Markers + reference

Salacca

2 species · Arecaceae · Arecales

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Species 2
Genome length 157–158 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1125 0.0053 1.00 54.2 yes View details
trnC-GCA-petN LSC 1109 0.0045 1.00 61.4 yes View details
psbM-trnD-GUC LSC 1050 0.0576 0.99 75.3 yes View details
trnD-GUC-trnY-GUA LSC 380 0.0105 1.00 60.2 yes View details
rps14 LSC 303 0.0033 1.00 40.7 yes View details
accD-psaI LSC 1136 0.0205 0.90 58.9 yes View details
rpl16 LSC 1617 0.0066 0.94 55.9 yes View details
ycf1 IRb 1344 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 394 0.0305 1.00 72.0 yes View details
ycf1 SSC 5565 0.0032 1.00 54.0 yes View details
rps19-psbA LSC 320 0.1042 0.45 67.1 no View details
rps14-psaB LSC 128 0.0367 0.85 71.5 yes View details
atpH-atpI LSC 801 0.0050 1.00 61.7 yes View details
rps15-ycf1 SSC 380 0.0132 1.00 61.7 yes View details
trnT-UGU-trnL-UAA LSC 736 0.0041 1.00 61.1 yes View details
rbcL-accD LSC 812 0.0025 0.99 60.8 yes View details
petA-psbJ LSC 1033 0.0029 1.00 60.8 yes View details
rpl32-trnL-UAG SSC 853 0.0012 0.99 60.8 yes View details
psaA-ycf3 LSC 636 0.0031 1.00 60.6 yes View details
trnP-UGG LSC 74 0.0135 1.00 60.3 yes View details
ndhC-trnV-UAC LSC 1267 0.0024 1.00 60.1 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
rps16_p1 rps16 GCAAGAAAAAGGCAAATTGTGT CCGGTTGAGCCAATGACTAT 1298–1305 1.000 54.7
rps16_p2 rps16 GCAAGAAAAAGGCAAATTGTGT GGTATACACACCGGTTGAGC 1308–1315 1.000 54.5
rps16_p3 rps16 GCAAGAAAAAGGCAAATTGTGT GTATACACACCGGTTGAGCC 1307–1314 1.000 54.5
rps16_p4 rps16 AGCAAGAAAAAGGCAAATTGTG CCGGTTGAGCCAATGACTAT 1299–1306 1.000 52.5
rps16_p5 rps16 CAGCAAGAAAAAGGCAAATTGT CCGGTTGAGCCAATGACTAT 1300–1307 1.000 52.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 890–894 1.000 75.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 862–866 1.000 75.5
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 973–977 1.000 75.3
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 945–949 1.000 75.3
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 946–950 1.000 74.8
trnC-GCA-petN_p1 trnC-GCA-petN TTGTATCAGATTTGGCGGCA TAAAGCAGCCCAAGTGAGAC 1225–1226 1.000 77.9
trnC-GCA-petN_p2 trnC-GCA-petN TTGTATCAGATTTGGCGGCA ACCATTAAAGCAGCCCAAGT 1230–1231 1.000 76.9
trnC-GCA-petN_p3 trnC-GCA-petN TGTATCAGATTTGGCGGCAT TAAAGCAGCCCAAGTGAGAC 1224–1225 1.000 76.1
trnC-GCA-petN_p4 trnC-GCA-petN TATCAGATTTGGCGGCATGG TAAAGCAGCCCAAGTGAGAC 1222–1223 1.000 75.8
trnC-GCA-petN_p5 trnC-GCA-petN TGTATCAGATTTGGCGGCAT ACCATTAAAGCAGCCCAAGT 1229–1230 1.000 75.1
psbM-trnD-GUC_p1 psbM-trnD-GUC GTCTCACTTGGGCTGCTTTA AGTTCAATCGGTCAGAGCAC 1789–1796 1.000 81.1
psbM-trnD-GUC_p2 psbM-trnD-GUC GTCTCACTTGGGCTGCTTTA AATTCTTCCTGGGTCGATGC 2271–2291 1.000 80.9
psbM-trnD-GUC_p3 psbM-trnD-GUC GTCTCACTTGGGCTGCTTTA TGGGGGTAGAGAGGAAGTTG 2319–2339 1.000 80.8
psbM-trnD-GUC_p4 psbM-trnD-GUC ACTTGGGCTGCTTTAATGGT AATTCTTCCTGGGTCGATGC 2266–2286 1.000 79.9
psbM-trnD-GUC_p5 psbM-trnD-GUC GTCTCACTTGGGCTGCTTTA TCTCTTTCAAGGAGGCAACG 2355–2375 1.000 79.8
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 559–572 1.000 79.7
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT AATTCTTCCTGGGTCGATGC 502–515 1.000 79.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 526–539 1.000 77.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 562–575 1.000 77.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 563–576 1.000 77.1
rps14_p1 rps14 TCTTTGCCTACCCCCAAAAC TTGATTGCCTCGACATCAGG 782–794 1.000 82.2
rps14_p2 rps14 TCTTTGCCTACCCCCAAAAC GTATGGGCGTGGATGTTCTT 1022–1034 1.000 81.6
rps14_p3 rps14 TCTTTGCCTACCCCCAAAAC TGCACGTGGTTCCAAGTTAA 1335–1347 1.000 81.1
rps14_p4 rps14 TCTTTGCCTACCCCCAAAAC ATGGGCTCATGAACGTACAC 930 0.500 59.8
rps14_p5 rps14 AAGGTTATGAGCCTTGCGAG ATGGGCTCATGAACGTACAC 801 0.500 59.6

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
Salacca ramosiana NC_029954.1 157047 View on NCBI ↗
Salacca zalacca NC_063109.1 158295 View on NCBI ↗