Markers + reference

Picconia

2 species · Oleaceae · Lamiales

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Species 2
Genome length 155–155 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 447 0.0112 1.00 54.5 yes View details
matK LSC 1521 0.0046 1.00 48.5 yes View details
matK-rps16 LSC 1642 0.0055 1.00 51.5 yes View details
trnQ(UUG)-psbK LSC 335 0.0120 1.00 51.4 yes View details
rpoB-trnC(GCA) LSC 1181 0.0059 1.00 56.2 yes View details
psbM-trnD(GUC) LSC 643 0.0093 1.00 58.4 yes View details
ycf1 IRb 1164 0.0026 1.00 50.3 no View details
rpl32-trnL(UAG) SSC 542 0.0185 1.00 56.2 yes View details
ndhA SSC 2194 0.0041 1.00 60.1 yes View details
ycf1 SSC 5637 0.0055 1.00 55.8 yes View details
petD-rpoA LSC 184 0.0166 0.98 63.6 yes View details
psbE-petL LSC 1180 0.0068 1.00 62.6 yes View details
rbcL-accD LSC 672 0.0045 0.99 62.2 yes View details
psaA-ycf3 LSC 734 0.0041 1.00 61.1 yes View details
rpl20-rps12 LSC 800 0.0038 1.00 61.0 yes View details
rpl2-trnH(GUG) IRa 75 0.0159 0.84 60.9 no View details
trnV(GAC) IRb 72 0.0139 1.00 60.5 yes View details
trnV(GAC) IRa 72 0.0139 1.00 60.5 yes View details
trnR(ACG)-trnN(GUU) IRb 575 0.0035 1.00 60.4 yes View details
trnN(GUU)-trnR(ACG) IRa 575 0.0035 1.00 60.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(GUG)-psbA_p1 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 627 1.000 77.2
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 572 1.000 76.9
trnH(GUG)-psbA_p3 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 628 1.000 76.8
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 573 1.000 76.7
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 573 1.000 76.4
matK_p1 matK CTACTGGAGGAGCAGCAATG CGGTACAAAACCCTGTTCGA 2777–2782 1.000 78.8
matK_p2 matK CTACTGGAGGAGCAGCAATG TCGGTACAAAACCCTGTTCG 2778–2783 1.000 78.8
matK_p3 matK CTACTGGAGGAGCAGCAATG AACGGTAGAGTACTCGGCTT 2960–2965 1.000 78.5
matK_p4 matK CTACTGGAGGAGCAGCAATG ACGGTAGAGTACTCGGCTTT 2959–2964 1.000 78.5
matK_p5 matK CTACTGGAGGAGCAGCAATG ATACGGGAAGGACTTCTCCC 2599–2604 1.000 78.2
matK-rps16_p1 matK-rps16 CCCTGATCATGAGCAAGTCC GGAACTTCGACCTAATCAAACG 1779–1783 1.000 59.7
matK-rps16_p2 matK-rps16 CCTGATCATGAGCAAGTCCA GGAACTTCGACCTAATCAAACG 1778–1782 1.000 54.3
matK-rps16_p3 matK-rps16 ACCCTGATCATGAGCAAGTC GGAACTTCGACCTAATCAAACG 1780–1784 1.000 54.3
matK-rps16_p4 matK-rps16 CCCTGATCATGAGCAAGTCC GAACTTCGACCTAATCAAACGA 1778–1782 1.000 52.3
matK-rps16_p5 matK-rps16 CCCTGATCATGAGCAAGTCC ACTTCGACCTAATCAAACGA 1776–1780 1.000 52.0
trnQ(UUG)-psbK_p1 trnQ(UUG)-psbK GACCAAAACCCGTTGCCTTA ACTACTCGAATAAAGGGCAGA 432–433 1.000 52.9
trnQ(UUG)-psbK_p2 trnQ(UUG)-psbK GAATAGCGGGACCAAAACCC ACTACTCGAATAAAGGGCAGA 441–442 1.000 51.1
trnQ(UUG)-psbK_p3 trnQ(UUG)-psbK GACCAAAACCCGTTGCCTTA AACTACTCGAATAAAGGGCAGA 433–434 1.000 50.8
trnQ(UUG)-psbK_p4 trnQ(UUG)-psbK GACCAAAACCCGTTGCCTTA ACTACTCGAATAAAGGGCAGAA 432–433 1.000 50.8
trnQ(UUG)-psbK_p5 trnQ(UUG)-psbK ATATGGCTCTGGGACGGAAG ACTACTCGAATAAAGGGCAGA 474–475 1.000 50.7
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1264–1269 1.000 71.7
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1269–1274 1.000 71.1
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) CTCATTTCCATCCCCGAGC AAAGGATTTGCAGTCCTCCG 1245–1250 1.000 71.0
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1263–1268 1.000 70.6
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) ATTCCCTCATTTCCATCCCC AAAGGATTTGCAGTCCTCCG 1250–1255 1.000 70.4
psbM-trnD(GUC)_p1 psbM-trnD(GUC) AGAATGAATAGTGCAGTCGC TTCAATTGGTCAGAGCACCG 754–756 1.000 60.4
psbM-trnD(GUC)_p2 psbM-trnD(GUC) AGAATGAATAGTGCAGTCGC GTTCAATTGGTCAGAGCACC 755–757 1.000 56.2
psbM-trnD(GUC)_p3 psbM-trnD(GUC) AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 775–777 1.000 55.9
psbM-trnD(GUC)_p4 psbM-trnD(GUC) AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 767–769 1.000 55.8
psbM-trnD(GUC)_p5 psbM-trnD(GUC) AGAATGAATAGTGCAGTCGC TCAATTGGTCAGAGCACCG 753–755 1.000 54.4

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
Picconia azorica NC_042428.1 155350 View on NCBI ↗
Picconia excelsa NC_042466.1 155355 View on NCBI ↗