Markers + reference

Parinari

4 species · Chrysobalanaceae · Malpighiales

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Species 4
Genome length 162–163 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 411 0.0328 0.95 71.7 yes View details
trnK-UUU-trnQ-UUG LSC 1421 0.0041 1.00 51.0 yes View details
atpA LSC 1533 0.0010 1.00 36.9 yes View details
trnT-UGU-trnL-UAA LSC 454 0.0011 1.00 47.6 yes View details
petA-psbJ LSC 804 0.0039 1.00 47.3 yes View details
rpl32-trnL-UAG SSC 1296 0.0077 0.98 58.4 yes View details
ccsA-ndhD SSC 287 0.0210 1.00 61.0 yes View details
ndhD SSC 1503 0.0024 1.00 46.1 yes View details
ndhE SSC 306 0.0000 1.00 21.6 yes View details
ycf3-trnS-GGA LSC 477 0.0053 0.95 64.6 yes View details
petN-psbM LSC 1088 0.0018 1.00 62.1 yes View details
ndhC-trnV-UAC LSC 1162 0.0019 0.99 61.9 yes View details
trnR-ACG-trnN-GUU IRb 642 0.0016 0.98 61.7 yes View details
trnN-GUU-trnR-ACG IRa 642 0.0016 0.98 61.7 yes View details
rps19-trnH-GUG LSC 52 0.0224 1.00 61.4 no View details
psaJ-rpl33 LSC 498 0.0064 1.00 61.0 yes View details
rpl20-rps12 LSC 825 0.0022 1.00 60.7 yes View details
psbM-trnD-GUC LSC 999 0.0015 1.00 60.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCCTCTAGATCTAGCAGCTGT 465–486 1.000 77.3
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCCTCTAGATCTAGCAGCTGT 466–487 1.000 77.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCCCTCTAGATCTAGCAGCTG 466–487 1.000 77.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT AGATCTAGCAGCTGTCGAAG 459–480 1.000 77.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCCCTCTAGATCTAGCAGCTG 467–488 1.000 76.9
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT TGAATAGAAATGGGGCGTGG 1536–1547 1.000 78.9
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT TGAATAGAAATGGGGCGTGG 1535–1546 1.000 78.9
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1478–1489 1.000 78.7
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1477–1488 1.000 78.7
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC TGAATAGAAATGGGGCGTGG 1522–1533 1.000 76.6
trnG-GCC_p1 trnG-GCC TCCCTTACCCGATACTCGAC ACAACAAAGAACAACAAAGCA 1558–1568 1.000 51.5
trnG-GCC_p2 trnG-GCC TCCCTTACCCGATACTCGAC GAACAACAAAGAACAACAAAGCA 1560–1570 1.000 50.5
trnG-GCC_p3 trnG-GCC TCCCTTACCCGATACTCGAC TGAACAACAAAGAACAACAAAGC 1561–1571 1.000 50.5
trnG-GCC_p4 trnG-GCC CGCCAACAAATCATAGCAGC ACAACAAAGAACAACAAAGCA 1773–1783 1.000 50.2
trnG-GCC_p5 trnG-GCC TCCCTTACCCGATACTCGAC AACAACAAAGAACAACAAAGCA 1559–1569 1.000 49.6
atpA_p1 atpA TGGAAAAGCGTCCATTGTCT GAACTACGCAATGGGACCAT 2309–2394 1.000 81.0
atpA_p2 atpA TGGAAAAGCGTCCATTGTCT AGAGTCCTCCGAGTATTCCG 2612–2697 1.000 80.6
atpA_p3 atpA TGGAAAAGCGTCCATTGTCT GAGTCCTCCGAGTATTCCGA 2611–2696 1.000 80.6
atpA_p4 atpA TGGAAAAGCGTCCATTGTCT AAGAACTACGCAATGGGACC 2311–2396 1.000 80.4
atpA_p5 atpA TGGAAAAGCGTCCATTGTCT TCATGTTTGGTTCGGGAAGG 2433–2518 1.000 80.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT GCGCTGTTCATTCTTGTTCC 1224–1252 1.000 80.0
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT GCGCTGTTCATTCTTGTTCC 1163–1191 1.000 78.5
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 1233–1261 1.000 78.2
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 1234–1262 1.000 77.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ACTGCGCTGTTCATTCTTGT 1227–1255 1.000 77.1
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACAAGAATGAACAGCGC TTCAATTGGTCAGAGCACCG 1115–1122 1.000 76.7
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT TTCAATTGGTCAGAGCACCG 1106–1113 1.000 74.8
psbM-trnD-GUC_p3 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA TTCAATTGGTCAGAGCACCG 1105–1112 1.000 73.9
psbM-trnD-GUC_p4 psbM-trnD-GUC ACAAGAATGAACAGCGCAGT TTCAATTGGTCAGAGCACCG 1112–1119 1.000 73.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGAACAGCGCAGTAGCAA TTCAATTGGTCAGAGCACCG 1107–1114 1.000 73.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Parinari campestris NC_024067.1 162637 View on NCBI ↗
Parinari capensis NC_030581.1 162487 View on NCBI ↗
Parinari curatellifolia NC_030582.1 162647 View on NCBI ↗
Parinari oblongifolia NC_030583.1 162512 View on NCBI ↗