Markers + reference

Aiouea

2 species · Lauraceae · Laurales

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Species 2
Genome length 153–153 kb
Candidate markers 263
Primer pairs 90

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4158 0.0005 1.00 54.1 yes View details
petN-psbM LSC 1063 0.0019 1.00 59.8 yes View details
rps4-trnT-UGU LSC 339 0.0059 1.00 56.7 yes View details
petA-psbJ LSC 1142 0.0123 1.00 65.8 yes View details
ycf2 LSC 6993 0.0026 1.00 41.2 yes View details
rpl32-trnL-UAG SSC 1394 0.0022 1.00 53.6 yes View details
ccsA SSC 951 0.0000 1.00 27.4 yes View details
trnL-CAA-ycf2 IRa 339 0.0442 1.00 63.9 yes View details
ycf2 IRa 3168 0.0019 1.00 41.5 no View details
ccsA-ndhD SSC 222 0.0225 1.00 65.5 yes View details
trnL-UAG-trnI-CAU SSC 43 0.0233 1.00 61.7 yes View details
accD-psaI LSC 590 0.0017 0.99 60.3 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
matK-trnK-UUU LSC 720 0.0014 1.00 59.5 yes View details
rpl20-rps12 LSC 749 0.0013 1.00 59.5 yes View details
ndhK LSC 858 0.0012 1.00 59.4 yes View details
ycf4-cemA LSC 910 0.0011 1.00 59.4 yes View details
atpF LSC 1282 0.0008 1.00 59.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TTGTTGCCGAAATCCATCCA GTCGGGCAATCGAATCTCTT 869 1.000 79.0
matK-trnK-UUU_p2 matK-trnK-UUU TGTTGCCGAAATCCATCCAT GTCGGGCAATCGAATCTCTT 868 1.000 78.5
matK-trnK-UUU_p3 matK-trnK-UUU TTGTTGCCGAAATCCATCCA AACGGTAGAGTACTCGGCTT 792 1.000 78.1
matK-trnK-UUU_p4 matK-trnK-UUU TTGTTGCCGAAATCCATCCA ACGGTAGAGTACTCGGCTTT 791 1.000 78.1
matK-trnK-UUU_p5 matK-trnK-UUU TTGTTGCCGAAATCCATCCA ATGGGTTGCTAACTCAACGG 807 1.000 78.0
trnG-UCC_p1 trnG-UCC AACATGTCAGCACCCCAATT TCCGATTTCTTTCACGTTCTGA 1037–1038 1.000 63.9
trnG-UCC_p2 trnG-UCC ACATGTCAGCACCCCAATTT TCCGATTTCTTTCACGTTCTGA 1036–1037 1.000 63.9
trnG-UCC_p3 trnG-UCC AACATGTCAGCACCCCAATT CCGATTTCTTTCACGTTCTGAC 1036–1037 1.000 63.6
trnG-UCC_p4 trnG-UCC ACATGTCAGCACCCCAATTT CCGATTTCTTTCACGTTCTGAC 1035–1036 1.000 63.6
trnG-UCC_p5 trnG-UCC TGTCAGCACCCCAATTTTCA TCCGATTTCTTTCACGTTCTGA 1033–1034 1.000 63.4
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA GGGGGCGAAGTGATACAAAA 1444 1.000 73.6
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA CAATCCAAAACAAAGGGGGC 1458 1.000 73.5
atpF_p3 atpF AATTTCGTCGGCTCGAATGG GGGGGCGAAGTGATACAAAA 1441 1.000 70.8
atpF_p4 atpF AATTTCGTCGGCTCGAATGG CAATCCAAAACAAAGGGGGC 1455 1.000 70.7
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA CAAAGGGGGCGAAGTGATAC 1448 1.000 70.0
rpoC2_p1 rpoC2 GGAACGGGGCATTAGTTCTT TTTCTGACCTCTCCGTGACT 248 1.000 79.3
rpoC2_p2 rpoC2 GGAACGGGGCATTAGTTCTT TTCGCTCCACAAGGATCAAG 304 1.000 78.5
rpoC2_p3 rpoC2 GGAACGGGGCATTAGTTCTT CGCTCCACAAGGATCAAGAT 302 1.000 76.7
rpoC2_p4 rpoC2 GGAACGGGGCATTAGTTCTT CCTTTTTCGCTCCACAAGGA 309 1.000 76.1
rpoC2_p5 rpoC2 GGAACGGGGCATTAGTTCTT TAGTGCCTTTTTCGCTCCAC 314 1.000 75.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTCT 1225 1.000 69.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTC 1225 1.000 68.9
petN-psbM_p3 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTCT 1246 1.000 67.6
petN-psbM_p4 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTC 1246 1.000 67.5
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTCT 1164 1.000 67.5
rps4-trnT-UGU_p1 rps4-trnT-UGU TCCCGAAACGTGATTGGTTT CTCAGAGGTTAGAGCATCGC 520 1.000 79.0
rps4-trnT-UGU_p2 rps4-trnT-UGU TTCCCGAAACGTGATTGGTT CTCAGAGGTTAGAGCATCGC 521 1.000 79.0
rps4-trnT-UGU_p3 rps4-trnT-UGU TTTCCCGAAACGTGATTGGT CTCAGAGGTTAGAGCATCGC 522 1.000 79.0
rps4-trnT-UGU_p4 rps4-trnT-UGU TCCCGAAACGTGATTGGTTT ATGGTCATCGGTTCGATTCC 488 1.000 78.2
rps4-trnT-UGU_p5 rps4-trnT-UGU TTCCCGAAACGTGATTGGTT ATGGTCATCGGTTCGATTCC 489 1.000 78.2

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
Aiouea chavarriana PV553478.1 152698 View on NCBI ↗
Aiouea montana OR264207.1 152682 View on NCBI ↗