Markers + reference

Nephelium

2 species · Sapindaceae · Sapindales

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Species 2
Genome length 161–161 kb
Candidate markers 274
Primer pairs 110

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR(TCT)-atpA LSC 260 0.0286 0.94 62.8 yes View details
atpH-atpI LSC 1203 0.0075 1.00 56.4 yes View details
psbM-trnD(GTC) LSC 1174 0.0085 1.00 63.6 yes View details
trnT(GGT)-psbD LSC 1519 0.0092 1.00 63.4 yes View details
psbC-trnS(TGA) LSC 238 0.0336 1.00 71.8 yes View details
trnS(TGA)-psbZ LSC 351 0.0086 1.00 52.0 yes View details
psbZ-trnG(GCC) LSC 558 0.0108 1.00 56.1 yes View details
accD-psaI LSC 729 0.0070 0.97 62.7 yes View details
petA-psbJ LSC 752 0.0175 0.99 59.0 yes View details
psbE-petL LSC 1346 0.0075 0.99 63.5 yes View details
petB LSC 1450 0.0055 1.00 62.3 yes View details
ndhF-rpl32 SSC 953 0.0085 0.99 61.5 yes View details
ccsA-ndhD SSC 304 0.0468 0.98 81.0 yes View details
trnT(TGT)-trnL(TAA) LSC 908 0.0057 0.96 65.6 yes View details
psaA-ycf3 LSC 808 0.0040 0.93 65.4 yes View details
ndhC-trnV(TAC) LSC 881 0.0058 0.98 63.6 yes View details
rpl20-rps12 LSC 726 0.0069 1.00 62.8 yes View details
trnR(ACG)-trnN(GTT) IRb 641 0.0047 0.99 62.5 yes View details
trnN(GTT)-trnR(ACG) IRa 641 0.0047 0.99 62.5 yes View details
rpoB-trnC(GCA) LSC 1211 0.0050 0.99 62.4 yes View details
psbL LSC 117 0.0171 1.00 62.3 yes View details
petN-psbM LSC 1278 0.0055 1.00 61.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnR(TCT)-atpA_p1 trnR(TCT)-atpA TGCAAAGCGTCCATTGTCTA GGATTCAGGAACAAATGGAACG 370–385 1.000 66.5
trnR(TCT)-atpA_p2 trnR(TCT)-atpA TGCAAAGCGTCCATTGTCTA AGGGATTCAGGAACAAATGGA 372–387 1.000 66.3
trnR(TCT)-atpA_p3 trnR(TCT)-atpA AATTCGGAATGCAAAGCGTC GGATTCAGGAACAAATGGAACG 379–394 1.000 65.7
trnR(TCT)-atpA_p4 trnR(TCT)-atpA AATTCGGAATGCAAAGCGTC AGGGATTCAGGAACAAATGGA 381–396 1.000 65.5
trnR(TCT)-atpA_p5 trnR(TCT)-atpA AATGCAAAGCGTCCATTGTC GGATTCAGGAACAAATGGAACG 372–387 1.000 65.0
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG AAGCGGCATTCAAGCTCTTA 1345–1350 1.000 79.4
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1324–1329 1.000 79.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT AAGCGGCATTCAAGCTCTTA 1367–1372 1.000 78.7
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 1346–1351 1.000 78.6
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC AAGCGGCATTCAAGCTCTTA 1371–1376 1.000 78.1
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) CCGGGGATTGTAGACATTCG AAAAGGATTTGCAGTCCCCC 1286–1296 1.000 77.1
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) CCGGGGATTGTAGACATTCG GCGACACCCAGATTTGAACT 1311–1321 1.000 76.1
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) CCCGGGGATTGTAGACATTC AAAAGGATTTGCAGTCCCCC 1287–1297 1.000 76.1
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) GGGGATTGTAGACATTCGCA AAAAGGATTTGCAGTCCCCC 1284–1294 1.000 75.5
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) CCCGGGGATTGTAGACATTC GCGACACCCAGATTTGAACT 1312–1322 1.000 75.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1440–1449 1.000 67.9
petN-psbM_p2 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1380–1389 1.000 67.7
petN-psbM_p3 petN-psbM GGGGAAGGAGTGGACTCTAG TGCTACTGCACTGTTCATTCT 1377–1386 1.000 67.4
petN-psbM_p4 petN-psbM CTTGGGCTGCGTTAATGGTA TGCTACTGCACTGTTCATTCT 1428–1437 1.000 67.1
petN-psbM_p5 petN-psbM TTGGGCTGCGTTAATGGTAG TGCTACTGCACTGTTCATTCT 1427–1436 1.000 67.1
psbM-trnD(GTC)_p1 psbM-trnD(GTC) AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1285–1297 1.000 59.0
psbM-trnD(GTC)_p2 psbM-trnD(GTC) AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1292–1304 1.000 55.8
psbM-trnD(GTC)_p3 psbM-trnD(GTC) AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1286–1298 1.000 54.8
psbM-trnD(GTC)_p4 psbM-trnD(GTC) GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1291–1303 1.000 53.3
psbM-trnD(GTC)_p5 psbM-trnD(GTC) AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1284–1296 1.000 52.9
trnT(GGT)-psbD_p1 trnT(GGT)-psbD GTGGTAGAGTAACGCCATGG TCTCCGTAACCAGTCATCCA 1652–1659 1.000 78.4
trnT(GGT)-psbD_p2 trnT(GGT)-psbD TCAGTGGTAGAGTAACGCCA TCTCCGTAACCAGTCATCCA 1655–1662 1.000 78.2
trnT(GGT)-psbD_p3 trnT(GGT)-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1683–1690 1.000 78.1
trnT(GGT)-psbD_p4 trnT(GGT)-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1686–1693 1.000 77.9
trnT(GGT)-psbD_p5 trnT(GGT)-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1685–1692 1.000 77.7

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
Nephelium lappaceum NC_053699.1 161356 View on NCBI ↗
Nephelium ramboutan-ake NC_070102.1 161265 View on NCBI ↗