Markers + reference

Eriostemon

2 species · Rutaceae · Sapindales

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Species 2
Genome length 157–157 kb
Candidate markers 272
Primer pairs 105

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 385 0.0674 0.89 78.8 yes View details
trnK-UUU-rps16 LSC 586 0.0189 0.99 69.8 yes View details
atpF-atpH LSC 487 0.0210 0.98 56.1 yes View details
atpH-atpI LSC 1135 0.0125 0.99 52.5 yes View details
trnC-GCA-petN LSC 727 0.0124 1.00 65.9 yes View details
clpP1 LSC 2089 0.0106 1.00 49.1 yes View details
rps3-rpl22 LSC 296 0.0211 0.96 53.5 yes View details
trnN-GUU-rpl32 SSC 4225 0.0057 1.00 48.1 yes View details
ndhA SSC 2238 0.0081 1.00 57.9 yes View details
ycf1 SSC 5481 0.0123 1.00 45.6 yes View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
psbC-trnS-UGA LSC 249 0.0363 1.00 73.7 yes View details
ycf15-trnL-CAA IRb 739 0.0108 1.00 65.0 yes View details
trnL-CAA-ycf15 IRa 739 0.0108 1.00 65.0 yes View details
petA-psbJ LSC 1071 0.0103 1.00 64.9 yes View details
ndhK LSC 684 0.0073 1.00 63.0 yes View details
trnR-ACG-trnN-GUU IRb 612 0.0066 1.00 62.8 yes View details
trnN-GUU-trnR-ACG IRa 612 0.0066 1.00 62.8 yes View details
petN-psbM LSC 1276 0.0125 1.00 61.8 yes View details
ndhE-ndhG SSC 252 0.0159 1.00 61.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACTTCCCTCTAGACCTAGCT 432–457 1.000 72.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACTTCCCTCTAGACCTAGCT 446–471 1.000 72.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACTTCCCTCTAGACCTAGCT 445–470 1.000 72.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ACTTCCCTCTAGACCTAGCT 447–472 1.000 72.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AACTTCCCTCTAGACCTAGCT 433–458 1.000 70.7
trnK-UUU_p1 trnK-UUU TAAAGGCGGTTTTCAGTGCT CCGATTCTATCTACCCATTCGA 2991 1.000 56.2
trnK-UUU_p2 trnK-UUU TAAAGGCGGTTTTCAGTGCT TCCGATTCTATCTACCCATTCG 2992 1.000 56.2
trnK-UUU_p3 trnK-UUU ACGTGTCAACCAATAATCCA TTGATCGTGGAGAAACGGAC 2968–2973 1.000 56.1
trnK-UUU_p4 trnK-UUU GTAAAGGCGGTTTTCAGTGC CCGATTCTATCTACCCATTCGA 2992 0.500 35.2
trnK-UUU_p5 trnK-UUU GTAAAGGCGGTTTTCAGTGC TCCGATTCTATCTACCCATTCG 2993 0.500 35.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 682–718 1.000 81.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CTCTCCCGAAGATTTGGACG ATTTCAAAGAAAGCGGGGGT 736–772 1.000 80.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCAACCTACAGGAACCGTTC 707–743 1.000 79.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCAAAGAAAGCGGGGGTTTT 679–715 1.000 79.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TTCAAAGAAAGCGGGGGTTT 680–716 1.000 79.8
atpF-atpH_p1 atpF-atpH TGGGTCCAGCCTATTCTTGA ATTTCTGCCGCTTCCGTTAT 900–902 1.000 81.5
atpF-atpH_p2 atpF-atpH GGTGCTTTGTCTGGACTTCA ATTTCTGCCGCTTCCGTTAT 1116–1119 1.000 81.1
atpF-atpH_p3 atpF-atpH TGGGTCCAGCCTATTCTTGA TAGTTACTTCGGCTGGGTGA 1028–1030 1.000 81.1
atpF-atpH_p4 atpF-atpH GGTGCTTTGTCTGGACTTCA TAGTTACTTCGGCTGGGTGA 1244–1247 1.000 80.8
atpF-atpH_p5 atpF-atpH GGTGCTTTGTCTGGACTTCA GTTACTTCGGCTGGGTGAAT 1242–1245 1.000 80.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT AGCCTTGCTCACGTCAATAG 1492–1501 1.000 81.0
atpH-atpI_p2 atpH-atpI GGAGATTCCTGCCAAGAAGG AGCCTTGCTCACGTCAATAG 2004–2019 1.000 80.7
atpH-atpI_p3 atpH-atpI CCCTCGTTTGTTGCAACATC AGCCTTGCTCACGTCAATAG 1939–1954 1.000 80.7
atpH-atpI_p4 atpH-atpI CCTCGTTTGTTGCAACATCC AGCCTTGCTCACGTCAATAG 1938–1953 1.000 80.7
atpH-atpI_p5 atpH-atpI CTCGTTTGTTGCAACATCCC AGCCTTGCTCACGTCAATAG 1937–1952 1.000 80.7
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT ACGAGCGAAAGGGAAAATGT 849–850 1.000 77.1
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCATACTACGAGCGAAAGGG 856–857 1.000 76.9
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCATACTACGAGCGAAAGG 857–858 1.000 76.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CCCCATACTACGAGCGAAAG 858–859 1.000 76.9
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 811–812 1.000 76.8

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
Eriostemon australasius NC_081876.1 157114 View on NCBI ↗
Eriostemon banksii NC_081877.1 157307 View on NCBI ↗