Markers + reference

Castanea

5 species · Fagaceae · Fagales

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Species 5
Genome length 161–161 kb
Candidate markers 265
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 432 0.0231 1.00 69.6 yes View details
trnK-UUU-rps16 LSC 1062 0.0130 0.98 61.0 yes View details
rps16 LSC 1181 0.0068 0.98 51.8 yes View details
psbC-trnS-UGA LSC 267 0.0184 1.00 61.4 yes View details
psbZ-trnG-UCC LSC 607 0.0099 1.00 53.3 yes View details
rbcL-accD LSC 599 0.0267 1.00 75.5 yes View details
accD-psaI LSC 697 0.0063 1.00 48.3 yes View details
psbE-petL LSC 1331 0.0089 1.00 66.1 yes View details
clpP LSC 2082 0.0037 1.00 48.3 yes View details
ndhF SSC 2280 0.0047 1.00 55.4 yes View details
ndhA SSC 2143 0.0043 1.00 61.6 yes View details
trnS-GCU-trnG-GCC LSC 1024 0.0045 0.96 65.0 yes View details
trnE-UUC-trnT-GGU LSC 1010 0.0051 1.00 64.2 yes View details
ycf3-trnS-GGA LSC 929 0.0019 1.00 63.3 yes View details
petA-psbJ LSC 1026 0.0039 0.99 62.5 yes View details
rpl32-trnL-UAG SSC 1176 0.0043 0.99 60.0 yes View details
ndhF-rpl32 SSC 946 0.0061 0.99 59.4 yes View details
rpl14-rpl16 LSC 151 0.0061 0.97 58.0 yes View details
rps4-trnT-UGU LSC 339 0.0100 1.00 57.2 yes View details
trnT-UGU-trnL-UAA LSC 847 0.0057 1.00 55.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 537–557 1.000 79.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 538–558 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 551–571 1.000 79.3
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 552–572 1.000 79.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 550–570 1.000 79.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGCGGGAGTTTTTATGGA 1114–1162 1.000 76.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGCGGGAGTTTTTATGGAA 1113–1161 1.000 76.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCGGGAGTTTTTATGGA 1113–1161 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCGGGAGTTTTTATGGAA 1112–1160 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGCGGGAGTTTTTATGGAAC 1111–1159 1.000 75.9
rps16_p1 rps16 CCCCCTCTTTTGTTCTATTCA ACAGCAACCTACTAGGAAATGT 1198–1225 1.000 42.6
rps16_p2 rps16 CCCCCTCTTTTGTTCTATTCA ACAGCAACCTACTAGGAAATGTT 1198–1225 1.000 42.6
rps16_p3 rps16 CCCCCTCTTTTGTTCTATTCA CTGTTTACAGCAACCTACTAGGA 1204–1231 1.000 42.6
rps16_p4 rps16 CCCCCTCTTTTGTTCTATTCA TGTTTACAGCAACCTACTAGGA 1203–1230 1.000 42.6
rps16_p5 rps16 CCCCCTCTTTTGTTCTATTCA CAGCAACCTACTAGGAAATGT 1197–1224 1.000 42.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATT 1084–1131 1.000 77.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATT 1083–1130 1.000 77.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TAGTCCACTCAGCCATCTCC CGAAGGACCCCTTAACCATT 1071–1118 1.000 76.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACCATTT 1084–1131 1.000 75.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACCATTT 1083–1130 1.000 75.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU ACTTCCTTGCGTAGTACCCT GAACCGATGACTTACGCCTT 1150–1157 1.000 81.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU ACTTCCTTGCGTAGTACCCT CCATGGCGTTACTCTACCAC 1129–1136 1.000 80.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU ACTTCCTTGCGTAGTACCCT TGGCGTTACTCTACCACTGA 1126–1133 1.000 80.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 1107–1114 1.000 80.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU ACTTCCTTGCGTAGTACCCT CCGATGACTTACGCCTTACC 1147–1154 1.000 80.1
psbC-trnS-UGA_p1 psbC-trnS-UGA TTTATGGCATGCAGGAAGGG GGTTGATAGCTCCGGTCTTG 440–451 1.000 80.3
psbC-trnS-UGA_p2 psbC-trnS-UGA TTTATGGCATGCAGGAAGGG GGGTTCGAATCCCTCTCTCT 386–397 1.000 79.4
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 413–424 1.000 79.2
psbC-trnS-UGA_p4 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 412–423 1.000 78.7
psbC-trnS-UGA_p5 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGGTTCGAATCCCTCTCTCT 359–370 1.000 78.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Castanea henryi NC_033881.1 160807 View on NCBI ↗
Castanea mollissima NC_014674.1 160799 View on NCBI ↗
Castanea pumila var. pumila KM360048.1 160603 View on NCBI ↗
Castanea sativa NC_054204.1 160938 View on NCBI ↗
Castanea seguinii NC_039749.1 160862 View on NCBI ↗