Markers + reference

Brahea

8 species · Arecaceae · Arecales

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Species 8
Genome length 158–159 kb
Candidate markers 271
Primer pairs 70

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 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5628 0.1688 0.88 76.7 yes View details
ycf1-rps15 SSC 388 0.2525 0.91 68.7 yes View details
ndhA SSC 2143 0.2092 0.78 68.1 yes View details
ndhG SSC 531 0.2238 0.82 59.8 yes View details
ndhE-psaC SSC 460 0.2708 0.94 70.3 yes View details
ndhD SSC 1506 0.2357 0.89 72.4 yes View details
ccsA SSC 966 0.2292 0.83 70.7 yes View details
trnL-UAG-rpl32 SSC 785 0.2207 0.87 76.6 yes View details
ycf1 IRa 1346 0.0000 1.00 26.2 no View details
rps19-psbA LSC 374 0.0307 0.67 72.0 no View details
ndhF SSC 2238 0.1966 0.78 70.2 yes View details
ndhH SSC 1182 0.2040 0.76 69.2 yes View details
ndhD-ccsA SSC 216 0.2447 0.95 63.3 yes View details
ndhI SSC 543 0.2180 0.80 61.9 yes View details
rpl32-ndhF SSC 355 0.1848 0.78 61.6 yes View details
ndhI-ndhG SSC 331 0.1819 0.80 59.9 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1_p1 ycf1 TCGATCCATGAATTGGGCAA CACTGCCACCGCATAGTAAT 871–898 0.500 59.4
ycf1_p2 ycf1 TTCGATCCATGAATTGGGCA CACTGCCACCGCATAGTAAT 872–899 0.500 59.4
ycf1_p3 ycf1 TCGATCCATGAATTGGGCAA TCAATGAATCCACTGCCACC 881–908 0.500 58.5
ycf1_p4 ycf1 TTCGATCCATGAATTGGGCA TCAATGAATCCACTGCCACC 882–909 0.500 58.5
ycf1_p5 ycf1 TCGATCCATGAATTGGGCAA TCGTCAATGAATCCACTGCC 884–911 0.500 57.7
ycf1-rps15_p1 ycf1-rps15 ACGGCAATATGCTTGTGGAT GGCTCAGCTCCAGCATAATT 1456–1458 0.500 60.0
ycf1-rps15_p2 ycf1-rps15 ACGGCAATATGCTTGTGGAT AACACCATGCATTGATGGGT 1203–1205 0.500 59.8
ycf1-rps15_p3 ycf1-rps15 ACGGCAATATGCTTGTGGAT ACCATGCATTGATGGGTGTT 1200–1202 0.500 59.8
ycf1-rps15_p4 ycf1-rps15 ACGGCAATATGCTTGTGGAT GAAGCTATACGGCTCAGCTC 1466–1468 0.500 59.7
ycf1-rps15_p5 ycf1-rps15 ACGGCAATATGCTTGTGGAT GAGAAGCTATACGGCTCAGC 1468–1470 0.500 59.7
ndhH_p1 ndhH CAGTTGGATATTCGGGAGCC CCAGCATATTCAGGCCCAAT 1524–1526 0.500 59.3
ndhH_p2 ndhH GGCTCCTGGCTTATTTGTCA CCAGCATATTCAGGCCCAAT 1580–1582 0.500 59.2
ndhH_p3 ndhH CAGTTGGATATTCGGGAGCC CCAACGGACCAGCATATTCA 1532–1534 0.500 59.0
ndhH_p4 ndhH GGCTCCTGGCTTATTTGTCA CCAACGGACCAGCATATTCA 1588–1590 0.500 58.9
ndhH_p5 ndhH CAGTTGGATATTCGGGAGCC TGTTCCAACGAATCACACGT 1892–1894 0.500 58.8
ndhA_p1 ndhA TGTCAGAGTAGAAGCCCCAA CGGGCATACACGAACACATA 2659–2660 0.500 59.2
ndhA_p2 ndhA ACTTTCCCCTGGAGATGGAA CGGGCATACACGAACACATA 2601–2602 0.500 59.0
ndhA_p3 ndhA TGGGAAGTCCAATGGCAAAA CGGGCATACACGAACACATA 2901–2902 0.500 58.7
ndhA_p4 ndhA GGGCATTATTGGTGGAGAGG ACCTTGCAGCTCGTATTGTT 2858–2859 0.500 58.5
ndhA_p5 ndhA TGTCAGAGTAGAAGCCCCAA ACCTTGCAGCTCGTATTGTT 2495–2496 0.500 58.3
ndhI_p1 ndhI TTTTGGGGGTGGAATCTGTG ACAAACCAGTGAAGTGACCC 1760 0.500 59.6
ndhI_p2 ndhI TTTTGGGGGTGGAATCTGTG TCCCAACGAAAAGGCAGAAA 1568 0.500 59.5
ndhI_p3 ndhI GGTTTTTGGGGGTGGAATCT ACAAACCAGTGAAGTGACCC 1763 0.500 59.4
ndhI_p4 ndhI TTTTGGGGGTGGAATCTGTG GGTCCAGGAAAGGAAAAGGG 1394 0.500 59.4
ndhI_p5 ndhI TTTTGGGGGTGGAATCTGTG GTCCAGGAAAGGAAAAGGGG 1393 0.500 59.4
ndhI-ndhG_p1 ndhI-ndhG TATGTGTTCGTGTATGCCCG ACAAACCAGTGAAGTGACCC 981 0.500 59.1
ndhI-ndhG_p2 ndhI-ndhG TATGTGTTCGTGTATGCCCG TCCCAACGAAAAGGCAGAAA 789 0.500 59.1
ndhI-ndhG_p3 ndhI-ndhG TATGTGTTCGTGTATGCCCG TGTGCGGCAGCTACAAAATA 854 0.500 58.0
ndhI-ndhG_p4 ndhI-ndhG GTGTTCGTGTATGCCCGATA ACAAACCAGTGAAGTGACCC 978 0.500 58.0
ndhI-ndhG_p5 ndhI-ndhG GTGTTCGTGTATGCCCGATA TCCCAACGAAAAGGCAGAAA 786 0.500 57.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Brahea aculeata NC_045079.1 158659 View on NCBI ↗
Brahea armata NC_045080.1 158356 View on NCBI ↗
Brahea brandegeei NC_029968.1 158733 View on NCBI ↗
Brahea decumbens NC_079710.1 158767 View on NCBI ↗
Brahea dulcis NC_079711.1 158650 View on NCBI ↗
Brahea edulis NC_045081.1 158736 View on NCBI ↗
Brahea pimo NC_079712.1 158515 View on NCBI ↗
Brahea sarukhanii NC_045082.1 158653 View on NCBI ↗