Markers + reference

Matsumurella

5 species · Lamiaceae · Lamiales

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Species 5
Genome length 152–152 kb
Candidate markers 270
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 685 0.0114 1.00 52.8 yes View details
atpH-atpI LSC 999 0.0099 1.00 59.9 yes View details
psbE-petL LSC 931 0.0086 1.00 64.2 yes View details
psaJ-rpl33 LSC 473 0.0090 1.00 53.0 yes View details
petD LSC 1222 0.0063 0.99 43.1 yes View details
ndhF SSC 2223 0.0065 1.00 41.3 yes View details
ccsA SSC 972 0.0086 1.00 50.3 yes View details
ndhD SSC 1503 0.0025 1.00 45.7 yes View details
ndhA SSC 2166 0.0066 1.00 56.4 yes View details
rps15-ycf1 SSC 317 0.0126 1.00 47.9 yes View details
ycf1 SSC 5547 0.0065 1.00 42.3 yes View details
ndhD-psaC SSC 116 0.0534 1.00 70.5 yes View details
ndhC-trnV-UAC LSC 965 0.0066 1.00 64.8 yes View details
trnT-UGU-trnL-UAA LSC 672 0.0086 1.00 63.8 yes View details
petA-psbJ LSC 1045 0.0092 1.00 60.2 yes View details
rpl32-trnL-UAG SSC 722 0.0089 1.00 59.0 yes View details
trnK-UUU-rps16 LSC 821 0.0041 1.00 58.8 yes View details
trnF-GAA-ndhJ LSC 663 0.0064 1.00 57.6 yes View details
rpl20-rps12 LSC 768 0.0055 1.00 56.4 yes View details
atpB-rbcL LSC 781 0.0058 1.00 55.7 yes View details
rbcL LSC 1467 0.0049 1.00 54.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTTCCGCCTAATCAA 890–1014 1.000 70.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATCAA 889–1013 1.000 70.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGGAACTTCCGCCTAATCAA 904–1028 1.000 69.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGGAACTTCCGCCTAATCAA 899–1023 1.000 69.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATCAAA 889–1013 1.000 68.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 754–762 1.000 53.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 753–761 1.000 53.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 757–765 1.000 52.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 756–764 1.000 52.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 755–763 1.000 52.4
trnG-UCC_p1 trnG-UCC CAATCCGACGCTTTAGTCCA CCCTCTTGCGGTAGAAGAAC 2068–2076 1.000 81.3
trnG-UCC_p2 trnG-UCC AATCCGACGCTTTAGTCCAC CCCTCTTGCGGTAGAAGAAC 2067–2075 1.000 81.3
trnG-UCC_p3 trnG-UCC CAATCCGACGCTTTAGTCCA TTCAGGAACAAATGGACCGG 1868–1876 1.000 80.8
trnG-UCC_p4 trnG-UCC AATCCGACGCTTTAGTCCAC TTCAGGAACAAATGGACCGG 1867–1875 1.000 80.8
trnG-UCC_p5 trnG-UCC ACTCAGCCATCTCTCCCAAT CCCTCTTGCGGTAGAAGAAC 2049–2057 1.000 80.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1126–1133 1.000 80.5
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1142–1149 1.000 79.6
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CCCGTCATGTTCCTTGGATT 1127–1134 1.000 79.3
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC CCCGTCATGTTCCTTGGATT 1141–1148 1.000 79.1
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG CCCGTCATGTTCCTTGGATT 1136–1143 1.000 78.7
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGTTTCCCACACTAAGGCTC 772–778 1.000 78.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 733–739 1.000 78.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG GGTTTCCCACACTAAGGCTC 823–829 1.000 77.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT GGTTTCCCACACTAAGGCTC 804–810 1.000 77.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG CCGTAGCGTCTACCGATTTC 784–790 1.000 77.3
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 355–805 1.000 84.2
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CTACATTGGGAATGGTCGGG AGTTGGATAGGATGGCCCTT 372–822 1.000 83.9
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TGCTACATTGGGAATGGTCG AGTTGGATAGGATGGCCCTT 374–824 1.000 83.9
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 319–769 1.000 83.8
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA GATAATCATCCGCGCCTGAA 394–844 1.000 83.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Matsumurella chinensis PP056237.1 151955 View on NCBI ↗
Matsumurella kwangtungensis OR565917.1 152216 View on NCBI ↗
Matsumurella szechuanensis OR565946.1 152230 View on NCBI ↗
Matsumurella tuberifera OR565922.1 152133 View on NCBI ↗
Matsumurella yangsoensis OR565945.1 151681 View on NCBI ↗