Markers + reference

Hedlundia

6 species · Rosaceae · Rosales

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Species 6
Genome length 159–160 kb
Candidate markers 259
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 679 0.0170 1.00 51.1 yes View details
trnT-GGU-psbD LSC 1419 0.0082 1.00 59.6 yes View details
ndhC-trnV-UAC LSC 707 0.0129 0.96 60.7 yes View details
psaJ-rpl33 LSC 464 0.0022 1.00 39.4 yes View details
rpl33-rps18 LSC 222 0.0195 1.00 57.1 yes View details
rpl22 LSC 426 0.0041 1.00 30.7 yes View details
ndhF-rpl32 SSC 1120 0.0078 0.98 70.0 yes View details
rpl32-trnL-UAG SSC 1436 0.0065 1.00 42.1 yes View details
rps15-ycf1 SSC 405 0.0091 1.00 36.7 yes View details
rpoB-trnC-GCA LSC 1218 0.0032 1.00 61.6 yes View details
rpl22-rps19 LSC 66 0.0202 1.00 58.9 yes View details
atpH-atpI LSC 1176 0.0035 1.00 57.0 yes View details
petA-psbJ LSC 998 0.0035 1.00 56.9 yes View details
psbA-trnK-UUU LSC 276 0.0080 1.00 55.2 yes View details
trnK-UUU-rps16 LSC 942 0.0035 1.00 55.1 yes View details
psbE-petL LSC 1237 0.0027 1.00 51.9 yes View details
ndhD SSC 1503 0.0022 1.00 50.9 yes View details
ycf3-trns-GGA LSC 613 0.0011 1.00 50.7 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
psbA-trnK-UUU_p1 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC CGGTTTGGGGAGGGATTTTT 422–436 1.000 79.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC AAAATGCAAGCACGGTTTGG 434–448 1.000 79.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACTCCATCCGACTAGTTCCG 365–379 1.000 78.5
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGTTTGGGGAGGGATTTTT 442–456 1.000 78.0
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC TGAAAAATGCAAGCACGGTT 437–451 1.000 77.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1014–1029 1.000 81.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1013–1028 1.000 81.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1023–1038 1.000 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1069–1084 1.000 79.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1068–1083 1.000 79.6
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG ACAATCTCAATCATCCCCGC 963–1337 1.000 85.5
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG ACAATCTCAATCATCCCCGC 966–1340 1.000 85.3
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TTCGGTTTCCAGGGTAGGAT 1143–1517 1.000 85.2
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TCAGACCGGCCATTAATGTG 1168–1542 1.000 85.1
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG TCAGACCGGCCATTAATGTG 1171–1545 1.000 84.9
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1252–1286 1.000 81.4
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1218–1252 1.000 81.4
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1282–1316 1.000 80.5
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1248–1282 1.000 80.5
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1219–1253 1.000 80.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC CCGGATTTGAACTGGGGAAA 1367–1375 1.000 79.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC AAAAGGATTTGCAGTCCCCC 1349–1357 1.000 77.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1301–1309 1.000 77.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCTGTTAAGCCCTGCTCAA CCGGATTTGAACTGGGGAAA 1373–1381 1.000 76.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCCTCTGTTAAGCCCTGC CCGGATTTGAACTGGGGAAA 1377–1385 1.000 76.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1563–1621 1.000 83.3
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1566–1624 1.000 83.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1565–1623 1.000 83.1
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1553–1611 1.000 83.1
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TAGGCCAGACCAACCTACAA 1568–1626 1.000 82.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Hedlundia arranensis NC_085645.1 160091 View on NCBI ↗
Hedlundia austriaca NC_085584.1 159483 View on NCBI ↗
Hedlundia borbasii NC_085590.1 159999 View on NCBI ↗
Hedlundia hybrida NC_085646.1 160199 View on NCBI ↗
Hedlundia mougeotii NC_085647.1 160149 View on NCBI ↗
Hedlundia persica NC_085662.1 160116 View on NCBI ↗