Markers + reference

Sapindus

3 species · Sapindaceae · Sapindales

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Species 3
Genome length 160–160 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 215 0.0000 1.00 21.4 yes View details
atpA LSC 1524 0.0018 1.00 59.8 yes View details
atpH-atpI LSC 1253 0.0022 0.99 61.1 yes View details
rpoC2 LSC 4125 0.0013 1.00 44.9 yes View details
trnF-GAA-ndhJ LSC 835 0.0032 1.00 60.9 yes View details
psbE-petL LSC 1407 0.0024 0.98 61.9 yes View details
rpl36-rps8 LSC 489 0.0048 1.00 59.6 yes View details
rpl16-rps3 LSC 1214 0.0016 1.00 59.9 yes View details
ndhF-rpl32 SSC 736 0.0027 1.00 55.5 yes View details
ycf1 SSC 5640 0.0012 1.00 53.3 yes View details
trnH-GUG-psbA LSC 718 0.0011 0.88 61.6 yes View details
trnG-UCC-trnfM-CAU LSC 186 0.0036 1.00 60.5 yes View details
petA-psbJ LSC 774 0.0009 0.99 60.5 yes View details
trnR-ACG-trnN-GUU IRb 677 0.0020 1.00 60.0 yes View details
trnN-GUU-trnR-ACG IRa 677 0.0020 1.00 60.0 yes View details
accD LSC 1491 0.0013 1.00 59.6 yes View details
psbM-trnD-GUC LSC 753 0.0009 1.00 59.5 yes View details
trnK-UUU-rps16 LSC 834 0.0000 1.00 59.0 yes View details
psbZ-trnG-UCC LSC 526 0.0025 1.00 59.0 yes View details
clpP LSC 2136 0.0009 1.00 58.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCACAGAAAACGAATCCGCT 722–809 1.000 76.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCACAGAAAACGAATCCGCT 736–823 1.000 76.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCACAGAAAACGAATCCGCT 735–822 1.000 76.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCACAGAAAACGAATCCGCT 737–824 1.000 76.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACGAATCCGCTAATGAAGGT 713–800 1.000 75.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCGACAGTATGGACGAATC ATTTCAAAGAAAGCGGGGGT 990–999 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAAGCGGGGGT 928–937 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 927–936 1.000 78.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCCGACAGTATGGACGAAT ATTTCAAAGAAAGCGGGGGT 991–1000 1.000 78.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACTCTCCCGACAGTATGGAC ATTTCAAAGAAAGCGGGGGT 995–1004 1.000 78.2
trnR-UCU-atpA_p1 trnR-UCU-atpA TGCAAAGCGTCCATTGTCTA TGGAACGTTTTCTACTTCAGGA 325–360 1.000 57.2
trnR-UCU-atpA_p2 trnR-UCU-atpA AATTCGGAATGCAAAGCGTC TGGAACGTTTTCTACTTCAGGA 334–369 1.000 56.5
trnR-UCU-atpA_p3 trnR-UCU-atpA AATGCAAAGCGTCCATTGTC TGGAACGTTTTCTACTTCAGGA 327–362 1.000 55.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GAATGCAAAGCGTCCATTGT TGGAACGTTTTCTACTTCAGGA 328–363 1.000 55.8
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGCAAAGCGTCCATTG TGGAACGTTTTCTACTTCAGGA 329–364 1.000 55.7
atpA_p1 atpA AAAGATTAAGAGTGATCGAATTT TGACACGTTTGAGGTGATGG 1646 1.000 40.2
atpA_p2 atpA AAGATTAAGAGTGATCGAATTTT TGACACGTTTGAGGTGATGG 1645 1.000 40.2
atpA_p3 atpA AGATTAAGAGTGATCGAATTTTT TGACACGTTTGAGGTGATGG 1644 1.000 40.2
atpA_p4 atpA AAGATTAAGAGTGATCGAATTTT GACACGTTTGAGGTGATGGA 1644 1.000 40.2
atpA_p5 atpA AGATTAAGAGTGATCGAATTTTT GACACGTTTGAGGTGATGGA 1643 1.000 40.2
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG AGTGGTTCCGATACCTGTCA 1424–1434 1.000 80.2
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG AAGCGGCATTCAAGCTCTTA 1385–1395 1.000 79.8
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1364–1374 1.000 79.7
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT AGTGGTTCCGATACCTGTCA 1446–1456 1.000 79.5
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT AAGCGGCATTCAAGCTCTTA 1407–1417 1.000 79.2
rpoC2_p1 rpoC2 TCGAGATACCTGAATGGGGC AATCATCAAGTGCGACACCA 241 1.000 71.6
rpoC2_p2 rpoC2 TCGAGATACCTGAATGGGGC ATCATCAAGTGCGACACCAA 240 1.000 71.6
rpoC2_p3 rpoC2 TCGAGATACCTGAATGGGGC TCATCAAGTGCGACACCAAT 239 1.000 71.6
rpoC2_p4 rpoC2 CGAGATACCTGAATGGGGCA ATCATCAAGTGCGACACCAA 239 1.000 69.3
rpoC2_p5 rpoC2 CGAGATACCTGAATGGGGCA TCATCAAGTGCGACACCAAT 238 1.000 69.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Sapindus delavayi NC_053829.1 159861 View on NCBI ↗
Sapindus mukorossi NC_025554.1 160481 View on NCBI ↗
Sapindus rarak OL840056.1 160401 View on NCBI ↗