Markers + reference

Phebalium

5 species · Rutaceae · Sapindales

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Species 5
Genome length 157–157 kb
Candidate markers 274
Primer pairs 100

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0032 1.00 46.6 yes View details
rps16 LSC 1172 0.0074 1.00 61.3 yes View details
trnS-GCU-trnG-UCC LSC 801 0.0111 1.00 58.5 yes View details
atpF-atpH LSC 480 0.0212 1.00 66.0 yes View details
psbZ-trnG-GCC LSC 541 0.0233 1.00 66.5 yes View details
trnT-UGU-trnL-UAA LSC 1010 0.0101 1.00 61.9 yes View details
trnF-GAA-ndhJ LSC 471 0.0134 1.00 53.8 yes View details
petA-psbJ LSC 1067 0.0114 1.00 67.5 yes View details
rpl32-trnL-UAG SSC 584 0.0125 1.00 54.8 yes View details
rps15-ycf1 SSC 366 0.0099 0.99 47.3 yes View details
ycf1 SSC 5493 0.0075 1.00 43.4 yes View details
trnH-GUG-psbA IRa 335 0.0307 0.99 66.5 no View details
trnR-ACG-trnN-GUU IRb 614 0.0047 1.00 62.9 yes View details
trnN-GUU-trnR-ACG IRa 614 0.0046 1.00 62.8 yes View details
trnC-GCA-petN LSC 658 0.0089 0.98 62.4 yes View details
ndhH-rps15 SSC 101 0.0187 0.98 62.4 yes View details
rps12-trnV-GAC IRb 1776 0.0034 1.00 61.3 yes View details
trnV-GAC-rps12 IRa 1776 0.0033 1.00 61.3 yes View details
psbE-petL LSC 1383 0.0056 1.00 61.1 yes View details
psaA-ycf3 LSC 750 0.0081 0.99 60.7 yes View details
rps18-rpl20 LSC 194 0.0072 0.98 59.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GGGTCGGTATGGATCCGTTA ACATAGGGAAAGCTGTGTGC 1512–1563 1.000 76.2
psbA_p2 psbA GGGTCGGTATGGATCCGTTA CATAGGGAAAGCTGTGTGCA 1511–1562 1.000 76.2
psbA_p3 psbA GGGTCGGTATGGATCCGTTA AGGGCGGATTTGGTATTTGG 1769–1820 1.000 75.4
psbA_p4 psbA GGGTCGGTATGGATCCGTTA GGGCGGATTTGGTATTTGGA 1768–1819 1.000 75.4
psbA_p5 psbA GGGTCGGTATGGATCCGTTA TATGCTTGGGAGTCCCTGAT 1160–1176 0.800 66.8
rps16_p1 rps16 ACTCCTCCACACCCTCTTTT TCCCTCCATCTACAAGGAAA 1299–1312 1.000 57.7
rps16_p2 rps16 ACTCCTCCACACCCTCTTTT TTCCCTCCATCTACAAGGAA 1300–1313 1.000 57.7
rps16_p3 rps16 TAAGACTCCTCCACACCCTC TCCCTCCATCTACAAGGAAA 1303–1316 1.000 57.3
rps16_p4 rps16 TAAGACTCCTCCACACCCTC TTCCCTCCATCTACAAGGAA 1304–1317 1.000 57.3
rps16_p5 rps16 ACTCCTCCACACCCTCTTTT TCCCTCCATCTACAAGGAAAA 1299–1312 1.000 56.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA AGGGGATTACTTGAACGAATCA 879–911 1.000 59.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA GGGGATTACTTGAACGAATCAC 878–910 1.000 58.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGGGGATTACTTGAACGAATCA 937–969 1.000 57.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGGATTACTTGAACGAATCAC 936–968 1.000 57.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC AGGGGATTACTTGAACGAATCA 876–908 1.000 56.9
atpF-atpH_p1 atpF-atpH GCCAGTGAACCAAAGAAACG TGGACTGGTTGTAGCATTAGC 538–579 1.000 77.9
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGACTGGTTGTAGCATTAGC 564–605 1.000 77.8
atpF-atpH_p3 atpF-atpH TGGCCAGTGAACCAAAGAAA TGGACTGGTTGTAGCATTAGC 540–581 1.000 77.7
atpF-atpH_p4 atpF-atpH AATGGCCAGTGAACCAAAGA TGGACTGGTTGTAGCATTAGC 542–583 1.000 75.8
atpF-atpH_p5 atpF-atpH ATGGCCAGTGAACCAAAGAA TGGACTGGTTGTAGCATTAGC 541–582 1.000 75.8
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT ACGAGCGAAAGGGAAAATGT 769–796 1.000 80.7
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 731–758 1.000 80.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCATACTACGAGCGAAAGGG 776–803 1.000 80.4
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCATACTACGAGCGAAAGG 777–804 1.000 80.4
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCCATACTACGAGCGAAAG 778–805 1.000 80.4
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CGGATGGTTGGTCGAGTAAC TCTTCTCCTTGGCAAAGAGA 665–687 1.000 67.0
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTTGCTTCTCCGGATGGTTG TCTTCTCCTTGGCAAAGAGA 675–697 1.000 66.1
psbZ-trnG-GCC_p3 psbZ-trnG-GCC ATTTGCTTCTCCGGATGGTT TCTTCTCCTTGGCAAAGAGA 676–698 1.000 65.7
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CGGATGGTTGGTCGAGTAAC TCTTCTCCTTGGCAAAGAGAA 665–687 1.000 65.2
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTTGCTTCTCCGGATGGTTG TCTTCTCCTTGGCAAAGAGAA 675–697 1.000 64.3

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
Phebalium clavatum NC_081890.1 157111 View on NCBI ↗
Phebalium elegans NC_081891.1 157194 View on NCBI ↗
Phebalium longifolium NC_081892.1 157309 View on NCBI ↗
Phebalium tuberculosum NC_081893.1 157198 View on NCBI ↗
Phebalium whitei NC_081894.1 156908 View on NCBI ↗