Markers + reference

Discocleidion

2 species · Euphorbiaceae · Malpighiales

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Species 2
Genome length 167–168 kb
Candidate markers 269
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 434 0.0305 0.98 70.4 yes View details
trnS-GCU-trnG-GCC LSC 933 0.0292 0.51 61.3 yes View details
trnE-UUC-trnT-GGU LSC 2638 0.0662 0.95 85.7 yes View details
ndhC-trnV-UAC LSC 805 0.0531 0.98 89.5 yes View details
accD-psaI LSC 1575 0.0285 0.80 74.1 yes View details
ycf1-ndhF SSC 1177 0.0934 0.83 78.1 yes View details
psbC-trnS-UGA LSC 238 0.0294 1.00 69.4 yes View details
trnG-GCC-trnR-UCU LSC 846 0.0102 0.93 68.8 yes View details
trnV-UAC LSC 39 0.0256 1.00 67.2 yes View details
psaA-ycf3 LSC 792 0.0066 0.96 66.2 yes View details
trnH-GUG-psbA LSC 552 0.0081 0.90 65.7 yes View details
trnG-UCC-trnfM-CAU LSC 200 0.0156 0.96 65.3 yes View details
rps16-trnQ-UUG LSC 1004 0.0081 0.99 64.4 yes View details
psbZ-trnG-UCC LSC 618 0.0177 0.92 64.1 yes View details
rpl16-rps3 LSC 1468 0.0049 0.97 64.1 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 80 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 CCTCTAGACCTAGCTGCTGT 581–619 1.000 83.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 595–633 1.000 82.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 594–632 1.000 82.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 596–634 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 584–622 1.000 82.9
psbA-trnK-UUU_p1 psbA-trnK-UUU AAACGACCCCATAGGCTTTC CTATCCGACTAGTTCCGGGT 516–523 1.000 82.1
psbA-trnK-UUU_p2 psbA-trnK-UUU GAAACGACCCCATAGGCTTT CTATCCGACTAGTTCCGGGT 517–524 1.000 82.1
psbA-trnK-UUU_p3 psbA-trnK-UUU CCAGTTACAGAAACGACCCC CTATCCGACTAGTTCCGGGT 526–533 1.000 81.4
psbA-trnK-UUU_p4 psbA-trnK-UUU AAACGACCCCATAGGCTTTC CGGCTTGGAGAGGGATTTTT 568–576 1.000 80.8
psbA-trnK-UUU_p5 psbA-trnK-UUU GAAACGACCCCATAGGCTTT CGGCTTGGAGAGGGATTTTT 569–577 1.000 80.8
trnK-UUU_p1 trnK-UUU AGCATTTCATCTGATTTCAATATGA TGATTGTGTGATGCGCTTCA 2769–2777 1.000 40.7
trnK-UUU_p2 trnK-UUU AGCATTTCATCTGATTTCAATATGA GATTGTGTGATGCGCTTCAA 2768–2776 1.000 40.7
trnK-UUU_p3 trnK-UUU AGCATTTCATCTGATTTCAATATGA TTGATTGTGTGATGCGCTTC 2770–2778 1.000 40.7
trnK-UUU_p4 trnK-UUU GCATTTCATCTGATTTCAATATGA TGATTGTGTGATGCGCTTCA 2768–2776 1.000 40.7
trnK-UUU_p5 trnK-UUU AGCATTTCATCTGATTTCAATATG TGATTGTGTGATGCGCTTCA 2769–2777 1.000 40.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACGTTGCTTTCTACCCCATC GAAATTCAAATGGGGCGTGG 1123–1128 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTTGCTTTCTACCCCATCGT GAAATTCAAATGGGGCGTGG 1121–1126 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTCAAATGGGGCGTGG 1130–1135 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACGTTGCTTTCTACCCCATC GAGGTTCGAATCCTTCCGTC 1065–1070 1.000 79.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTTGCTTTCTACCCCATCGT GAGGTTCGAATCCTTCCGTC 1063–1068 1.000 79.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTCATCGGAATATGGAGCCG 625–1056 1.000 81.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TTCATCGGAATATGGAGCCG 624–1055 1.000 81.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAGCCGAGGATCCCTTAACT 611–1042 1.000 80.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAGCCGAGGATCCCTTAACT 610–1041 1.000 80.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TTCCAAGTCATCACCGGAAC TTCATCGGAATATGGAGCCG 698–1129 1.000 80.1
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 868–926 1.000 68.1
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 871–929 1.000 67.8
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 874–932 1.000 67.4
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 877–935 1.000 67.2
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 872–930 1.000 65.6

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
Discocleidion rufescens PP968730.1 167327 View on NCBI ↗
Discocleidion ulmifolium PQ009256.1 168208 View on NCBI ↗