Markers + reference

Thesium

4 species · Thesiaceae · Santalales

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Species 4
Genome length 137–141 kb
Candidate markers 247
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 458 0.0938 0.95 81.4 yes View details
rps16-trnQ-UUG LSC 1133 0.0557 0.98 84.9 yes View details
trnG-UCC-trnR-UCU LSC 319 0.0956 0.97 80.5 yes View details
trnR-UCU-atpA LSC 199 0.0511 0.98 77.0 yes View details
petN-psbM LSC 781 0.0578 0.93 82.4 yes View details
ycf1 IRb 522 0.0383 0.98 73.9 no View details
rpl32-trnL-UAG SSC 501 0.0978 0.93 80.8 yes View details
psaC-rps15 SSC 633 0.0571 0.96 86.1 yes View details
ycf1 SSC 5592 0.0438 1.00 68.8 yes View details
ycf4-cemA LSC 690 0.0529 1.00 83.5 yes View details
rpl16-rps3 LSC 181 0.0589 1.00 80.7 yes View details
trnS-GCU-trnG-UCC LSC 352 0.0638 0.94 80.6 yes View details
petA-psbJ LSC 479 0.0483 0.99 80.3 yes View details
psbK-psbI LSC 441 0.0493 0.96 79.3 yes View details
trnD-GUC-trnY-GUA LSC 414 0.0396 0.99 77.5 yes View details
ycf1-rpl32 SSC 112 0.1101 1.00 77.4 yes View details
rps15-ycf1 SSC 339 0.0669 1.00 77.3 yes View details
trnG-GCC-trnM-CAU LSC 181 0.0635 0.96 77.2 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 85 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 CGTAGCTGCCCATGGTTATT 790–828 1.000 90.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCATGGTTCCTTGGTAACC 893–931 1.000 88.8
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAATGGGAGCTTAGCTTC 1148–1186 1.000 87.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 902–940 0.750 73.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 901–939 0.750 73.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATCCTGTCCTTCAAGTCGC GTTCGAATCCTTCCGTTCCA 1186–1401 1.000 89.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTTCCA 1173–1388 1.000 89.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCTGTCCTTCAAGTCGC TTCGAATCCTTCCGTTCCAG 1185–1400 1.000 87.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AATCCTGTCCTTCAAGTCGC AGGTTCGAATCCTTCCGTTC 1188–1403 1.000 87.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATCCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTT 1189–1404 1.000 87.2
psbK-psbI_p1 psbK-psbI TCAAAACCCAGTGCCTTACC TGGACTAAAGCGGTGGATTG 1219–1242 0.750 71.7
psbK-psbI_p2 psbK-psbI TCAAAACCCAGTGCCTTACC GTGGACTAAAGCGGTGGATT 1220–1243 0.750 71.6
psbK-psbI_p3 psbK-psbI GCCAAATTACCCGAAGCCTA TAGCCGGCCTGTATTAGTGA 918–926 0.500 62.7
psbK-psbI_p4 psbK-psbI TCAAAACCCAGTGCCTTACC TAGCCGGCCTGTATTAGTGA 1376–1397 0.500 62.1
psbK-psbI_p5 psbK-psbI CTCCGAATGCTGGGATCAAA TAGCCGGCCTGTATTAGTGA 1391–1412 0.500 61.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCACCGCTTTAGTCCA ACGAATCACACTTTTACCACT 404–679 1.000 61.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCACCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 403–678 1.000 61.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCAGAAAGGGAAAGAGAGGG ACGAATCACACTTTTACCACT 464–739 1.000 60.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTCGTACAGCGGATTAGCAA ACGAATCACACTTTTACCACT 421–696 1.000 60.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AACTCGTACAGCGGATTAGC ACGAATCACACTTTTACCACT 423–698 1.000 60.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU TTCCAAGCTAATGATGCGGG AGAAGACCTATGTCCTATCCA 377–420 1.000 54.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU GCTAATGATGCGGGTTCGAT AGAAGACCTATGTCCTATCCA 371–414 1.000 52.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCAAGCTAATGATGCGGGTT AGAAGACCTATGTCCTATCCA 375–418 1.000 52.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AATGATGCGGGTTCGATTCC AGAAGACCTATGTCCTATCCA 368–411 1.000 52.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AAGCTAATGATGCGGGTTCG AGAAGACCTATGTCCTATCCA 373–416 1.000 52.0
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTCCCGCTATCCGCTTTAC AGACATTCACGGAAGAAGCC 687–716 1.000 89.9
trnR-UCU-atpA_p2 trnR-UCU-atpA ATTCCCGCTATCCGCTTTAC GGAAGAAGCCGAATCCCTTT 677–706 1.000 89.6
trnR-UCU-atpA_p3 trnR-UCU-atpA ATTCCCGCTATCCGCTTTAC ATTGGAACTGGCGCAATTTG 974–1003 1.000 88.7
trnR-UCU-atpA_p4 trnR-UCU-atpA ATTCCCGCTATCCGCTTTAC ATGAAACAAGTAGCCGGCAA 1000–1029 1.000 88.3
trnR-UCU-atpA_p5 trnR-UCU-atpA ATTCCCGCTATCCGCTTTAC TCAAGAGCAAATGGAACGCT 648–673 0.750 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Thesium alpinum PP622700.1 137095 View on NCBI ↗
Thesium bavarum PP622701.1 138399 View on NCBI ↗
Thesium chinense NC_065651.1 138495 View on NCBI ↗
Thesium decaryanum OR712484.1 141066 View on NCBI ↗