Markers + reference

Pritchardia

2 species · Arecaceae · Arecales

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Species 2
Genome length 158–158 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 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 40.0 yes View details
atpI-rps2 LSC 307 0.0100 0.98 60.6 yes View details
rpoC1 LSC 2793 0.0004 1.00 56.3 yes View details
petN-psbM LSC 837 0.0012 1.00 59.4 yes View details
trnD-GUC-trnY-GUA LSC 383 0.0104 1.00 60.2 yes View details
psaC-ndhE SSC 541 0.0134 0.97 68.2 yes View details
trnT-UGU-trnL-UAA LSC 964 0.0000 0.99 59.4 yes View details
rpl16 LSC 1532 0.0000 0.99 59.2 yes View details
rps4-trnT-UGU LSC 384 0.0000 0.86 56.5 yes View details
ndhI-ndhA SSC 103 0.0000 0.85 54.7 yes View details
matK-trnK-UUU LSC 813 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 711 0.0000 1.00 40.0 yes View details
rps16 LSC 1136 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 1031 0.0000 1.00 40.0 yes View details
trnS-GCU-trnG-UCC LSC 651 0.0000 1.00 40.0 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 80 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
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA AACGGTAGAGTACTCGGCTT 916 1.000 61.8
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA ACGGTAGAGTACTCGGCTTT 915 1.000 61.8
matK-trnK-UUU_p3 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA GGGTTGCTAACTCAACGGTA 929 1.000 59.4
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA TTCGGGTTGCTAACTCAACG 932 1.000 59.1
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGAT ACGGTAGAGTACTCGGCTTT 915 1.000 58.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 882 1.000 70.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 881 1.000 70.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 884 1.000 70.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 883 1.000 70.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 825 1.000 69.5
rps16_p1 rps16 GCAAGAAAAAGGCAAATTGTGT CCGGTTGAGCCAATGACTAT 1309 1.000 54.3
rps16_p2 rps16 GCAAGAAAAAGGCAAATTGTGT TATACACACACCGGTTGAGC 1319 1.000 54.0
rps16_p3 rps16 AGCAAGAAAAAGGCAAATTGTG CCGGTTGAGCCAATGACTAT 1310 1.000 52.2
rps16_p4 rps16 AGCAAGAAAAAGGCAAATTGTG TATACACACACCGGTTGAGC 1320 1.000 51.8
rps16_p5 rps16 GCAAGAAAAAGGCAAATTGTGT GGTATACACACACCGGTTGA 1321 1.000 51.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1122 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1120 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1128 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1129 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTCGAAATGGGGCGTG 1181 1.000 79.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGGAATATGAAACTGAAAGACCC 797 1.000 51.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 725 1.000 51.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ATGAAACTGAAAGACCCCTT 791 1.000 51.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 728 1.000 50.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 727 1.000 50.3

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
Pritchardia pacifica NC_067842.1 157661 View on NCBI ↗
Pritchardia thurstonii NC_029955.1 157909 View on NCBI ↗