Markers + reference

Tripterygium

2 species · Celastraceae · Celastrales

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Species 2
Genome length 159–159 kb
Candidate markers 273
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 411 0.0122 1.00 61.8 yes View details
psbA LSC 1062 0.0028 1.00 49.5 yes View details
rps16 LSC 294 0.0034 1.00 40.7 yes View details
atpF LSC 1235 0.0041 1.00 51.1 yes View details
psbM-trnD-GUC LSC 464 0.0065 1.00 60.1 yes View details
trnE-UUC-trnT-GGU LSC 611 0.0458 1.00 85.1 yes View details
psbZ-trnG-GCC LSC 698 0.0143 1.00 67.1 yes View details
petB LSC 1402 0.0057 1.00 51.5 yes View details
ycf1 IRb 936 0.0000 1.00 25.8 yes View details
ndhF-rpl32 SSC 935 0.0043 0.99 60.1 yes View details
ccsA SSC 972 0.0051 1.00 55.1 yes View details
ycf1 SSC 5703 0.0023 1.00 52.3 no View details
ycf1-ndhF SSC 31 0.1852 0.87 80.5 yes View details
rpl14-rpl16 LSC 141 0.0214 0.99 65.5 yes View details
infA-rps8 LSC 147 0.0204 1.00 64.2 yes View details
trnR-ACG-trnN-GUU IRb 605 0.0066 1.00 62.6 yes View details
trnN-GUU-trnR-ACG IRa 605 0.0066 1.00 62.6 yes View details
trnF-GAA-ndhJ LSC 813 0.0050 0.99 62.3 yes View details
cemA LSC 690 0.0058 1.00 62.1 yes View details
petA-psbJ LSC 905 0.0055 1.00 61.9 yes View details
rbcL-accD LSC 598 0.0050 1.00 61.6 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 105 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 CTACTGTCGAAGTTCCAGCC 465–473 1.000 79.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTACTGTCGAAGTTCCAGCC 479–487 1.000 79.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTACTGTCGAAGTTCCAGCC 478–486 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTACTGTCGAAGTTCCAGCC 480–488 1.000 79.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT CTACTGTCGAAGTTCCAGCC 485–493 1.000 79.7
psbA_p1 psbA CGAACTCGTATACACTAAAACCG TGCTTGGGAGTCCCTGATAA 1135 1.000 51.2
psbA_p2 psbA AAACCGAACTCGTATACACT TGCTTGGGAGTCCCTGATAA 1139 1.000 49.3
psbA_p3 psbA CCGAACTCGTATACACTAAAACC TGCTTGGGAGTCCCTGATAA 1136 1.000 48.4
psbA_p4 psbA AAAACCGAACTCGTATACACT TGCTTGGGAGTCCCTGATAA 1140 1.000 48.1
psbA_p5 psbA AAAAACCGAACTCGTATACACT TGCTTGGGAGTCCCTGATAA 1141 1.000 46.3
rps16_p1 rps16 AAAAGCTGCTAGTCGCACTT GATGCGCTTTTCATCCCATG 1619–1620 1.000 78.3
rps16_p2 rps16 AAAGCCGAGTACTCTACCGT GATGCGCTTTTCATCCCATG 1598–1599 1.000 77.9
rps16_p3 rps16 AAGCCGAGTACTCTACCGTT GATGCGCTTTTCATCCCATG 1597–1598 1.000 77.9
rps16_p4 rps16 AAAAGCTGCTAGTCGCACTT AAAAGCTTACGCCCACATCT 1555–1556 1.000 77.7
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT AAAAGCTTACGCCCACATCT 1533–1534 1.000 77.3
atpF_p1 atpF GGCTCGAATGGTTACCATGA AGTCGACAAATAGAGAATTAGTCT 1362–1366 1.000 40.6
atpF_p2 atpF GGCTCGAATGGTTACCATGA AAGTCGACAAATAGAGAATTAGTCT 1363–1367 1.000 40.6
atpF_p3 atpF ACTAATTTCGTCGGCTCGAA AGTCGACAAATAGAGAATTAGTCT 1374–1378 1.000 40.6
atpF_p4 atpF GGCTCGAATGGTTACCATGA AGTCGACAAATAGAGAATTAGTC 1362–1366 1.000 40.6
atpF_p5 atpF GGCTCGAATGGTTACCATGA GTCGACAAATAGAGAATTAGTCT 1361–1365 1.000 40.6
psbM-trnD-GUC_p1 psbM-trnD-GUC CGCCCTGACTTTGACTGATA TTCAATTGGTCAGAGCACCG 632–634 1.000 71.4
psbM-trnD-GUC_p2 psbM-trnD-GUC TATCGCCCTGACTTTGACTG TTCAATTGGTCAGAGCACCG 635–637 1.000 71.4
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCGCCCTGACTTTGACTGA TTCAATTGGTCAGAGCACCG 634–636 1.000 68.6
psbM-trnD-GUC_p4 psbM-trnD-GUC TCGCCCTGACTTTGACTGAT TTCAATTGGTCAGAGCACCG 633–635 1.000 68.6
psbM-trnD-GUC_p5 psbM-trnD-GUC TTATCGCCCTGACTTTGACTG TTCAATTGGTCAGAGCACCG 636–638 1.000 68.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 714 1.000 81.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 693 1.000 80.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGGGCTTACTGAGAATCCCT GAACCGATGACTTACGCCTT 785 1.000 80.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 693 1.000 80.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGGGCTTACTGAGAATCCCT CCATGGCGTTACTCTACCAC 764 1.000 80.3

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
Tripterygium regelii NC_061597.1 159144 View on NCBI ↗
Tripterygium wilfordii NC_061612.1 158916 View on NCBI ↗