Markers + reference

Carya

10 species · Juglandaceae · Fagales

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Species 10
Genome length 158–161 kb
Candidate markers 274
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1376 0.0057 0.98 48.5 yes View details
psbC-trnS-UGA LSC 241 0.0195 1.00 51.3 yes View details
psbZ-trnG-GCC LSC 617 0.0139 0.96 54.1 yes View details
ndhC-trnV-UAC LSC 596 0.0130 1.00 64.7 yes View details
rrn4.5S IRb 271 0.0295 1.00 59.0 yes View details
rrn5S-trnR-ACG IRb 241 0.0024 1.00 43.5 yes View details
ycf1 IRb 1093 0.0120 1.00 44.0 no View details
ndhF SSC 2226 0.0024 1.00 33.6 yes View details
ndhF-rpl32 SSC 965 0.0105 1.00 51.3 yes View details
ndhA SSC 2284 0.0048 1.00 44.1 yes View details
ycf1 SSC 5658 0.0039 1.00 39.1 yes View details
rrn5-rrn4.5S IRa 257 0.0309 1.00 60.2 yes View details
rrn4.5S IRa 103 0.0000 1.00 28.5 no View details
atpH-atpI LSC 1306 0.0048 1.00 65.1 yes View details
ycf1-ndhF SSC 188 0.0739 0.99 63.9 yes View details
psbE-petL LSC 1430 0.0055 1.00 60.3 yes View details
trnT-UGU-trnL-UAA LSC 892 0.0046 1.00 59.7 yes View details
trnS-GCU-trnS-CGA LSC 849 0.0054 1.00 59.6 yes View details
rps15-ycf1 SSC 446 0.0054 0.99 58.2 yes View details
rpl2-trnH-GUG IRa 96 0.0127 0.99 57.7 no View details
atpA-atpF LSC 74 0.0296 0.96 54.7 yes View details
matK-rps16 LSC 1650 0.0045 1.00 52.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 ACTCCCGAAAGATAAGTGGG TCAAAGAAGGCGGGAGTTTT 1766–1990 1.000 69.3
matK-rps16_p2 matK-rps16 ACTCCCGAAAGATAAGTGGG TTCAAAGAAGGCGGGAGTTT 1767–1991 1.000 69.3
matK-rps16_p3 matK-rps16 CTCCCGAAAGATAAGTGGGT TCAAAGAAGGCGGGAGTTTT 1765–1989 1.000 69.3
matK-rps16_p4 matK-rps16 CTCCCGAAAGATAAGTGGGT TTCAAAGAAGGCGGGAGTTT 1766–1990 1.000 69.3
matK-rps16_p5 matK-rps16 CTCCCGAAAGATAAGTGGGT TTTCAAAGAAGGCGGGAGTT 1767–1991 1.000 69.3
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AATGGCGGATGTCAGAATCC GAGGTTCGAATCCTTCCGTC 1628–1685 1.000 84.4
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AATGGCGGATGTCAGAATCC AGCAGCTTGCCAAACAAAAG 2279–2334 1.000 83.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AATGGCGGATGTCAGAATCC CTTACAGCAGCTTGCCAAAC 2284–2339 1.000 83.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG GATTCCCGCGTGATACACTT AGCAGCTTGCCAAACAAAAG 2599–2661 1.000 82.9
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GATTCCCGCGTGATACACTT CTTACAGCAGCTTGCCAAAC 2604–2666 1.000 82.9
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA GGAACGAATCACACTTTTACCA 871–971 1.000 60.8
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA TGGAACGAATCACACTTTTACC 872–972 1.000 60.8
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC GGAACGAATCACACTTTTACCA 870–970 1.000 60.8
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC TGGAACGAATCACACTTTTACC 871–971 1.000 60.8
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA ACAAAAGCGGAAAGAGAGGG GGAACGAATCACACTTTTACCA 931–1031 1.000 60.0
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC CACGCTGTTAGAAATAACCGA 212 0.100 22.3
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG CACGCTGTTAGAAATAACCGA 210 0.100 22.3
atpA-atpF_p3 atpA-atpF ACTTGAAGTACGGTACCGGT CACGCTGTTAGAAATAACCGA 203 0.100 20.0
atpA-atpF_p4 atpA-atpF TCGCCTACTTGAAGTACGGT CACGCTGTTAGAAATAACCGA 209 0.100 19.4
atpA-atpF_p5 atpA-atpF CGTCGCCTACTTGAAGTACG CACGCTGTTAGAAATAACCGA 211 0.100 19.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1332–1446 1.000 84.0
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1417–1531 1.000 83.9
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1302–1416 1.000 83.6
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC CGAATCCATGGAGGGTCATC 1387–1501 1.000 83.5
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1333–1447 1.000 82.8
psbC-trnS-UGA_p1 psbC-trnS-UGA TTATGGCATGCAGGAAGAGC GGTTGATAGCTCCGGTCTTG 412–418 1.000 80.3
psbC-trnS-UGA_p2 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 385–391 1.000 79.5
psbC-trnS-UGA_p3 psbC-trnS-UGA TTATGGCATGCAGGAAGAGC GGGTTCGAATCCCTCTCTCT 358–364 1.000 79.5
psbC-trnS-UGA_p4 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGGTTCGAATCCCTCTCTCT 331–337 1.000 78.8
psbC-trnS-UGA_p5 psbC-trnS-UGA TTATGGCATGCAGGAAGAGC TGGTTGATAGCTCCGGTCTT 413–419 1.000 77.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Carya cordiformis NC_067508.1 160796 View on NCBI ↗
Carya dabieshanensis NC_067502.1 160233 View on NCBI ↗
Carya floridana NC_067503.1 160760 View on NCBI ↗
Carya glabra NC_067504.1 160652 View on NCBI ↗
Carya illinoinensis NC_041449.1 160819 View on NCBI ↗
Carya ovalis NC_067509.1 160822 View on NCBI ↗
Carya palmeri NC_067505.1 160672 View on NCBI ↗
Carya poilanei NC_067868.1 158036 View on NCBI ↗
Carya texana NC_067506.1 160745 View on NCBI ↗
Carya tomentosa NC_067507.1 160784 View on NCBI ↗