Markers + reference

Chuniophoenix

3 species · Arecaceae · Arecales

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Species 3
Genome length 154–155 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0006 1.00 35.5 yes View details
psbK-psbI LSC 401 0.0083 1.00 52.2 yes View details
trnS-GCU-trnG-GCC LSC 1013 0.0041 0.64 46.7 yes View details
petN-psbM LSC 772 0.0078 1.00 52.8 yes View details
psbC LSC 1422 0.0023 1.00 36.6 yes View details
petA-psbJ LSC 1028 0.0071 1.00 50.9 yes View details
petD LSC 1245 0.0011 1.00 42.7 yes View details
ndhF-rpl32 SSC 436 0.0107 0.50 46.2 yes View details
ccsA SSC 969 0.0007 1.00 35.8 yes View details
psaC SSC 246 0.0000 1.00 19.9 yes View details
rps15 SSC 273 0.0049 1.00 28.6 yes View details
rps19-psbA IRa 252 0.0839 0.58 76.2 no View details
trnT-UGU-trnL-UAA LSC 1075 0.0008 0.73 56.5 yes View details
psbC-trnS-UGA LSC 136 0.0343 1.00 54.4 yes View details
psaC-ndhE SSC 700 0.0021 0.46 53.2 yes View details
accD-psaI LSC 979 0.0009 0.78 53.0 yes View details
petD-rpoA LSC 181 0.0184 1.00 50.7 yes View details
psbM-trnD-GUC LSC 1020 0.0020 1.00 49.7 yes View details
rbcL-accD LSC 795 0.0042 1.00 48.9 yes View details
atpH-atpI LSC 832 0.0032 1.00 48.3 yes View details
trnR-ACG-trnN-GUU IRb 588 0.0000 1.00 47.2 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 105 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 73.5
psbA_p4 psbA TGCTCCATTCCTTCAACGAT ATACGTGTGCTTGGGAGTTC 1154 1.000 73.0
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGTGCTTGGGAGTTCTTGA 1150 1.000 71.2
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA TCGCGCAATGCAATTCAATT 2916–2937 1.000 72.0
trnK-UUU_p2 trnK-UUU GCCAATGTCAACCAATCTCA TCGCGCAATGCAATTCAATT 2915–2936 1.000 67.5
trnK-UUU_p3 trnK-UUU TGCCAATGTCAACCAATCTC TCGCGCAATGCAATTCAATT 2916–2937 1.000 67.5
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCTCA GTCGCGCAATGCAATTCAAT 2917–2938 1.000 66.3
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTCA TCAATGTTTTGACGGGGTCG 2933–2954 1.000 65.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 478–527 1.000 82.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 475–524 1.000 80.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 476–525 1.000 80.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 477–526 1.000 80.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGCCCTGGATCATT 477–526 1.000 79.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 720–1087 1.000 55.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 723–1090 1.000 54.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 722–1089 1.000 54.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 776–1143 1.000 54.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 721–1088 1.000 53.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 921–923 1.000 75.4
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 893–895 1.000 75.4
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 1004–1006 1.000 75.3
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 976–978 1.000 75.3
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 977–979 1.000 74.7
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 928–945 1.000 69.0
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 923–940 1.000 68.0
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 873–890 1.000 67.8
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 932–949 1.000 66.0
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 931–948 1.000 65.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Chuniophoenix hainanensis NC_067826.1 155276 View on NCBI ↗
Chuniophoenix nana NC_029966.1 153806 View on NCBI ↗
Chuniophoenix suoitienensis NC_079775.1 153584 View on NCBI ↗