Markers + reference

Callitropsis

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 127–128 kb
Candidate markers 244
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 244 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD-rpl23 Genome 1242 0.0174 0.88 71.4 yes View details
psaJ-rpl33 Genome 315 0.0317 1.00 71.1 yes View details
rps12-clpP Genome 1249 0.0323 0.94 81.7 yes View details
clpP-trnP-GGG Genome 277 0.0289 1.00 55.5 yes View details
ycf1 Genome 7026 0.0077 1.00 42.0 yes View details
ycf2 Genome 7410 0.0058 0.99 48.8 yes View details
trnV-GAC-rrn16 Genome 460 0.0239 1.00 61.6 yes View details
rrn16-trnI-GAU Genome 949 0.0286 1.00 75.6 yes View details
ndhF-rpl32 Genome 759 0.0225 1.00 63.4 yes View details
atpE-rbcL Genome 433 0.0069 1.00 77.0 no View details
ccsA-ycf1 Genome 35 0.0571 1.00 69.8 yes View details
rps4 Genome 624 0.0112 1.00 65.2 yes View details
trnP-GGG-trnL-UAG Genome 136 0.0403 0.91 64.7 yes View details
ycf4-cemA Genome 467 0.0150 1.00 64.6 yes View details
chlN-ndhJ Genome 473 0.0148 1.00 64.6 yes View details
trnH-GUG-chlL Genome 649 0.0093 1.00 64.5 yes View details
rpl16 Genome 1244 0.0088 1.00 63.8 yes View details
infA-rpl36 Genome 35 0.0286 1.00 63.8 yes View details
ndhC-trnV-UAC Genome 761 0.0040 0.98 63.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
accD-rpl23_p1 accD-rpl23 CATGGTTCCACGAGCTCTTT TTGATCCCGAATCGACATTT 1333–1409 1.000 60.8
accD-rpl23_p2 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATT 1334–1410 1.000 60.8
accD-rpl23_p3 accD-rpl23 CATGGTTCCACGAGCTCTTT TTTGATCCCGAATCGACATTT 1334–1410 1.000 59.3
accD-rpl23_p4 accD-rpl23 CATGGTTCCACGAGCTCTTT ATTTGATCCCGAATCGACAT 1335–1411 1.000 58.9
accD-rpl23_p5 accD-rpl23 ATGGTTCCACGAGCTCTTTT TTGATCCCGAATCGACATTT 1332–1408 1.000 57.7
rpl16_p1 rpl16 AAACATCTTGGAGCAGTGCT CCAATTGTTACCTCGGCAGA 1348–1353 1.000 77.5
rpl16_p2 rpl16 AAACATCTTGGAGCAGTGCT CTCCAATTGTTACCTCGGCA 1350–1355 1.000 77.5
rpl16_p3 rpl16 AAACATCTTGGAGCAGTGCT TCCAATTGTTACCTCGGCAG 1349–1354 1.000 77.5
rpl16_p4 rpl16 AAACATCTTGGAGCAGTGCT CCTCCAATTGTTACCTCGGC 1351–1356 1.000 73.4
rpl16_p5 rpl16 AAACATCTTGGAGCAGTGCT TCCTCCAATTGTTACCTCGG 1352–1357 1.000 69.8
infA-rpl36_p1 infA-rpl36 CATCCCGTCAAACGAAAGGA CTACGAATTAGGCGGCACTT 136 1.000 78.5
infA-rpl36_p2 infA-rpl36 CCCGTCAAACGAAAGGATGA CTACGAATTAGGCGGCACTT 133 1.000 78.5
infA-rpl36_p3 infA-rpl36 TCCCGTCAAACGAAAGGATG CTACGAATTAGGCGGCACTT 134 1.000 78.5
infA-rpl36_p4 infA-rpl36 ACGAAAGGATGATGCTACCG CTACGAATTAGGCGGCACTT 125 1.000 78.3
infA-rpl36_p5 infA-rpl36 GATGATGCTACCGATGAGGC CTACGAATTAGGCGGCACTT 118 1.000 77.9
ycf4-cemA_p1 ycf4-cemA ATTTGACCTTGCGCGAAATG TGGCAACTTCCAATTCGTGA 647 1.000 80.5
ycf4-cemA_p2 ycf4-cemA GAAAATTTGACCTTGCGCGA TGGCAACTTCCAATTCGTGA 651 1.000 80.3
ycf4-cemA_p3 ycf4-cemA AGAAAATTTGACCTTGCGCG TGGCAACTTCCAATTCGTGA 652 1.000 80.2
ycf4-cemA_p4 ycf4-cemA ATTTGACCTTGCGCGAAATG CTCGTTAGCTCTGCCCAAAA 606 1.000 79.2
ycf4-cemA_p5 ycf4-cemA GAAAATTTGACCTTGCGCGA CTCGTTAGCTCTGCCCAAAA 610 1.000 79.0
psaJ-rpl33_p1 psaJ-rpl33 ATATCTTTCCACAGCGCCTG TTACATTTCCACCCTTGGCC 449 1.000 80.9
psaJ-rpl33_p2 psaJ-rpl33 CATATCTTTCCACAGCGCCT TTACATTTCCACCCTTGGCC 450 1.000 80.9
psaJ-rpl33_p3 psaJ-rpl33 ACATATCTTTCCACAGCGCC TTACATTTCCACCCTTGGCC 451 1.000 78.6
psaJ-rpl33_p4 psaJ-rpl33 GCGCCTGTGTTAGCTACTTT TTACATTTCCACCCTTGGCC 436 1.000 76.8
psaJ-rpl33_p5 psaJ-rpl33 ATATCTTTCCACAGCGCCTG CATTTCCACCCTTGGCCAT 446 1.000 73.4
rps12-clpP_p1 rps12-clpP GCATACTCCCTTCCGTTGAG GCAGGTTGTTTTTCTAGCGC 1428–1479 1.000 83.1
rps12-clpP_p2 rps12-clpP TTTCTTATCGGCTGTCTCGC GCAGGTTGTTTTTCTAGCGC 1376–1427 1.000 83.0
rps12-clpP_p3 rps12-clpP CTTATCGGCTGTCTCGCATT GCAGGTTGTTTTTCTAGCGC 1373–1424 1.000 82.5
rps12-clpP_p4 rps12-clpP TATCGGCTGTCTCGCATTTC GCAGGTTGTTTTTCTAGCGC 1371–1422 1.000 82.5
rps12-clpP_p5 rps12-clpP TTATCGGCTGTCTCGCATTT GCAGGTTGTTTTTCTAGCGC 1372–1423 1.000 81.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Callitropsis nootkatensis NC_026295.1 127150 View on NCBI ↗
Callitropsis vietnamensis NC_026298.1 127541 View on NCBI ↗