Markers + reference

Glyptopetalum

2 species · Celastraceae · Celastrales

Back to catalogue

Species 2
Genome length 157–158 kb
Candidate markers 273
Primer pairs 110

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 390 0.0449 0.97 82.1 yes View details
trnK-UUU-rps16 LSC 583 0.0312 0.99 62.7 yes View details
rps16-trnQ-UUG LSC 1029 0.0219 0.98 67.0 yes View details
trnS-GCU-trnG-UCC LSC 886 0.0235 0.96 74.1 yes View details
trnG-UCC-trnR-UCU LSC 425 0.0256 0.92 65.2 yes View details
psbM-trnD-GUC LSC 462 0.0814 0.93 81.4 yes View details
trnD-GUC-trnY-GUA LSC 448 0.0184 0.97 55.3 yes View details
psbZ-trnG-GCC LSC 741 0.0419 0.87 75.8 yes View details
accD LSC 1500 0.0175 0.99 60.4 yes View details
petD-rpoA LSC 222 0.0811 1.00 85.1 yes View details
rpl32-trnL-UAG SSC 475 0.0254 0.99 60.6 yes View details
rps15 SSC 279 0.0179 1.00 49.0 yes View details
ycf1 SSC 5634 0.0168 0.99 57.3 yes View details
infA-rps8 LSC 142 0.0563 1.00 82.0 yes View details
atpF-atpH LSC 330 0.0404 0.98 78.6 yes View details
trnL-UAG-ccsA SSC 70 0.0429 1.00 77.1 yes View details
psbT-psbN LSC 60 0.0500 1.00 76.7 yes View details
psbI-trnS-GCU LSC 232 0.0354 0.97 74.9 yes View details
rpl22-rps19 LSC 113 0.0617 0.72 73.1 yes View details
psbC-trnS-UGA LSC 262 0.0349 0.98 72.2 yes View details
ccsA-ndhD SSC 252 0.0585 0.81 69.7 yes View details
rpoB-trnC-GCA LSC 1005 0.0143 0.97 69.2 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 110 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 GCGCTAACCTTGGTATGGAA 507–634 1.000 82.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 521–648 1.000 82.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 520–647 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 522–649 1.000 82.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT GCGCTAACCTTGGTATGGAA 527–654 1.000 82.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG CGATCGCGAAGAGAAGGAAA 1047 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTAGAACCCCCAACCCTCAT 1404 1.000 81.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA CGATCGCGAAGAGAAGGAAA 1303–1306 1.000 80.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTCATCTCCACCCCCTAA TTAGAACCCCCAACCCTCAT 1660–1663 1.000 80.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 GCATTTTGTTTTGCGCCAAG TTTAGAACCCCCAACCCTCA 1405 1.000 80.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG GAGGTTCGAATCCTTCCGTC 1142–1145 1.000 82.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA GAGGTTCGAATCCTTCCGTC 1145–1148 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTTCCTTCTCTTCGCGATCG AATAGAATATGGGGCGTGGC 1199–1202 1.000 80.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGTTTTCCTTCTCTTCGCGA AATAGAATATGGGGCGTGGC 1202–1205 1.000 79.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGATCGAACATCAATTGCA GAGGTTCGAATCCTTCCGTC 1129–1132 1.000 79.1
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA GTTCTTCGTACCGAGGGTTC 289–306 1.000 73.7
psbI-trnS-GCU_p2 psbI-trnS-GCU AATCCCGGACGCGAAGAATA TGGACTAAAGCGTCGGATTG 326–343 1.000 73.3
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA TGGACTAAAGCGTCGGATTG 325–342 1.000 73.3
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCCGGACGCGAAGAATA GTGGACTAAAGCGTCGGATT 327–344 1.000 73.3
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCCGGACGCGAAGAATAA GTGGACTAAAGCGTCGGATT 326–343 1.000 73.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TAATCCAACCGAGGGATCCC 979–999 1.000 80.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TAATCCAACCGAGGGATCCC 978–998 1.000 80.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC TAATCCAACCGAGGGATCCC 981–1001 1.000 77.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG TAATCCAACCGAGGGATCCC 974–994 1.000 77.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TAATCCAACCGAGGGATCCC 970–990 1.000 76.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATAAATTGCGTCCATGCGTC 531–555 1.000 79.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG ATAAATTGCGTCCATGCGTC 534–558 1.000 78.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC ATAAATTGCGTCCATGCGTC 535–559 1.000 76.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AATAAATTGCGTCCATGCGTC 532–556 1.000 76.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AATAAATTGCGTCCATGCGTC 535–559 1.000 76.5

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
Glyptopetalum feddei NC_065708.1 157441 View on NCBI ↗
Glyptopetalum fengii NC_065715.1 157543 View on NCBI ↗