655 0.875 82.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 881–1124 0.875 84.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG TACCGCTGAGTTAAAAGGGC 916–1159 0.875 81.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCGTTGCCTCCTTGAAAGAG TACCGCTGAGTTAAAAGGGC 882–1125 0.875 79.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 853–1096 0.875 77.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA ACCGCTGAGTTAAAAGGGC 880–1123 0.875 76.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Trachydium involucellatum PP530891.1 164112 View on NCBI ↗
Trachydium nyalamense PZ166665.1 155836 View on NCBI ↗
Trachydium simplicifolium NC_083207.1 155735 View on NCBI ↗
Trachydium souliei NC_083195.1 168331 View on NCBI ↗
Trachydium subnudum NC_071814.1 145696 View on NCBI ↗
Trachydium tibetanicum PZ168396.1 168352 View on NCBI ↗
Trachydium trifoliatum PZ166664.1 153750 View on NCBI ↗
Trachydium variabile NC_083199.1 159914 View on NCBI ↗