Markers + reference

Scorpiothyrsus

3 species · Melastomataceae · Myrtales

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Species 3
Genome length 156–156 kb
Candidate markers 262
Primer pairs 95

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 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0031 1.00 34.5 yes View details
rps16 LSC 1061 0.0132 1.00 57.7 yes View details
rpoB-trnC-GCA LSC 1354 0.0163 1.00 61.7 yes View details
trnfM-CAU-rps14 LSC 172 0.0465 1.00 74.0 yes View details
trnF-GAA-ndhJ LSC 876 0.0114 1.00 54.2 yes View details
rbcL-accD LSC 623 0.0194 1.00 73.1 yes View details
rpl33-rps18 LSC 224 0.0239 1.00 57.2 yes View details
rpl14-rps3 LSC 1738 0.0096 1.00 59.8 yes View details
ycf1 IRb 1899 0.0042 1.00 39.5 no View details
ndhF-rpl32 SSC 888 0.0359 0.98 72.2 yes View details
rps15-ycf1 SSC 359 0.0325 1.00 64.9 yes View details
ycf1 SSC 5625 0.0109 1.00 51.3 yes View details
trnH-GUG-psbA LSC 232 0.0524 0.99 89.8 yes View details
psbT-psbN LSC 72 0.0926 1.00 69.0 yes View details
petD-rpoA LSC 236 0.0254 1.00 68.0 yes View details
atpF-atpH LSC 522 0.0128 0.99 66.9 yes View details
ndhC-trnV-UAC LSC 671 0.0140 1.00 65.4 yes View details
trnS-GCU-trnR-UCU LSC 1819 0.0134 1.00 65.0 yes View details
trnE-UUC-trnT-GGU LSC 685 0.0156 1.00 64.9 yes View details
ndhK-ndhC LSC 54 0.0370 1.00 63.6 yes View details
rpl2-trnH-GUG IRa 137 0.0049 1.00 63.3 no 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 95 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 290–298 1.000 86.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 340–348 1.000 85.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 354–362 1.000 85.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 353–361 1.000 85.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 355–363 1.000 85.1
psbA_p1 psbA GATCCACTTGGCTACATCCG AACACAAAACTACTGGCCGT 2034–2042 1.000 80.3
psbA_p2 psbA GATCCACTTGGCTACATCCG ACAAAACTACTGGCCGTGTT 2031–2039 1.000 80.3
psbA_p3 psbA CAATCCACTGCCTTGATCCA AACACAAAACTACTGGCCGT 2048–2056 1.000 80.2
psbA_p4 psbA CAATCCACTGCCTTGATCCA ACAAAACTACTGGCCGTGTT 2045–2053 1.000 80.2
psbA_p5 psbA AATCCACTGCCTTGATCCAC ACAAAACTACTGGCCGTGTT 2044–2052 1.000 80.2
rps16_p1 rps16 AAAATTTCCCCCTTATCCTTT ATACCAGTTAAAACCCGGGG 1115–1145 1.000 42.0
rps16_p2 rps16 AAATTTCCCCCTTATCCTTTT ATACCAGTTAAAACCCGGGG 1114–1144 1.000 42.0
rps16_p3 rps16 AATTTCCCCCTTATCCTTTTT ATACCAGTTAAAACCCGGGG 1113–1143 1.000 42.0
rps16_p4 rps16 AGGGGGATCTACTAGAAAAA ATACCAGTTAAAACCCGGGG 1152–1182 1.000 41.9
rps16_p5 rps16 AGGGGGATCTACTAGAAAAA ACATACCAGTTAAAACCCGGG 1154–1184 1.000 41.9
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1933–1952 1.000 70.9
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1932–1951 1.000 70.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1940–1959 1.000 69.0
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1939–1958 1.000 69.0
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1934–1953 1.000 68.9
atpF-atpH_p1 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGATTGGTTGTCGCTTTAGC 599–607 1.000 78.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GGATTGGTTGTCGCTTTAGC 631–639 1.000 77.0
atpF-atpH_p3 atpF-atpH GGCCCAAGGAAAGGAAAGAA CGGAGGGAAAAATACGAGGT 664–672 1.000 76.6
atpF-atpH_p4 atpF-atpH GGCCCAAGGAAAGGAAAGAA GCGGAGGGAAAAATACGAGG 665–673 1.000 76.4
atpF-atpH_p5 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGCGGAGGGAAAAATACGAG 666–674 1.000 76.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCACTTCCATCCACCAGCAT CCGGATTTGAACTGGGGAAA 1436–1470 1.000 74.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCACTTCCATCCACC CCGGATTTGAACTGGGGAAA 1441–1475 1.000 74.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GACATTCCCTCACTTCCATCC CCGGATTTGAACTGGGGAAA 1445–1479 1.000 74.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTCCCTCACTTCCATCCA CCGGATTTGAACTGGGGAAA 1443–1477 1.000 74.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCACTTCCATCCAC CCGGATTTGAACTGGGGAAA 1442–1476 1.000 74.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Scorpiothyrsus erythrotrichus MZ434958.1 156050 View on NCBI ↗
Scorpiothyrsus oligotrichus MK994794.1 156105 View on NCBI ↗
Scorpiothyrsus shangszeensis MK994866.1 156371 View on NCBI ↗