Markers + reference

Hydriastele

2 species · Arecaceae · Arecales

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Species 2
Genome length 159–159 kb
Candidate markers 271
Primer pairs 90

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 0.0009 1.00 54.6 yes View details
trnK-UUU-rps16 LSC 720 0.0056 1.00 59.9 yes View details
petN-psbM LSC 440 0.0137 1.00 63.5 yes View details
trnD-GUC-trnY-GUA LSC 384 0.0130 1.00 58.7 yes View details
accD LSC 1533 0.0046 0.99 49.6 yes View details
psbE-petL LSC 1279 0.0031 1.00 47.3 yes View details
rpl32-trnL-UAG SSC 789 0.0051 0.99 62.3 yes View details
psaC-ndhE SSC 579 0.0123 0.99 66.7 yes View details
ycf1 SSC 5433 0.0050 1.00 55.4 yes View details
rps19-psbA LSC 253 0.1818 0.87 90.1 no View details
trnR-UCU-atpA LSC 91 0.0220 1.00 65.1 yes View details
psbC-trnS-UGA LSC 137 0.0219 1.00 65.1 yes View details
trnF-GAA-ndhJ LSC 720 0.0042 1.00 61.6 yes View details
ccsA-ndhD SSC 218 0.0139 0.99 61.4 yes View details
rbcL-accD LSC 804 0.0037 1.00 60.9 yes View details
trnS-GCU-trnG-UCC LSC 1266 0.0024 1.00 60.5 yes View details
atpF-atpH LSC 527 0.0038 0.99 60.5 yes View details
petA LSC 963 0.0031 1.00 60.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TCAAACAATGGAGCAATACCCA GTGCTTGGGAGTCCTTGAAA 1196 1.000 62.1
psbA_p2 psbA CAAACAATGGAGCAATACCCA GTGCTTGGGAGTCCTTGAAA 1195 1.000 62.0
psbA_p3 psbA TCAAACAATGGAGCAATACCCA AATACGTGTGCTTGGGAGTC 1203 1.000 61.5
psbA_p4 psbA CAAACAATGGAGCAATACCCA AATACGTGTGCTTGGGAGTC 1202 1.000 61.4
psbA_p5 psbA TCAAACAATGGAGCAATACCC GTGCTTGGGAGTCCTTGAAA 1196 1.000 59.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 889–891 1.000 70.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 888–890 1.000 70.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 891–893 1.000 70.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 890–892 1.000 70.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 832–834 1.000 70.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1335–1340 1.000 51.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1338–1343 1.000 50.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1337–1342 1.000 50.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1391–1396 1.000 50.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1336–1341 1.000 50.0
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACTTCAGGAACAAGCGTCAA 153 1.000 64.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAAGCGTCAACTT 150 1.000 64.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAAGCGTCAACT 151 1.000 64.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AACAAGCGTCAACTTCTCCC 145 1.000 64.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TACCAAGACATTCACCGAGC 225 1.000 64.1
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 645–650 1.000 79.7
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAAGGAA ATTTATGGACTGGTCGTGGC 617–622 1.000 75.5
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAAGGAAA ATTTATGGACTGGTCGTGGC 617–622 1.000 72.3
atpF-atpH_p4 atpF-atpH GTGACCCAAGGAAAGGAAAGA ATTTATGGACTGGTCGTGGC 615–620 1.000 70.9
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAGGAAAGGA ATTTATGGACTGGTCGTGGC 618–623 1.000 70.9
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 595–596 1.000 68.2
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 590–591 1.000 67.2
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 540–541 1.000 67.0
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 599–600 1.000 65.2
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 598–599 1.000 64.5

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
Hydriastele microcarpa NC_079783.1 158675 View on NCBI ↗
Hydriastele microspadix NC_079784.1 158618 View on NCBI ↗