Markers + reference

Eriocaulon

14 species · Eriocaulaceae · Poales

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Species 14
Genome length 150–152 kb
Candidate markers 272
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 598 0.0784 0.97 81.6 yes View details
trnS-GGA-trnG-UCC LSC 1377 0.0731 0.97 84.0 yes View details
atpH-atpI LSC 1055 0.0744 0.98 82.4 yes View details
petN-psbM LSC 724 0.0759 0.94 86.6 yes View details
trnE-UUC-trnT-GGU LSC 654 0.0829 0.95 84.4 yes View details
trnF-GAA-ndhJ LSC 709 0.0634 0.84 77.1 yes View details
ndhC-trnV-UAC LSC 722 0.0619 0.99 84.2 yes View details
petA-psbJ LSC 691 0.0726 0.94 80.4 yes View details
rpl32-trnL-UAG SSC 408 0.0812 0.97 78.8 yes View details
psaC-ndhE SSC 563 0.0741 0.94 79.7 yes View details
rps15-ycf1 SSC 436 0.0760 0.98 79.9 yes View details
ycf1 SSC 5115 0.0464 1.00 75.7 yes View details
ycf3-trnS-GCU LSC 582 0.0544 0.99 88.3 yes View details
psbM-trnD-GUC LSC 914 0.0539 0.99 88.1 yes View details
trnT-GGU-psbD LSC 755 0.0512 0.99 85.0 yes View details
rpoB-trnC-GCA LSC 773 0.0538 1.00 84.9 yes View details
psbE-petL LSC 877 0.0487 0.99 84.6 yes View details
ycf4-cemA LSC 639 0.0635 0.98 83.5 yes View details
rps16-trnQ-UUG LSC 386 0.0835 0.95 82.9 yes View details
atpB-rbcL LSC 906 0.0472 0.97 82.4 yes View details
trnT-UGU-trnL-UAA LSC 662 0.0570 0.98 82.1 yes View details
psaA-ycf3 LSC 637 0.0412 1.00 81.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGCCGTCTATCGAATCGTTG 877–915 1.000 86.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CCGTCTATCGAATCGTTGCA 875–913 1.000 86.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCTATCCCAATGAGCCGTCT 889–927 0.929 83.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG ATCCGTTTTTCTTGAGCCGT 958–996 0.929 83.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TCTATCCCAATGAGCCGTCT 887–925 0.929 82.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TAGTTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 405–479 1.000 90.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 395–469 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACATCGTTTCAAGCGAAG GAGGTTCGAATCCTTCCGTC 375–449 1.000 89.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACCACATCGTTTCAAGCGAA GAGGTTCGAATCCTTCCGTC 376–450 1.000 88.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TACCACATCGTTTCAAGCGA GAGGTTCGAATCCTTCCGTC 377–451 1.000 87.9
trnS-GGA-trnG-UCC_p1 trnS-GGA-trnG-UCC GTTTGGCAAGCTGCTGTAAG CATCGTTAGCTTGGAAGGCT 2044–2153 1.000 91.3
trnS-GGA-trnG-UCC_p2 trnS-GGA-trnG-UCC GTTTGGCAAGCTGCTGTAAG CGTTAGCTTGGAAGGCTAGG 2041–2150 1.000 91.1
trnS-GGA-trnG-UCC_p3 trnS-GGA-trnG-UCC AGCTGCTGTAAGTTTTCGCT CATCGTTAGCTTGGAAGGCT 2036–2145 1.000 90.8
trnS-GGA-trnG-UCC_p4 trnS-GGA-trnG-UCC GTTTGGCAAGCTGCTGTAAG CGTTAGAGATTGGGCAGGTC 2619–2735 0.571 73.9
trnS-GGA-trnG-UCC_p5 trnS-GGA-trnG-UCC GTTTGGCAAGCTGCTGTAAG ATTGCGTGCCTACTTACGAG 2657–2662 0.214 48.1
atpH-atpI_p1 atpH-atpI CTTCGGGTTGTCTCGCAATA ATTAGCCGCGGCCTATATTG 835–1614 1.000 91.8
atpH-atpI_p2 atpH-atpI CTTCGGGTTGTCTCGCAATA CATTAGCCGCGGCCTATATT 836–1615 1.000 91.8
atpH-atpI_p3 atpH-atpI AAGTCGGGTGTATCTGGGAA ATTAGCCGCGGCCTATATTG 1100–1909 0.857 85.7
atpH-atpI_p4 atpH-atpI AAGTCGGGTGTATCTGGGAA CATTAGCCGCGGCCTATATT 1101–1910 0.857 85.7
atpH-atpI_p5 atpH-atpI CTTCGGGTTGTCTCGCAATA TATGACCCTTGGGTTCCCTT 1372–2042 0.571 74.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCTTACCTCTTGGCCATGTC 1292–1367 1.000 91.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AAAGGATTTGCAGTCCCCTG 1312–1387 1.000 91.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG CCTTACCTCTTGGCCATGTC 1308–1383 1.000 91.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTGTTTCCTACTCACGCGAG AAAGGATTTGCAGTCCCCTG 1328–1403 1.000 90.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCAAAAATAAGCCTGCCGGT CCTTACCTCTTGGCCATGTC 1045–1120 0.929 88.1
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC ACGTCAAAACAGTTAGCCAA 671–778 0.929 70.7
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT ACGTCAAAACAGTTAGCCAA 670–777 0.929 70.7
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT ACGTCAAAACAGTTAGCCAA 668–775 0.929 69.8
petN-psbM_p4 petN-psbM AGTATGGGGAAGGAGTGGAC ACGTCAAAACAGTTAGCCAAA 671–778 0.929 68.9
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT ACGTCAAAACAGTTAGCCAAA 670–777 0.929 68.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Eriocaulon alpestre NC_061338.1 151372 View on NCBI ↗
Eriocaulon australe NC_061339.1 151584 View on NCBI ↗
Eriocaulon brownianum NC_061340.1 151432 View on NCBI ↗
Eriocaulon buergerianum NC_042211.1 151434 View on NCBI ↗
Eriocaulon cinereum NC_061304.1 150725 View on NCBI ↗
Eriocaulon faberi NC_066095.1 151361 View on NCBI ↗
Eriocaulon fistulosum NC_066092.1 151415 View on NCBI ↗
Eriocaulon henryanum NC_061341.1 151010 View on NCBI ↗
Eriocaulon miquelianum NC_066097.1 151344 View on NCBI ↗
Eriocaulon nantoense NC_066099.1 151389 View on NCBI ↗
Eriocaulon nepalense NC_066096.1 150973 View on NCBI ↗
Eriocaulon oryzetorum NC_066100.1 150255 View on NCBI ↗
Eriocaulon schochianum NC_061342.1 150450 View on NCBI ↗
Eriocaulon truncatum NC_066093.1 151052 View on NCBI ↗