Markers + reference

Pistacia

7 species · Anacardiaceae · Sapindales

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Species 7
Genome length 161–161 kb
Candidate markers 268
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 565 0.0104 1.00 64.6 yes View details
trnS-GCU-trnG-UCC LSC 753 0.0058 1.00 52.7 yes View details
trnR-UCU-atpA LSC 204 0.0107 1.00 43.4 yes View details
atpF LSC 1312 0.0028 1.00 43.5 yes View details
petN-psbM LSC 705 0.0057 1.00 52.1 yes View details
trnT-UGU-trnL-UAA LSC 999 0.0060 1.00 58.3 yes View details
petD-rpoA LSC 281 0.0269 1.00 62.2 yes View details
rpoA LSC 987 0.0012 1.00 34.2 yes View details
rps19-rpl2 LSC 233 0.0108 1.00 36.7 yes View details
rpl32-trnL-UAG SSC 1225 0.0043 1.00 56.4 yes View details
ccsA-ndhD SSC 376 0.0123 1.00 64.7 yes View details
trnK-UUU-rps16 LSC 1112 0.0042 0.98 64.3 yes View details
trnF-GAA-ndhJ LSC 769 0.0016 1.00 62.5 yes View details
trnT-GGU-psbD LSC 1558 0.0021 1.00 61.5 yes View details
psbM-trnD-GUC LSC 1275 0.0049 0.97 57.5 yes View details
psaI-pafII LSC 457 0.0042 1.00 54.7 yes View details
rps16-trnQ-UUG LSC 1514 0.0033 1.00 53.9 yes View details
ccsA SSC 969 0.0036 1.00 53.0 yes View details
trnV-UAC-trnM-CAU LSC 198 0.0111 1.00 52.7 yes View details
psaA-pafI LSC 698 0.0023 1.00 52.5 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 TTCCCTCTAGACCTAGCTGC 632–636 0.857 75.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 646–650 0.857 75.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 645–649 0.857 75.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 647–651 0.857 75.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 681–685 0.857 72.9
trnK-UUU_p1 trnK-UUU AAGGAATGCCCATTTATATAGA TGTTCCGACTCGATTAGAAA 2806–2846 1.000 41.9
trnK-UUU_p2 trnK-UUU TGAATGAATGAAGATGAAGTAAGT TGTTCCGACTCGATTAGAAA 2837–2877 1.000 41.9
trnK-UUU_p3 trnK-UUU AAAGGAATGCCCATTTATATAGA TGTTCCGACTCGATTAGAAA 2807–2847 1.000 41.9
trnK-UUU_p4 trnK-UUU AAGGAATGCCCATTTATATAGA TGTTCCGACTCGATTAGAAAA 2806–2846 1.000 41.9
trnK-UUU_p5 trnK-UUU AGGAATGCCCATTTATATAGAT TGTTCCGACTCGATTAGAAA 2805–2845 1.000 41.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTATGGACGAACCCTTTGCT TATTTCAAAGAAGGCGGGGG 1238–1262 1.000 80.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1183–1207 1.000 80.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1182–1206 1.000 80.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TATTTCAAAGAAGGCGGGGG 1192–1216 1.000 79.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACTCTCCCGATGGTATGGAC TATTTCAAAGAAGGCGGGGG 1250–1274 1.000 79.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1645–1664 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATTGAAATGGGGCGTGG 1656–1675 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1587–1606 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1598–1617 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAAATTGAAATGGGGCGTGG 1666–1685 1.000 77.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCACT 826–849 1.000 71.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TAGCAATCCGCCGCTTTAAT ACGAATCGCACTTTTACCACT 824–847 1.000 71.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCAC 826–849 1.000 71.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAGCAATCCGCCGCTTTAAT ACGAATCGCACTTTTACCAC 824–847 1.000 71.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 875–898 1.000 70.3
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 301 1.000 67.4
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACCGAGGAAGCAGAA 309 1.000 67.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACCGAGGAAGC 313 1.000 67.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAAGCAGAAGCCCTTTTG 300 1.000 65.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 299 1.000 65.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Pistacia atlantica NC_086667.1 160761 View on NCBI ↗
Pistacia chinensis NC_046786.1 160618 View on NCBI ↗
Pistacia integerrima NC_085419.1 160689 View on NCBI ↗
Pistacia khinjuk NC_086668.1 160567 View on NCBI ↗
Pistacia terebinthus subsp. terebinthus OR884998.1 160731 View on NCBI ↗
Pistacia vera NC_034998.1 160674 View on NCBI ↗
Pistacia weinmaniifolia NC_037471.1 160767 View on NCBI ↗