Markers + reference

Cupressus

4 species · Cupressaceae · Cupressales

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Species 4
Genome length 128–129 kb
Candidate markers 243
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 243 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD-rpl23 Genome 1366 0.0256 0.99 80.1 yes View details
rpoA Genome 1041 0.0328 0.98 71.7 yes View details
rps12-clpP Genome 1196 0.0183 1.00 59.5 yes View details
ycf1 Genome 7149 0.0162 1.00 42.2 yes View details
ycf2 Genome 7536 0.0067 1.00 49.1 yes View details
rrn16-trnI-GAU Genome 866 0.0143 0.95 72.7 yes View details
trnV-GAC-rrn16 Genome 733 0.0152 0.99 71.4 yes View details
atpE-rbcL Genome 433 0.0035 1.00 70.6 no View details
psbD-trnT-GGU Genome 865 0.0064 1.00 61.7 yes View details
ycf1-trnL-CAA Genome 884 0.0196 0.93 60.8 yes View details
psbM-petN Genome 603 0.0124 1.00 60.6 yes View details
trnA-UGC-rrn23 Genome 143 0.0082 1.00 60.4 yes View details
rrn4.5-rrn5 Genome 318 0.0110 1.00 59.0 yes View details
rps15-ndhH Genome 113 0.0147 1.00 58.8 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accD-rpl23_p1 accD-rpl23 CATGGTTCCACGAGCTCTTT TTGATCCCGAATCGACATTT 1471–1718 1.000 62.7
accD-rpl23_p2 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATT 1472–1719 1.000 62.7
accD-rpl23_p3 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATTT 1472–1719 1.000 61.2
accD-rpl23_p4 accD-rpl23 CATGGTTCCACGAGCTCTTT ATTTGATCCCGAATCGACAT 1473–1720 1.000 60.8
accD-rpl23_p5 accD-rpl23 ATGGTTCCACGAGCTCTTTT TTGATCCCGAATCGACATTT 1470–1717 1.000 59.6
rpoA_p1 rpoA TATGCTACGTGGCAATGGTC CGTCGTCCAGTAGCTACAAC 1564–1915 1.000 85.4
rpoA_p2 rpoA TATGCTACGTGGCAATGGTC AATGGCTTCAGTACCTGCAG 1637–1988 1.000 85.0
rpoA_p3 rpoA CCATTTGCTGCTCAGATTGC CGTCGTCCAGTAGCTACAAC 1641–1992 1.000 84.9
rpoA_p4 rpoA CCAGCACTGCGAGCTATTTA CGTCGTCCAGTAGCTACAAC 1533–1884 0.750 75.0
rpoA_p5 rpoA CCAGCACTGCGAGCTATTTA AATGGCTTCAGTACCTGCAG 1606–1957 0.750 74.6
rps12-clpP_p1 rps12-clpP GCATACTCCCTTCCGTTGAG CCCGTGTAGAAGGAAAGCTC 1561–1673 1.000 83.0
rps12-clpP_p2 rps12-clpP GCATACTCCCTTCCGTTGAG CCGTGTAGAAGGAAAGCTCC 1560–1672 1.000 83.0
rps12-clpP_p3 rps12-clpP GCATACTCCCTTCCGTTGAG CGTGTAGAAGGAAAGCTCCC 1559–1671 1.000 83.0
rps12-clpP_p4 rps12-clpP TTTCTTATCGGCTGTCTCGC CCGTGTAGAAGGAAAGCTCC 1508–1620 1.000 82.9
rps12-clpP_p5 rps12-clpP TTTCTTATCGGCTGTCTCGC CGTGTAGAAGGAAAGCTCCC 1507–1619 1.000 82.9
ycf1_p1 ycf1 TTAGACGTAGGCCTAGTCCG TGGATACCGAGACCAGAGTC 803–860 1.000 89.1
ycf1_p2 ycf1 TTAGACGTAGGCCTAGTCCG CGAATGGGAGCAAGATTGGA 480–534 0.750 74.0
ycf1_p3 ycf1 TGAAAAACGTACGCTTGGGA CGAATGGGAGCAAGATTGGA 1002–1056 0.750 73.7
ycf1_p4 ycf1 TCTCCAGGATGCTTGCAATC CGAATGGGAGCAAGATTGGA 1146–1200 0.750 73.6
ycf1_p5 ycf1 CTCTCCAGGATGCTTGCAAT CGAATGGGAGCAAGATTGGA 1147–1201 0.750 73.6
ycf1-trnL-CAA_p1 ycf1-trnL-CAA CAAGTTCTTCTCGAGGACCG CATTTTGAGTGTCGCGTGTC 1639–1767 1.000 85.7
ycf1-trnL-CAA_p2 ycf1-trnL-CAA CAAGTTCTTCTCGAGGACCG GACATTTTGAGTGTCGCGTG 1641–1769 1.000 85.7
ycf1-trnL-CAA_p3 ycf1-trnL-CAA TGGATGAGAAGACCACCAGT CATTTTGAGTGTCGCGTGTC 1141–1269 1.000 85.6
ycf1-trnL-CAA_p4 ycf1-trnL-CAA TTTGAAGCCAAGGGTGTCTC CATTTTGAGTGTCGCGTGTC 1264–1384 0.750 74.4
ycf1-trnL-CAA_p5 ycf1-trnL-CAA TTTGAAGCCAAGGGTGTCTC GACATTTTGAGTGTCGCGTG 1266–1386 0.750 74.4
ycf2_p1 ycf2 ACTTCCGTCTCTGAAAAGGG GCAGAAGAAGAATTTGCTCGT 221–227 1.000 68.0
ycf2_p2 ycf2 ACTTCCGTCTCTGAAAAGGG AGCAGAAGAAGAATTTGCTCG 222–228 1.000 65.7
ycf2_p3 ycf2 AACTTCCGTCTCTGAAAAGGG GCAGAAGAAGAATTTGCTCGT 222–228 1.000 65.7
ycf2_p4 ycf2 CTTCCGTCTCTGAAAAGGGA GCAGAAGAAGAATTTGCTCGT 220–226 1.000 65.7
ycf2_p5 ycf2 ACTTCCGTCTCTGAAAAGGG GCAGAAGAAGAATTTGCTCGTT 221–227 1.000 65.3

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
Cupressus chengiana NC_034788.1 128151 View on NCBI ↗
Cupressus gigantea NC_028155.1 128244 View on NCBI ↗
Cupressus jiangensis NC_036939.1 128286 View on NCBI ↗
Cupressus sempervirens NC_026296.1 129150 View on NCBI ↗