Markers + reference

Polyopes

3 species · Halymeniaceae · Halymeniales

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Species 3
Genome length 196–202 kb
Candidate markers 458
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 458 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf20-cpcG Genome 659 0.2544 1.00 84.6 yes View details
trnS-GCU-trnD-GUC Genome 6216 0.0965 0.48 62.5 yes View details
orf65-ycf45 Genome 1484 0.2876 0.31 69.1 yes View details
psaD-acsF Genome 835 0.2715 0.98 78.7 yes View details
petA-tatC Genome 589 0.2646 0.75 76.1 yes View details
atpA-sufC Genome 1083 0.2710 0.18 62.3 yes View details
orf12 Genome 1350 0.1996 0.99 79.7 yes View details
ycf80-trnR-CCG Genome 770 0.1038 0.99 86.8 yes View details
rpl11-trnW-CCA Genome 678 0.1726 1.00 85.9 yes View details
ycf22-psaC Genome 1148 0.1133 1.00 83.2 yes View details
rpl21-rpl32 Genome 878 0.0926 1.00 81.8 yes View details
ompR-psbD Genome 405 0.1163 1.00 80.7 yes View details
rrn16-ompR Genome 531 0.1387 1.00 80.6 yes View details
gltB-rpoZ Genome 372 0.0914 1.00 79.7 yes View details
rps1 Genome 618 0.0777 1.00 79.7 yes View details
ycf65-groEL Genome 618 0.1235 1.00 79.2 yes View details
petA Genome 975 0.0995 1.00 79.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf80-trnR-CCG_p1 ycf80-trnR-CCG TCAAGCCTTTTCGCCATACA CTGGTGGTCGAAGGTTCAAA 1261 0.333 51.5
ycf80-trnR-CCG_p2 ycf80-trnR-CCG TCAAGCCTTTTCGCCATACA ATCGGGCATGTAACTCAGTG 1303 0.333 49.3
ycf80-trnR-CCG_p3 ycf80-trnR-CCG TCAAGCCTTTTCGCCATACA GATTCCGATTCTGGTGGTCG 1271 0.333 48.4
ycf80-trnR-CCG_p4 ycf80-trnR-CCG TCAAGCCTTTTCGCCATACA ATTCTGGTGGTCGAAGGTTC 1264 0.333 48.0
ycf80-trnR-CCG_p5 ycf80-trnR-CCG TCAAGCCTTTTCGCCATACA GATTCTGGTGGTCGAAGGTT 1265 0.333 48.0
ycf20-cpcG_p1 ycf20-cpcG ACAACAAGAAGGTATGCAGCA TATTGTGGCCAGGTCCTGTA 1474–1480 0.667 69.2
ycf20-cpcG_p2 ycf20-cpcG ACAAGAAGGTATGCAGCATGT TATTGTGGCCAGGTCCTGTA 1471 0.333 44.4
ycf20-cpcG_p3 ycf20-cpcG ACAAGAAGGTATGCAGCATGT GGCCAGGTCCTGTAAATCAG 1465 0.333 44.4
ycf20-cpcG_p4 ycf20-cpcG ACAAGAAGGTATGCAGCATGT ACAAAGGGTTTTAGGGCGAG 1728 0.333 44.0
ycf20-cpcG_p5 ycf20-cpcG ACAACAAGAAGGTATGCAGCA GGCCAGGTCCTGTAAATCAG 1468 0.333 43.9
ycf22-psaC_p1 ycf22-psaC CGCTGCCCTGACTAAATCAT TGGGTGTAAGCGTTGTGAAA 1551–1562 0.667 70.4
ycf22-psaC_p2 ycf22-psaC CGCTGCCCTGACTAAATCAT TTGGGTGTAAGCGTTGTGAA 1552–1563 0.667 70.4
ycf22-psaC_p3 ycf22-psaC CGCTGCCCTGACTAAATCAT TGCAGGTATGACAGGTGGTA 2179–2190 0.667 69.6
ycf22-psaC_p4 ycf22-psaC CGCTGCCCTGACTAAATCAT GGACGTAACATAGGTGCAGG 2193–2204 0.667 69.5
ycf22-psaC_p5 ycf22-psaC CGCTGCCCTGACTAAATCAT GCCAAGCAGGACGTAACATA 2201 0.333 52.9
gltB-rpoZ_p1 gltB-rpoZ AACCAACACCACATGCATCT TGGTTGAACAAGCTGTGGTT 1079–1102 1.000 88.4
gltB-rpoZ_p2 gltB-rpoZ AACCAACACCACATGCATCT AGGACACTAGAGTCTCCAGC 1209 0.667 67.1
gltB-rpoZ_p3 gltB-rpoZ AACCAACACCACATGCATCT GGACACTAGAGTCTCCAGCA 1208 0.667 66.9
gltB-rpoZ_p4 gltB-rpoZ AACCAACACCACATGCATCT TTGTGTAAGCATTGCCACCT 1121 0.333 53.3
gltB-rpoZ_p5 gltB-rpoZ TTATACCTGCCCCATCACCA TTGTGTAAGCATTGCCACCT 1247 0.333 52.5
rpl21-rpl32_p1 rpl21-rpl32 AACCCACATTTGCCTTCCAT GCTGGCTCTTGGGCTTTATA 1351–1353 1.000 86.3
rpl21-rpl32_p2 rpl21-rpl32 ACCCACATTTGCCTTCCATT GCTGGCTCTTGGGCTTTATA 1350–1352 1.000 86.3
rpl21-rpl32_p3 rpl21-rpl32 AACCCACATTTGCCTTCCAT ACACCTGTTTTAGCAGCTGG 1366–1368 1.000 86.0
rpl21-rpl32_p4 rpl21-rpl32 ACCCACATTTGCCTTCCATT ACACCTGTTTTAGCAGCTGG 1365–1367 1.000 86.0
rpl21-rpl32_p5 rpl21-rpl32 ATTTTCCTGGCTGAACCCAC GCTGGCTCTTGGGCTTTATA 1364–1366 1.000 83.6
rrn16-ompR_p1 rrn16-ompR GAGCCAGGATCAAACTCTCC GCACTTACAACTTCGTAGCC 577–597 1.000 76.8
rrn16-ompR_p2 rrn16-ompR TGCATGTGTTAGGCATACCG GCACTTACAACTTCGTAGCC 611–631 1.000 76.7
rrn16-ompR_p3 rrn16-ompR GAGCCAGGATCAAACTCTCC GCACTTACAACTTCGTAGCCA 577–597 1.000 73.4
rrn16-ompR_p4 rrn16-ompR GAGCCAGGATCAAACTCTCC TGCACTTACAACTTCGTAGCC 578–598 1.000 73.4
rrn16-ompR_p5 rrn16-ompR TGCATGTGTTAGGCATACCG GCACTTACAACTTCGTAGCCA 611–631 1.000 73.2

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
Polyopes affinis NC_084249.1 196173 View on NCBI ↗
Polyopes constrictus PV055143.1 195850 View on NCBI ↗
Polyopes polyideoides PP338773.1 201550 View on NCBI ↗