Markers + reference

Abeliophyllum

2 species · Oleaceae · Lamiales

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Species 2
Genome length 156–156 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 6 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4179 0.0134 1.00 61.6 yes View details
ycf3 LSC 1960 0.0041 1.00 60.1 yes View details
rbcL LSC 1434 0.0021 1.00 60.0 yes View details
rpl20-rps12 LSC 792 0.0013 1.00 54.6 yes View details
petD LSC 1196 0.0000 1.00 31.9 yes View details
rps19 LSC 279 0.0000 1.00 27.4 yes View details
rpl2 IRb 1492 0.0013 1.00 59.5 yes View details
rpl2 IRa 1492 0.0013 1.00 59.5 yes View details
matK-trnK-UUU LSC 711 0.0014 1.00 59.6 yes View details
trnT-UGU-trnL-UAA LSC 737 0.0014 1.00 59.5 yes View details
trnK-UUU-rps16 LSC 844 0.0012 1.00 59.4 yes View details
rpoB-trnC-GCA LSC 1195 0.0008 1.00 59.2 yes View details
ndhH SSC 1182 0.0008 1.00 59.2 yes View details
psbM-trnD-GUC LSC 1046 0.0000 1.00 59.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CCTGATCATGAGCAAGTGCA AACGGTAGAGTACTCGGCTT 841 1.000 76.7
matK-trnK-UUU_p2 matK-trnK-UUU CCTGATCATGAGCAAGTGCA ACGGTAGAGTACTCGGCTTT 840 1.000 76.7
matK-trnK-UUU_p3 matK-trnK-UUU ACCCTGATCATGAGCAAGTG AACGGTAGAGTACTCGGCTT 843 1.000 75.4
matK-trnK-UUU_p4 matK-trnK-UUU ACCCTGATCATGAGCAAGTG ACGGTAGAGTACTCGGCTTT 842 1.000 75.4
matK-trnK-UUU_p5 matK-trnK-UUU CCTGATCATGAGCAAGTGCA GGGTTGCTAACTCAACGGTA 854 1.000 74.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATTCCTCGCTTCATCCA GGTGCTCAACCTACAGGAAC 1016 1.000 78.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 968 1.000 77.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 967 1.000 77.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 977 1.000 76.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 954 1.000 74.9
rpoC2_p1 rpoC2 TACGACACGGATCGGGATTA CCATTTTCCTGGAGAGACCG 950 0.500 59.5
rpoC2_p2 rpoC2 TACGACACGGATCGGGATTA GGGTTCAGGATTGCTCTCTG 458 0.500 59.4
rpoC2_p3 rpoC2 TACGACACGGATCGGGATTA CCACCAGGAACAGGAAAACA 898 0.500 59.2
rpoC2_p4 rpoC2 TACGACACGGATCGGGATTA ACCACCAGGAACAGGAAAAC 899 0.500 59.2
rpoC2_p5 rpoC2 AATGTTACGACACGGATCGG CCATTTTCCTGGAGAGACCG 955 0.500 59.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1278 1.000 71.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1283 1.000 70.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1277 1.000 70.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AAAAGGATTTGCAGTCCCCC 1260 1.000 69.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1285 1.000 68.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1178–1199 1.000 55.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1170–1191 1.000 55.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 1171–1192 1.000 53.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGCGGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 1170–1191 1.000 53.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 1179–1200 1.000 53.4
ycf3_p1 ycf3 TGACTGATGGTGCCAACAAA TCCCACGAGAGGTAATGAGA 2103 1.000 73.2
ycf3_p2 ycf3 TTGACTGATGGTGCCAACAA TCCCACGAGAGGTAATGAGA 2104 1.000 73.2
ycf3_p3 ycf3 TTTGACTGATGGTGCCAACA TCCCACGAGAGGTAATGAGA 2105 1.000 73.2
ycf3_p4 ycf3 ACTGATGGTGCCAACAAACA TCCCACGAGAGGTAATGAGA 2101 1.000 71.9
ycf3_p5 ycf3 TGACTGATGGTGCCAACAAA TCCCACGAGAGGTAATGAGAA 2103 1.000 71.0

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
Abeliophyllum distichum NC_031445.1 155982 View on NCBI ↗
Abeliophyllum distichum f. lilacinum MW426545.1 156015 View on NCBI ↗