Markers + reference

Parasassafras

2 species · Lauraceae · Laurales

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Species 2
Genome length 153–153 kb
Candidate markers 255
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 393 0.0000 1.00 35.7 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rpl2 LSC 1496 0.0000 1.00 25.3 yes View details
rpl2-rpl23 LSC 146 0.0068 1.00 56.4 yes View details
matK-trnK-UUU LSC 713 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 820 0.0000 1.00 40.0 yes View details
rps16 LSC 1110 0.0000 1.00 40.0 yes View details
trnS-GCU-trnG-UCC LSC 816 0.0000 1.00 40.0 yes View details
atpA LSC 1524 0.0000 1.00 40.0 yes View details
atpF LSC 1281 0.0000 1.00 40.0 yes View details
atpH-atpI LSC 658 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCAGT 459 1.000 78.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCAGT 473 1.000 78.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCAGT 472 1.000 78.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCAGT 474 1.000 78.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 462 1.000 78.4
psbA_p1 psbA TTGATCCTTCAACGACTCGT AATCTGTGTGCTTGGGAGTC 1151 1.000 69.7
psbA_p2 psbA TTGATCCTTCAACGACTCGT TGGGAGTCCCTGAGAATTGA 1139 1.000 68.5
psbA_p3 psbA ATTGATCCTTCAACGACTCGT AATCTGTGTGCTTGGGAGTC 1152 1.000 65.7
psbA_p4 psbA ATTGATCCTTCAACGACTCGT TGGGAGTCCCTGAGAATTGA 1140 1.000 64.5
psbA_p5 psbA TTGATCCTTCAACGACTCGT CTTGGGAGTCCCTGAGAATTG 1141 1.000 63.2
matK-trnK-UUU_p1 matK-trnK-UUU TTGTTGCCGAAATCCATCCA GTCGGGCAATCGAATCTCTT 868 1.000 78.9
matK-trnK-UUU_p2 matK-trnK-UUU TTGTTGCCGAAATCCATCCA ATCGTATCTACACACCCCGT 830 1.000 78.8
matK-trnK-UUU_p3 matK-trnK-UUU TGTTGCCGAAATCCATCCAT GTCGGGCAATCGAATCTCTT 867 1.000 78.4
matK-trnK-UUU_p4 matK-trnK-UUU TGTTGCCGAAATCCATCCAT ATCGTATCTACACACCCCGT 829 1.000 78.4
matK-trnK-UUU_p5 matK-trnK-UUU TTGTTGCCGAAATCCATCCA TCGTATCTACACACCCCGTT 829 1.000 78.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 952 1.000 78.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 951 1.000 78.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT AAAAAGGCGCTCAACCTACA 973 1.000 78.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 961 1.000 77.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 955 1.000 76.8
rps16_p1 rps16 GGGTCATGTGAGAGCAACAA ACCGATTGAGCCAATGACTA 1290 1.000 68.2
rps16_p2 rps16 GGGTCATGTGAGAGCAACAA TACCGATTGAGCCAATGACT 1291 1.000 68.2
rps16_p3 rps16 TGATACGGGGTCATGTGAGA ACCGATTGAGCCAATGACTA 1297 1.000 67.8
rps16_p4 rps16 TGATACGGGGTCATGTGAGA TACCGATTGAGCCAATGACT 1298 1.000 67.8
rps16_p5 rps16 GGGTCATGTGAGAGCAACAA TCAATTCCATACCGGTCCAA 1251 1.000 67.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCACT 890 1.000 69.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACGCTTTTACCAC 890 1.000 69.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACGCTTTTACCAC 891 1.000 67.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGAATCACGCTTTTACCACT 889 1.000 67.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACGCTTTTACCACT 876 1.000 66.8

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
Parasassafras cf. confertiflorum ZFL-2021 MT621615.1 152555 View on NCBI ↗
Parasassafras confertiflorum NC_042696.1 152555 View on NCBI ↗