Markers + reference

Copernicia

3 species · Arecaceae · Arecales

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Species 3
Genome length 157–158 kb
Candidate markers 272
Primer pairs 85

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 793 0.0420 1.00 81.9 yes View details
trnT-UGU-trnL-UAA LSC 1053 0.0126 0.95 60.9 yes View details
accD LSC 1482 0.0103 1.00 50.4 yes View details
accD-psaI LSC 285 0.0537 0.94 71.9 yes View details
rpl22 LSC 327 0.0000 1.00 20.4 yes View details
ycf2-trnL-CAA IRb 603 0.0376 1.00 82.7 yes View details
ndhF-rpl32 SSC 277 0.0385 1.00 68.4 yes View details
psaC-ndhE SSC 740 0.0487 0.92 85.6 yes View details
trnL-CAA-ycf2 IRa 603 0.0381 1.00 83.0 yes View details
rpl22-rps19 IRb 203 0.0690 1.00 87.5 yes View details
psbC-trnS-UGA LSC 137 0.0487 1.00 83.5 yes View details
rps19-psbA LSC 237 0.0366 1.00 77.3 no View details
matK-trnK-UUU LSC 875 0.0122 1.00 71.9 yes View details
petN-psbM LSC 848 0.0134 1.00 67.5 yes View details
rpl16 LSC 1565 0.0038 1.00 65.5 yes View details
psbE-petL LSC 1283 0.0057 1.00 63.4 yes View details
atpB-rbcL LSC 770 0.0061 1.00 63.1 yes View details
rpoB-trnC-GCA LSC 1176 0.0051 1.00 62.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA AACGGTAGAGTACTCGGCTT 962–978 1.000 66.5
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA ACGGTAGAGTACTCGGCTTT 961–977 1.000 66.5
matK-trnK-UUU_p3 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA GTCGTGCAGTGCAATTCAAT 1052–1068 1.000 64.8
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA GGGTTGCTAACTCAACGGTA 975–991 1.000 64.1
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA TTCGGGTTGCTAACTCAACG 978–994 1.000 63.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 838–867 1.000 60.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 841–870 1.000 59.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 840–869 1.000 59.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 894–923 1.000 58.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 839–868 1.000 58.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1244–1263 1.000 73.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1245–1264 1.000 72.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TTTGTTGATCAGGCGACACC 1281–1300 1.000 71.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TTTGTTGATCAGGCGACACC 1282–1301 1.000 71.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA GACACCCGGATTTGAACTGG 1267–1286 1.000 70.6
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 988–1008 1.000 70.1
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 983–1003 1.000 69.2
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 933–953 1.000 69.0
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 992–1012 1.000 67.2
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 991–1011 1.000 66.4
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 244 1.000 81.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GGTTGATAGCTCCGGTCTTG 243 1.000 81.5
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 283 1.000 81.3
psbC-trnS-UGA_p4 psbC-trnS-UGA CTGTTCTTTCCATGACCCCC GATGGCCGAGTGGTTGATAG 254 1.000 80.8
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 294 1.000 80.6
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 907–1103 1.000 84.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 915–1111 1.000 83.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 939–1135 1.000 83.5
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 947–1143 1.000 82.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 930–1126 1.000 82.6

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
Copernicia alba NC_067828.1 157240 View on NCBI ↗
Copernicia baileyana NC_079722.1 158173 View on NCBI ↗
Copernicia prunifera NC_072145.1 157323 View on NCBI ↗