Markers + reference

Borassus

2 species · Arecaceae · Arecales

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Species 2
Genome length 160–160 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 28.8 yes View details
trnQ-UUG-psbK LSC 337 0.0000 1.00 27.8 yes View details
trnS-GCU-trnG-UCC LSC 1378 0.0061 0.96 66.1 yes View details
atpF LSC 1365 0.0022 1.00 60.1 yes View details
rpoB-trnC-GCA LSC 1220 0.0016 1.00 59.7 yes View details
petN-psbM LSC 759 0.0040 1.00 61.3 yes View details
ccsA SSC 969 0.0010 1.00 49.8 yes View details
rps15-ycf1 SSC 417 0.0072 1.00 59.1 yes View details
ycf1 SSC 5565 0.0014 1.00 53.3 yes View details
rps19-psbA LSC 262 0.0536 1.00 82.0 no View details
ccsA-ndhD SSC 210 0.0190 1.00 63.5 yes View details
petG-trnW-CCA LSC 119 0.0168 1.00 62.2 yes View details
rps3 LSC 666 0.0000 0.97 61.5 yes View details
rpl16 LSC 1657 0.0012 0.98 60.7 yes View details
matK-trnK-UUU LSC 791 0.0025 1.00 60.5 yes View details
trnF-GAA-ndhJ LSC 728 0.0014 0.99 60.2 yes View details
rps16 LSC 1117 0.0009 1.00 59.7 yes View details
rps2 LSC 711 0.0014 1.00 59.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTCCTTCAACGA GTGTGCTTGGGAGTTCTTGA 1151 1.000 75.3
psbA_p2 psbA TTGCTCCATTCCTTCAACGA ATACGTGTGCTTGGGAGTTC 1155 1.000 74.8
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGTGCTTGGGAGTTCTTGA 1150 1.000 73.4
psbA_p4 psbA TGCTCCATTCCTTCAACGAT ATACGTGTGCTTGGGAGTTC 1154 1.000 72.9
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGTGCTTGGGAGTTCTTGA 1150 1.000 71.2
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2860–2862 1.000 68.4
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2876–2878 1.000 65.0
trnK-UUU_p3 trnK-UUU GCCAATGTCAACCAATCTCA GTCGTGCAGTGCAATTCAAT 2859–2861 1.000 63.9
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTC GTCGTGCAGTGCAATTCAAT 2860–2862 1.000 63.9
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA GTTCAATGTTTTGACGGGGTC 2878–2880 1.000 63.1
matK-trnK-UUU_p1 matK-trnK-UUU ACGATCATGAGCAAATGGGT AACGGTAGAGTACTCGGCTT 918–920 1.000 75.6
matK-trnK-UUU_p2 matK-trnK-UUU ACGATCATGAGCAAATGGGT ACGGTAGAGTACTCGGCTTT 917–919 1.000 75.6
matK-trnK-UUU_p3 matK-trnK-UUU ACGATCATGAGCAAATGGGT GTCGTGCAGTGCAATTCAAT 999–1001 1.000 74.2
matK-trnK-UUU_p4 matK-trnK-UUU ACGATCATGAGCAAATGGGT GGGTTGCTAACTCAACGGTA 931–933 1.000 73.3
matK-trnK-UUU_p5 matK-trnK-UUU ACGATCATGAGCAAATGGGT TTCGGGTTGCTAACTCAACG 934–936 1.000 73.0
rps16_p1 rps16 GCAAGAAAAAGGCAAATTGTGT CGGTTGAGCCAACGACTATT 1280–1285 1.000 55.1
rps16_p2 rps16 GCAAGAAAAAGGCAAATTGTGT TATACACACACCGGTTGAGC 1291–1296 1.000 54.3
rps16_p3 rps16 ACAGCAAGAAAAAGGCAAATTG CGGTTGAGCCAACGACTATT 1283–1288 1.000 53.0
rps16_p4 rps16 AGCAAGAAAAAGGCAAATTGTG CGGTTGAGCCAACGACTATT 1281–1286 1.000 53.0
rps16_p5 rps16 CAGCAAGAAAAAGGCAAATTGT CGGTTGAGCCAACGACTATT 1282–1287 1.000 53.0
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG GGGCAATTTGGCGAAGAAAA 482 1.000 77.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATGGAAACGATCTGGGACG GGGCAATTTGGCGAAGAAAA 502 1.000 75.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA GGGCAATTTGGCGAAGAAAA 480 1.000 75.2
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT GGGCAATTTGGCGAAGAAAA 481 1.000 75.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GAGTAACGGGACCAAAACCC GGGCAATTTGGCGAAGAAAA 465 1.000 74.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACTGAGAGACCCCTTAACT 1490–1564 1.000 59.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACTGAGAGACCCCTTAACT 1491–1565 1.000 58.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG AACTGAGAGACCCCTTAACT 1546–1620 1.000 57.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACTGAGAGACCCCTTAACT 1538–1612 1.000 57.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG AAACTGAGAGACCCCTTAACT 1547–1621 1.000 56.6

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
Borassus flabellifer NC_079708.1 160018 View on NCBI ↗
Borassus madagascariensis NC_079709.1 160194 View on NCBI ↗