Markers + reference

Hesperocyparis

4 species · Cupressaceae · Cupressales

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Species 4
Genome length 127–127 kb
Candidate markers 242
Primer pairs 80

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 242 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 Genome 366 0.0096 1.00 51.2 yes View details
rps12-clpP Genome 1164 0.0026 1.00 63.0 yes View details
rrn16-trnI-GAU Genome 966 0.0047 1.00 61.9 yes View details
ndhF-rpl32 Genome 717 0.0028 0.99 51.5 yes View details
trnS-GGA-ycf3 Genome 695 0.0024 1.00 37.8 yes View details
ycf3 Genome 1917 0.0011 1.00 58.6 yes View details
psbM-petN Genome 605 0.0033 1.00 41.5 yes View details
ycf1-trnL-CAA Genome 897 0.0028 1.00 60.7 yes View details
rps12-trnV-GAC Genome 861 0.0012 1.00 59.7 yes View details
chlB-trnK-UUU Genome 1104 0.0005 1.00 59.6 yes View details
trnV-GAC-rrn16 Genome 552 0.0018 1.00 59.4 yes View details
trnH-GUG-chlL Genome 645 0.0020 0.77 57.9 no View details
rpoC2 Genome 3528 0.0004 1.00 55.1 yes View details
ycf2 Genome 7437 0.0003 1.00 55.0 yes View details
psbI-psbK Genome 605 0.0008 1.00 50.1 yes View details
accD-rpl23 Genome 1060 0.0000 1.00 50.0 yes View details
atpI-atpH Genome 563 0.0009 1.00 49.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accD-rpl23_p1 accD-rpl23 CATGGTTCCACGAGCTCTTT TTGATCCCGAATCGACATTT 1222–1227 1.000 56.1
accD-rpl23_p2 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATT 1223–1228 1.000 56.1
accD-rpl23_p3 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATTT 1223–1228 1.000 54.5
accD-rpl23_p4 accD-rpl23 CATGGTTCCACGAGCTCTTT ATTTGATCCCGAATCGACAT 1224–1229 1.000 54.2
accD-rpl23_p5 accD-rpl23 ATGGTTCCACGAGCTCTTTT TTGATCCCGAATCGACATTT 1221–1226 1.000 53.0
rps19_p1 rps19 TGTTTCAATTCTTCGTCGACG TCAATTTCATCTTCATCCTCCA 512–519 1.000 41.1
rps19_p2 rps19 GTTTCAATTCTTCGTCGACGT TCAATTTCATCTTCATCCTCCA 511–518 1.000 41.1
rps19_p3 rps19 TGTTTCAATTCTTCGTCGACG ATCAATTTCATCTTCATCCTCCA 513–520 1.000 41.1
rps19_p4 rps19 TGTTTCAATTCTTCGTCGACG TCAATTTCATCTTCATCCTCCAT 512–519 1.000 41.1
rps19_p5 rps19 GTTTCAATTCTTCGTCGACGT TCAATTTCATCTTCATCCTCCAT 511–518 1.000 41.1
rps12-clpP_p1 rps12-clpP GCATACTCCCTTCCGTTGAG GCAGGTTGTTTTTCTAGCGC 1326–1343 1.000 78.8
rps12-clpP_p2 rps12-clpP TTTCTTATCGGCTGTCTCGC GCAGGTTGTTTTTCTAGCGC 1274–1291 1.000 78.7
rps12-clpP_p3 rps12-clpP CTTATCGGCTGTCTCGCATT GCAGGTTGTTTTTCTAGCGC 1271–1288 1.000 78.2
rps12-clpP_p4 rps12-clpP TATCGGCTGTCTCGCATTTC GCAGGTTGTTTTTCTAGCGC 1269–1286 1.000 78.2
rps12-clpP_p5 rps12-clpP TTATCGGCTGTCTCGCATTT GCAGGTTGTTTTTCTAGCGC 1270–1287 1.000 76.9
ycf1-trnL-CAA_p1 ycf1-trnL-CAA CGGACCAATTGGCAATGTTG CATTTTGAGTGTCGCGTGTC 1033–1250 1.000 77.5
ycf1-trnL-CAA_p2 ycf1-trnL-CAA CGGACCAATTGGCAATGTTG GACATTTTGAGTGTCGCGTG 1035–1252 1.000 77.5
ycf1-trnL-CAA_p3 ycf1-trnL-CAA CGGACCAATTGGCAATGTTG ATTTTGAGTGTCGCGTGTCT 1032–1249 1.000 77.0
ycf1-trnL-CAA_p4 ycf1-trnL-CAA CGGACCAATTGGCAATGTTG TTTGAGTGTCGCGTGTCTAC 1030–1247 1.000 76.1
ycf1-trnL-CAA_p5 ycf1-trnL-CAA AAATACATTTGGGCCGGACC CATTTTGAGTGTCGCGTGTC 1047–1264 1.000 75.7
ycf2_p1 ycf2 TACTCGGGTTCATAGCGAGA AGAAATGCCGATCTTCGCTG 261 1.000 72.0
ycf2_p2 ycf2 TACTCGGGTTCATAGCGAGA AGCAGAAATGCCGATCTTCG 264 1.000 72.0
ycf2_p3 ycf2 TACTCGGGTTCATAGCGAGA CAGAAATGCCGATCTTCGCT 262 1.000 72.0
ycf2_p4 ycf2 GGGTTCATAGCGAGACAGAA AGAAATGCCGATCTTCGCTG 256 1.000 67.0
ycf2_p5 ycf2 GGGTTCATAGCGAGACAGAA CAGAAATGCCGATCTTCGCT 257 1.000 67.0
rps12-trnV-GAC_p1 rps12-trnV-GAC ATCGTACTCTGGCGACTTTG GACTTTCACCACGTCAAGGT 963–964 1.000 77.6
rps12-trnV-GAC_p2 rps12-trnV-GAC ATCGTACTCTGGCGACTTTG TGACTTTCACCACGTCAAGG 964–965 1.000 77.6
rps12-trnV-GAC_p3 rps12-trnV-GAC GCGTAAGGCAGAGTTTGGTT GACTTTCACCACGTCAAGGT 944–945 1.000 73.7
rps12-trnV-GAC_p4 rps12-trnV-GAC GCGTAAGGCAGAGTTTGGTT TGACTTTCACCACGTCAAGG 945–946 1.000 73.7
rps12-trnV-GAC_p5 rps12-trnV-GAC ATCGTACTCTGGCGACTTTG AGGTGACACTCTACCACTGA 947–948 1.000 72.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Hesperocyparis benthamii NC_039565.1 127007 View on NCBI ↗
Hesperocyparis glabra NC_026297.1 126993 View on NCBI ↗
Hesperocyparis lusitanica NC_039567.1 127113 View on NCBI ↗
Hesperocyparis stephensonii NC_061008.1 127186 View on NCBI ↗