Markers + reference

Phoenix

9 species · Arecaceae · Arecales

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Species 9
Genome length 158–159 kb
Candidate markers 269
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0017 1.00 35.2 yes View details
trnS-GCU-trnG-UCC LSC 1320 0.0132 0.98 64.1 yes View details
trnS-UGA-psbZ LSC 352 0.0022 1.00 29.5 yes View details
trnT-UGU-trnL-UAA LSC 981 0.0062 0.99 64.7 yes View details
accD-psaI LSC 617 0.0072 0.99 63.4 yes View details
petA-psbJ LSC 1009 0.0150 1.00 46.9 yes View details
rpl32-trnL-UAG SSC 736 0.0137 1.00 56.8 yes View details
ndhD SSC 1503 0.0017 1.00 37.2 yes View details
psaC-ndhE SSC 692 0.0073 1.00 61.2 yes View details
ycf1 SSC 5634 0.0030 1.00 49.1 yes View details
psbC-trnS-UGA LSC 137 0.0280 1.00 63.5 yes View details
rpl22-rps19 IRb 133 0.0272 1.00 60.1 yes View details
matK-trnK-UUU LSC 809 0.0040 0.99 58.5 yes View details
trnH-GUG-psbA IRa 661 0.0151 0.99 58.4 no View details
trnK-UUU-rps16 LSC 743 0.0059 0.99 58.3 yes View details
atpH-atpI LSC 826 0.0016 0.99 58.0 yes View details
trnT-GGU-psbD LSC 1061 0.0016 1.00 57.1 yes View details
trnG-GCC-trnfM-CAU LSC 211 0.0058 1.00 51.0 yes View details
matK LSC 1545 0.0040 1.00 50.4 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 TCCTTCAACGATTCATATACACT GTGTGCTTGGGAGTTCTTGA 1142 1.000 40.4
psbA_p2 psbA TCCTTCAACGATTCATATACAC GTGTGCTTGGGAGTTCTTGA 1142 1.000 40.4
psbA_p3 psbA CCTTCAACGATTCATATACACT GTGTGCTTGGGAGTTCTTGA 1141 1.000 40.4
psbA_p4 psbA TCCTTCAACGATTCATATACACT ATACGTGTGCTTGGGAGTTC 1146 1.000 40.3
psbA_p5 psbA TCCTTCAACGATTCATATACACT AATACGTGTGCTTGGGAGTT 1147 1.000 40.3
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGTGCAGTGCAAATCAAT 2874–2884 1.000 69.5
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2890–2900 1.000 66.0
trnK-UUU_p3 trnK-UUU GCCAATGTCAACCAATCTCA GTCGTGCAGTGCAAATCAAT 2873–2883 1.000 65.0
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTC GTCGTGCAGTGCAAATCAAT 2874–2884 1.000 65.0
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA GTTCAATGTTTTGACGGGGTC 2892–2902 1.000 64.1
matK_p1 matK TCTCATCACGTCAACAAACCA ATGAAATAGGTCCCGCCTCT 1606 1.000 70.1
matK_p2 matK GTCTCATCACGTCAACAAACC ATGAAATAGGTCCCGCCTCT 1607 1.000 67.4
matK_p3 matK TCTCATCACGTCAACAAACCA AATGAAATAGGTCCCGCCTC 1607 1.000 66.5
matK_p4 matK CTCATCACGTCAACAAACCA ATGAAATAGGTCCCGCCTCT 1605 1.000 65.9
matK_p5 matK TCTCATCACGTCAACAAACCA CGCCTCTGGTTCAAGTAGAA 1593 1.000 65.7
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 879–889 1.000 77.8
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 878–888 1.000 77.8
matK-trnK-UUU_p3 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA GTCGTGCAGTGCAAATCAAT 965–975 1.000 76.3
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT AACGGTAGAGTACTCGGCTT 876–886 1.000 76.0
matK-trnK-UUU_p5 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT ACGGTAGAGTACTCGGCTTT 875–885 1.000 76.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 891–920 1.000 73.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 890–919 1.000 73.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 893–922 1.000 73.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 892–921 1.000 73.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 834–863 1.000 73.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1364–1430 1.000 58.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1367–1433 1.000 57.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1366–1432 1.000 57.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1420–1486 1.000 56.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1365–1431 1.000 56.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Phoenix acaulis NC_079735.1 158156 View on NCBI ↗
Phoenix canariensis NC_051507.1 158477 View on NCBI ↗
Phoenix dactylifera NC_013991.2 158462 View on NCBI ↗
Phoenix loureiroi NC_079736.1 158204 View on NCBI ↗
Phoenix pusilla NC_079737.1 158498 View on NCBI ↗
Phoenix reclinata NC_079738.1 158479 View on NCBI ↗
Phoenix roebelenii NC_067830.1 158283 View on NCBI ↗
Phoenix rupicola NC_079739.1 158588 View on NCBI ↗
Phoenix theophrasti NC_079740.1 158429 View on NCBI ↗