Markers + reference

Plinia

2 species · Myrtaceae · Myrtales

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Species 2
Genome length 159–160 kb
Candidate markers 276
Primer pairs 100

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 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 564 0.0142 1.00 60.1 yes View details
atpH-atpI LSC 1116 0.0126 1.00 66.3 yes View details
petN-psbM LSC 982 0.0122 1.00 52.0 yes View details
trnT-GGU-psbD LSC 1396 0.0123 0.99 59.7 yes View details
psbZ-trnG-GCC LSC 863 0.0130 0.98 67.9 yes View details
trnF-GAA-ndhJ LSC 766 0.0131 1.00 65.0 yes View details
ndhC-trnV-UAC LSC 510 0.0179 0.98 64.9 yes View details
clpP-psbB LSC 405 0.0204 0.97 58.2 yes View details
ycf1 SSC 5616 0.0127 1.00 45.5 yes View details
ycf1 IRa 1143 0.0018 0.99 52.9 no View details
rps8-rpl14 LSC 192 0.0273 0.95 72.1 yes View details
psbT-psbN LSC 65 0.0308 1.00 70.2 yes View details
ccsA-trnL-UAG SSC 113 0.0354 1.00 69.3 yes View details
trnT-UGU-trnL-UAA LSC 1216 0.0126 0.98 67.9 yes View details
ycf4-cemA LSC 961 0.0105 0.99 65.4 yes View details
petA-psbJ LSC 993 0.0101 1.00 64.7 yes View details
psbM-trnD-GUC LSC 1071 0.0084 1.00 64.0 yes View details
trnP-UGG-psaJ LSC 410 0.0126 0.97 63.6 yes View details
ycf3-trnS-GGA LSC 833 0.0072 1.00 63.3 yes View details
ndhI-ndhG SSC 418 0.0144 1.00 63.2 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 100 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 AAAAAGGCGCTCAACCTACA 678–686 1.000 80.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 677–685 1.000 80.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 687–695 1.000 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 682–690 1.000 79.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 681–689 1.000 79.0
trnG-UCC_p1 trnG-UCC ACGTCCGATTACCTTTGTTTTG ATTCGAATACAGGTCTATCTAAT 913–917 1.000 40.7
trnG-UCC_p2 trnG-UCC CGTCCGATTACCTTTGTTTTGT ATTCGAATACAGGTCTATCTAAT 912–916 1.000 40.7
trnG-UCC_p3 trnG-UCC ACGTCCGATTACCTTTGTTT ATTCGAATACAGGTCTATCTAAT 913–917 1.000 40.7
trnG-UCC_p4 trnG-UCC ACGTCCGATTACCTTTGTTTT ATTCGAATACAGGTCTATCTAAT 913–917 1.000 40.7
trnG-UCC_p5 trnG-UCC TGATTACGTCCGATTACCTTTGT ATTCGAATACAGGTCTATCTAAT 918–922 1.000 40.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1204–1214 1.000 76.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1177–1187 1.000 76.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1260–1270 1.000 76.1
atpH-atpI_p4 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCAACTTTAGCCGCG 1242–1252 1.000 76.0
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT TAGGTGAATCCATGGAGGGT 1233–1243 1.000 75.6
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATGGAAACGTAAGAGCGGTC 1520–1524 1.000 80.9
petN-psbM_p2 petN-psbM CTCTACGCCAGTGATTCCAC ATGGAAACGTAAGAGCGGTC 1612–1616 1.000 80.3
petN-psbM_p3 petN-psbM CCCTTTTTGACTCTACGCCA ATGGAAACGTAAGAGCGGTC 1622–1626 1.000 79.5
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG ATGGAAACGTAAGAGCGGTC 1526–1530 1.000 79.4
petN-psbM_p5 petN-psbM TAGTGGTTGTGGAAAGTGGC ATGGAAACGTAAGAGCGGTC 2125 0.500 59.8
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 1181–1184 1.000 53.9
psbM-trnD-GUC_p2 psbM-trnD-GUC ACTAGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 1184–1187 1.000 52.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCAG TCAATTGGTTAGAGCACCGC 1188–1191 1.000 51.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAAGAGTGCA TCAATTGGTTAGAGCACCGC 1188–1191 1.000 51.1
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACTAGAATGAAGAGTGCAGT TCAATTGGTTAGAGCACCGC 1187–1190 1.000 51.1
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACGGTCTCTACGTAACCAGT 1523–1535 1.000 79.6
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACGGTCTCTACGTAACCAGT 1526–1538 1.000 79.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACGGTCTCTACGTAACCAGT 1500–1512 1.000 77.9
trnT-GGU-psbD_p4 trnT-GGU-psbD TGGGCCCTTTTAACTCAGTG ACGGTCTCTACGTAACCAGT 1540–1552 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCCCTTTTAACTCAGTGGT ACGGTCTCTACGTAACCAGT 1538–1550 1.000 77.8

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
Plinia aureana NC_039557.1 158918 View on NCBI ↗
Plinia edulis MN095408.1 159631 View on NCBI ↗