Markers + reference

Haslea

3 species · Naviculaceae · Naviculales

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Species 3
Genome length 119–121 kb
Candidate markers 332
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 332 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
OOD24_pgt005-orf125a LSC 1126 0.3091 0.20 65.7 yes View details
thiG-ycf35 SSC 1137 0.4251 0.97 78.9 yes View details
clpC-psbA SSC 1109 0.4509 0.95 79.4 yes View details
atpD LSC 564 0.0496 1.00 84.9 yes View details
rrf-psbY IRb 306 0.1499 0.97 82.8 yes View details
OOD24_pgt025-OOD24_pgt026 SSC 97 0.2361 0.99 82.7 yes View details
psbY-rrf IRa 306 0.1532 0.97 82.7 yes View details
OOD24_pgt026-clpC SSC 136 0.1299 1.00 81.8 yes View details
rbcR SSC 924 0.0801 1.00 81.1 yes View details
dnaK-rpl3 SSC 232 0.1135 1.00 80.8 yes View details
rps2 LSC 690 0.0698 1.00 80.7 yes View details
psaF LSC 558 0.0717 1.00 80.4 yes View details
OOD24_pgt007-OOD24_pgt008 LSC 136 0.1446 1.00 80.2 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpD_p1 atpD TTTCTCAATTTGTTCACGGA GGACCAAAAGAACGTGCAAC 731 1.000 46.1
atpD_p2 atpD TTTCTCAATTTGTTCACGGA ACAGTTGTTCGTGCACAAGA 758 1.000 45.1
atpD_p3 atpD TTCTCAATTTGTTCACGGAT GGACCAAAAGAACGTGCAAC 730 1.000 44.6
atpD_p4 atpD ATTTCTCAATTTGTTCACGGA GGACCAAAAGAACGTGCAAC 732 1.000 44.6
atpD_p5 atpD TTTCTCAATTTGTTCACGGAT GGACCAAAAGAACGTGCAAC 731 1.000 44.6
psaF_p1 psaF ATTGTCCAAAATGCGCACTG GGGCAAGTTAGCGTCTGAAT 1876 0.333 50.7
psaF_p2 psaF GTCCAAAATGCGCACTGAAA GGGCAAGTTAGCGTCTGAAT 1873 0.333 50.2
psaF_p3 psaF GTTGAGCCCATTTCGCAAAA GGGCAAGTTAGCGTCTGAAT 1729 0.333 50.1
psaF_p4 psaF TTGAGCCCATTTCGCAAAAC GGGCAAGTTAGCGTCTGAAT 1728 0.333 50.1
psaF_p5 psaF TGATCGACGATCTGTTGAGC GGGCAAGTTAGCGTCTGAAT 1665 0.333 49.7
OOD24_pgt005-orf125a_p1 OOD24_pgt005-orf125a ATCAGTGTAAGTGCTGCAGG TTGCTGGCTTTCCTTGTGAT 1503 0.333 52.5
OOD24_pgt005-orf125a_p2 OOD24_pgt005-orf125a ATCAGTGTAAGTGCTGCAGG TCGCTTACCACTATCGGCTA 1592 0.333 52.3
OOD24_pgt005-orf125a_p3 OOD24_pgt005-orf125a ATCAGTGTAAGTGCTGCAGG GAAGATGGATCTGCTGCACA 1804 0.333 52.2
OOD24_pgt005-orf125a_p4 OOD24_pgt005-orf125a ATCAGTGTAAGTGCTGCAGG GTGAAGATGGATCTGCTGCA 1806 0.333 52.2
OOD24_pgt005-orf125a_p5 OOD24_pgt005-orf125a ATCAGTGTAAGTGCTGCAGG TGAAGATGGATCTGCTGCAC 1805 0.333 52.2
OOD24_pgt007-OOD24_pgt008_p1 OOD24_pgt007-OOD24_pgt008 AACCTGTGACCTTCTGCTTG AAAATGGGCCGAGTTGGATT 276 1.000 87.9
OOD24_pgt007-OOD24_pgt008_p2 OOD24_pgt007-OOD24_pgt008 AACCTGTGACCTTCTGCTTG GATTTACAATCCGCCCCCTT 231 1.000 87.9
OOD24_pgt007-OOD24_pgt008_p3 OOD24_pgt007-OOD24_pgt008 TTGAACCTGTGACCTTCTGC GATTTACAATCCGCCCCCTT 234 1.000 87.9
OOD24_pgt007-OOD24_pgt008_p4 OOD24_pgt007-OOD24_pgt008 TTGAACCTGTGACCTTCTGC AAAATGGGCCGAGTTGGATT 279 1.000 87.8
OOD24_pgt007-OOD24_pgt008_p5 OOD24_pgt007-OOD24_pgt008 AGACACTCTACCGCTGAGTT AAAATGGGCCGAGTTGGATT 250 1.000 87.4
rps2_p1 rps2 AACAAGAGAAACAGCCTGCA AGTTATCTGTTTCCAAGCGGT 1468 0.333 41.5
rps2_p2 rps2 AACAAGAGAAACAGCCTGCA ACAACCCATTTTGCTTTTCGT 1266 0.333 40.6
rps2_p3 rps2 AAGAGAAACAGCCTGCATGT AGTTATCTGTTTCCAAGCGGT 1465 0.333 39.7
rps2_p4 rps2 ACAAGAGAAACAGCCTGCAT AGTTATCTGTTTCCAAGCGGT 1467 0.333 39.7
rps2_p5 rps2 AGAGAAACAGCCTGCATGTT AGTTATCTGTTTCCAAGCGGT 1464 0.333 39.7
rrf-psbY_p1 rrf-psbY AACCACACTGATCCATTCCG ATAATGCCCATGAAGCAGCA 454–465 1.000 90.5
rrf-psbY_p2 rrf-psbY CGGAACCACACTGATCCATT ATAATGCCCATGAAGCAGCA 457–468 1.000 90.5
rrf-psbY_p3 rrf-psbY AACCACACTGATCCATTCCG TAATGCCCATGAAGCAGCAA 453–464 1.000 89.9
rrf-psbY_p4 rrf-psbY AACCACACTGATCCATTCCG TGCCCATGAAGCAGCAATTA 450–461 1.000 89.9
rrf-psbY_p5 rrf-psbY CGGAACCACACTGATCCATT TGCCCATGAAGCAGCAATTA 453–464 1.000 89.9

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
Haslea karadagensis NC_067583.1 121340 View on NCBI ↗
Haslea nusantara NC_044491.1 120448 View on NCBI ↗
Haslea provincialis NC_067582.1 118665 View on NCBI ↗