Markers + reference

Latania

2 species · Arecaceae · Arecales

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Species 2
Genome length 160–160 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 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
petN-psbM LSC 733 0.0041 0.99 61.9 yes View details
trnD-GUC-trnY-GUA LSC 384 0.0130 1.00 61.7 yes View details
trnT-GGU-psbD LSC 1046 0.0019 1.00 60.3 yes View details
psbC LSC 1422 0.0000 1.00 31.1 yes View details
ndhC-trnV-UAC LSC 1941 0.0021 0.98 60.8 yes View details
rbcL LSC 1464 0.0020 1.00 59.9 yes View details
petA-psbJ LSC 1045 0.0077 1.00 63.2 yes View details
ccsA SSC 969 0.0000 1.00 30.9 yes View details
ccsA-ndhD SSC 216 0.0139 1.00 60.5 yes View details
psaC-ndhE SSC 757 0.0040 0.99 61.7 yes View details
psbC-trnS-UGA LSC 137 0.0219 1.00 65.1 yes View details
trnS-GCU-trnG-GCC LSC 1670 0.0007 0.91 62.5 yes View details
rps12-trnV-GAC IRb 1934 0.0005 0.97 61.3 yes View details
trnV-GAC-rps12 IRa 1934 0.0005 0.97 61.3 yes View details
rpl16 LSC 1619 0.0019 0.99 60.3 yes View details
trnT-UGU-trnL-UAA LSC 921 0.0022 1.00 60.0 yes View details
rps16 LSC 1117 0.0018 1.00 59.8 yes View details
accD-psaI LSC 988 0.0010 0.99 59.8 yes View details
cemA LSC 693 0.0014 1.00 59.6 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 GTGAATACAGCAAGAAAAAGGCA CGGTTGAGCCAACGACTATT 1297–1299 1.000 52.9
rps16_p2 rps16 TGTGAATACAGCAAGAAAAAGGC CGGTTGAGCCAACGACTATT 1298–1300 1.000 52.9
rps16_p3 rps16 TGAATACAGCAAGAAAAAGGCA CGGTTGAGCCAACGACTATT 1296–1298 1.000 52.3
rps16_p4 rps16 GTGAATACAGCAAGAAAAAGGCA TATACACACACCGGTTGAGC 1308–1310 1.000 52.1
rps16_p5 rps16 TGTGAATACAGCAAGAAAAAGGC TATACACACACCGGTTGAGC 1309–1311 1.000 52.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1599–1744 1.000 55.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1602–1747 1.000 54.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1601–1746 1.000 54.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1655–1800 1.000 53.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1600–1745 1.000 53.5
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 889–901 1.000 68.1
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 884–896 1.000 67.1
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 834–846 1.000 66.8
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 893–905 1.000 65.1
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 892–904 1.000 64.4
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 563 1.000 79.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTGCTCTGACCGATTGAACT AATTCTTCCTGGGTCGATGC 506 1.000 79.7
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 530 1.000 77.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 566 1.000 77.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 567 1.000 77.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1191–1196 1.000 78.0
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTCCGTAACCAATCATCC 1175–1180 1.000 77.9
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1194–1199 1.000 77.8
trnT-GGU-psbD_p4 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG ACAAAAACGAAACGGTCCCT 1210–1215 1.000 77.7
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCCTCCGTAACCAATCATCC 1178–1183 1.000 77.7
psbC_p1 psbC TTTCCCAAGAAATCCGTGCA ATAGCCGAGCCAGAACAGAA 1586 1.000 73.5
psbC_p2 psbC TTTCCCAAGAAATCCGTGCA TAGCCGAGCCAGAACAGAAA 1585 1.000 71.7
psbC_p3 psbC TTTCCCAAGAAATCCGTGCA GCCGAGCCAGAACAGAAAAA 1583 1.000 71.5
psbC_p4 psbC TTTCCCAAGAAATCCGTGCA ATAGCCGAGCCAGAACAGA 1586 1.000 71.1
psbC_p5 psbC GCAGCGGAAGATCCTGAATT ATAGCCGAGCCAGAACAGAA 1569 1.000 70.9

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
Latania lontaroides NC_067844.1 160122 View on NCBI ↗
Latania verschaffeltii NC_067829.1 159823 View on NCBI ↗